Starting phenix.real_space_refine on Wed Sep 17 16:12:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1v_39737/09_2025/8z1v_39737_neut.cif" } 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= 0.001 sd= 0.022 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 Fe 8 7.16 5 S 74 5.16 5 C 6139 2.51 5 N 1658 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9562 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2380 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain breaks: 1 Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2122 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 14, 'TRANS': 265} Chain: "C" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2481 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2563 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 23, 'TRANS': 301} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6711 SG CYS C 290 22.078 31.180 99.809 1.00151.77 S ATOM 6663 SG CYS C 284 18.109 34.615 95.541 1.00128.87 S ATOM 6903 SG CYS C 315 17.616 35.255 102.133 1.00142.04 S ATOM 6767 SG CYS C 297 15.308 30.150 99.252 1.00155.91 S ATOM 9218 SG CYS D 293 66.298 56.997 100.668 1.00146.86 S ATOM 9264 SG CYS D 299 61.661 59.918 104.969 1.00159.29 S ATOM 9325 SG CYS D 306 68.298 61.053 105.064 1.00167.47 S ATOM 9454 SG CYS D 323 65.448 55.497 107.415 1.00154.31 S Time building chain proxies: 2.37, per 1000 atoms: 0.25 Number of scatterers: 9562 At special positions: 0 Unit cell: (93.6, 94.64, 126.88, 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) Fe 8 26.01 S 74 16.00 O 1683 8.00 N 1658 7.00 C 6139 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: 1.00 Conformation dependent library (CDL) restraints added in 377.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 401 " pdb="FE3 SF4 C 401 " - pdb=" SG CYS C 315 " pdb="FE4 SF4 C 401 " - pdb=" SG CYS C 297 " pdb="FE1 SF4 C 401 " - pdb=" SG CYS C 290 " pdb="FE2 SF4 C 401 " - pdb=" SG CYS C 284 " pdb=" SF4 D 401 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 306 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 323 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 293 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 299 " Number of angles added : 24 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 60.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.943A pdb=" N LEU A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.936A pdb=" N LEU A 67 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 124 Proline residue: A 94 - end of helix removed outlier: 3.975A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.845A pdb=" N ALA A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 232 removed outlier: 4.731A pdb=" N LEU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 4.756A pdb=" N ILE A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.549A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 254 through 282 removed outlier: 4.090A pdb=" N ASN A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.514A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.921A pdb=" N TRP A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.521A pdb=" N VAL A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 removed outlier: 3.689A pdb=" N ARG B 28 " --> pdb=" O HIS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 89 through 127 removed outlier: 3.549A pdb=" N ARG B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 160 through 189 removed outlier: 3.832A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.088A pdb=" N ASN B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.604A pdb=" N THR B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 211 through 240 removed outlier: 4.823A pdb=" N ALA B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.966A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 260 through 265 removed outlier: 4.680A pdb=" N SER B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 293 removed outlier: 4.036A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.872A pdb=" N ILE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.019A pdb=" N LEU C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 149 No H-bonds generated for 'chain 'C' and resid 148 through 149' Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.864A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.855A pdb=" N VAL C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.685A pdb=" N PHE C 242 " --> pdb=" O HIS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.881A pdb=" N ARG C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.526A pdb=" N ARG D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 133 through 149 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.519A pdb=" N PHE D 162 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.648A pdb=" N MET D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 212 Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.628A pdb=" N HIS D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.896A pdb=" N THR D 307 " --> pdb=" O GLY D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.366A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.366A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.552A pdb=" N VAL C 35 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE C 225 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY C 37 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET C 227 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 39 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 234 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR C 228 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 45 removed outlier: 6.502A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 41 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE D 16 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 43 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN D 14 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.613A pdb=" N GLN D 102 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ASP D 186 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 104 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 183 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE D 218 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA D 185 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR D 50 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N MET D 233 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA D 52 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N MET D 235 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL D 54 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 242 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR D 236 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1515 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: 1.51 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4327 1.43 - 1.64: 5300 1.64 - 1.86: 117 1.86 - 2.07: 0 2.07 - 2.29: 24 Bond restraints: 9768 Sorted by residual: bond pdb=" CA ALA B 217 " pdb=" CB ALA B 217 " ideal model delta sigma weight residual 1.534 1.426 0.108 1.18e-02 7.18e+03 8.35e+01 bond pdb=" CE1 HIS D 227 " pdb=" NE2 HIS D 227 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.76e+01 bond pdb=" CA ALA D 52 " pdb=" CB ALA D 52 " ideal model delta sigma weight residual 1.529 1.419 0.110 1.34e-02 5.57e+03 6.74e+01 bond pdb=" CE1 HIS A 68 " pdb=" NE2 HIS A 68 " ideal model delta sigma weight residual 1.321 1.240 0.081 1.00e-02 1.00e+04 6.58e+01 bond pdb=" CD2 HIS D 227 " pdb=" NE2 HIS D 227 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.10e-02 8.26e+03 6.54e+01 ... (remaining 9763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9611 2.16 - 4.32: 2941 4.32 - 6.48: 513 6.48 - 8.64: 193 8.64 - 10.80: 23 Bond angle restraints: 13281 Sorted by residual: angle pdb=" C HIS D 227 " pdb=" N ILE D 228 " pdb=" CA ILE D 228 " ideal model delta sigma weight residual 122.66 129.78 -7.12 9.70e-01 1.06e+00 5.38e+01 angle pdb=" CA PHE D 217 " pdb=" CB PHE D 217 " pdb=" CG PHE D 217 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.02e+01 angle pdb=" CA ASN C 85 " pdb=" CB ASN C 85 " pdb=" CG ASN C 85 " ideal model delta sigma weight residual 112.60 119.64 -7.04 1.00e+00 1.00e+00 4.96e+01 angle pdb=" CA ASP C 7 " pdb=" CB ASP C 7 " pdb=" CG ASP C 7 " ideal model delta sigma weight residual 112.60 119.55 -6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" CA ASN D 202 " pdb=" CB ASN D 202 " pdb=" CG ASN D 202 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 ... (remaining 13276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5493 17.52 - 35.03: 315 35.03 - 52.54: 46 52.54 - 70.06: 13 70.06 - 87.57: 12 Dihedral angle restraints: 5879 sinusoidal: 2350 harmonic: 3529 Sorted by residual: dihedral pdb=" CA ARG B 88 " pdb=" C ARG B 88 " pdb=" N ASP B 89 " pdb=" CA ASP B 89 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP D 193 " pdb=" C ASP D 193 " pdb=" N VAL D 194 " pdb=" CA VAL D 194 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLN B 245 " pdb=" C GLN B 245 " pdb=" N PRO B 246 " pdb=" CA PRO B 246 " ideal model delta harmonic sigma weight residual 180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1121 0.145 - 0.289: 153 0.289 - 0.434: 49 0.434 - 0.579: 152 0.579 - 0.723: 66 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CG LEU B 285 " pdb=" CB LEU B 285 " pdb=" CD1 LEU B 285 " pdb=" CD2 LEU B 285 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CG LEU D 201 " pdb=" CB LEU D 201 " pdb=" CD1 LEU D 201 " pdb=" CD2 LEU D 201 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CG LEU D 313 " pdb=" CB LEU D 313 " pdb=" CD1 LEU D 313 " pdb=" CD2 LEU D 313 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 1538 not shown) Planarity restraints: 1696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " 0.151 2.00e-02 2.50e+03 7.69e-02 1.48e+02 pdb=" CG TRP A 293 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " -0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " 0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " -0.108 2.00e-02 2.50e+03 5.40e-02 7.29e+01 pdb=" CG TRP B 251 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " 0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " 0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " -0.074 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 316 " -0.081 2.00e-02 2.50e+03 6.02e-02 5.43e+01 pdb=" CG HIS C 316 " 0.093 2.00e-02 2.50e+03 pdb=" ND1 HIS C 316 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS C 316 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS C 316 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 316 " -0.049 2.00e-02 2.50e+03 ... (remaining 1693 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1769 2.81 - 3.33: 9426 3.33 - 3.86: 15116 3.86 - 4.38: 17325 4.38 - 4.90: 30386 Nonbonded interactions: 74022 Sorted by model distance: nonbonded pdb=" OG SER D 133 " pdb=" OE2 GLU D 135 " model vdw 2.288 3.040 nonbonded pdb=" N GLN D 312 " pdb=" OE1 GLN D 312 " model vdw 2.387 3.120 nonbonded pdb=" OE2 GLU D 123 " pdb=" OH TYR D 155 " model vdw 2.523 3.040 nonbonded pdb=" OE2 GLU B 187 " pdb=" OH TYR B 192 " model vdw 2.536 3.040 nonbonded pdb=" OE1 GLU C 80 " pdb=" NH1 ARG C 84 " model vdw 2.542 3.120 ... (remaining 74017 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: 2.860 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.780 Find NCS groups from input model: 0.080 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.026 0.224 9776 Z= 1.360 Angle : 2.223 13.776 13305 Z= 1.487 Chirality : 0.239 0.723 1541 Planarity : 0.014 0.128 1696 Dihedral : 12.466 87.571 3611 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 7.41 % 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 aren not related in a simple way. whole: -0.95 (0.22), residues: 1224 helix: -0.76 (0.17), residues: 665 sheet: -0.44 (0.49), residues: 91 loop : -0.14 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 62 TYR 0.089 0.016 TYR D 81 PHE 0.080 0.012 PHE D 162 TRP 0.151 0.018 TRP A 293 HIS 0.016 0.003 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.02517 ( 9768) covalent geometry : angle 2.21136 (13281) hydrogen bonds : bond 0.19261 ( 523) hydrogen bonds : angle 7.13389 ( 1515) metal coordination : bond 0.15961 ( 8) metal coordination : angle 5.84087 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 24 PHE cc_start: 0.7210 (t80) cc_final: 0.6996 (t80) REVERT: A 62 MET cc_start: 0.6855 (mtm) cc_final: 0.6506 (mtm) REVERT: A 151 MET cc_start: 0.7339 (mmm) cc_final: 0.7043 (mmm) REVERT: A 175 LEU cc_start: 0.8916 (mt) cc_final: 0.8702 (mp) REVERT: A 222 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6916 (mtp85) REVERT: A 247 ARG cc_start: 0.7411 (ttp80) cc_final: 0.6849 (ttp80) REVERT: A 296 ASP cc_start: 0.7424 (t0) cc_final: 0.7069 (t0) REVERT: A 300 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7648 (ttm-80) REVERT: B 60 GLN cc_start: 0.8488 (mt0) cc_final: 0.7562 (mt0) REVERT: B 61 PHE cc_start: 0.7161 (m-80) cc_final: 0.6771 (m-80) REVERT: B 62 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6424 (ptp90) REVERT: B 77 MET cc_start: 0.8014 (tpp) cc_final: 0.7644 (tpp) REVERT: B 84 ASP cc_start: 0.7280 (t0) cc_final: 0.6857 (t0) REVERT: B 115 MET cc_start: 0.6860 (mtp) cc_final: 0.6515 (mtp) REVERT: B 210 ASN cc_start: 0.8179 (m-40) cc_final: 0.7928 (m-40) REVERT: B 254 MET cc_start: 0.8177 (mtp) cc_final: 0.7914 (mtm) REVERT: C 15 ASP cc_start: 0.6594 (t70) cc_final: 0.6264 (t70) REVERT: C 41 GLU cc_start: 0.7048 (pt0) cc_final: 0.6641 (pt0) REVERT: C 50 SER cc_start: 0.7203 (m) cc_final: 0.6754 (p) REVERT: C 95 PHE cc_start: 0.8608 (m-80) cc_final: 0.8401 (m-80) REVERT: C 124 LYS cc_start: 0.7470 (tppp) cc_final: 0.7127 (tppp) REVERT: C 142 ASP cc_start: 0.7243 (t0) cc_final: 0.6496 (t0) REVERT: C 149 VAL cc_start: 0.7559 (t) cc_final: 0.7206 (p) REVERT: C 158 MET cc_start: 0.7492 (mmm) cc_final: 0.6965 (mmm) REVERT: C 168 ILE cc_start: 0.7800 (tp) cc_final: 0.7503 (tp) REVERT: C 173 LYS cc_start: 0.7455 (ttmt) cc_final: 0.7046 (ttmm) REVERT: C 198 GLU cc_start: 0.7474 (tp30) cc_final: 0.7242 (tp30) REVERT: C 202 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7665 (ttpp) REVERT: C 213 ASP cc_start: 0.7651 (t0) cc_final: 0.7152 (t0) REVERT: C 259 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7602 (mt-10) REVERT: C 319 LEU cc_start: 0.8015 (mp) cc_final: 0.7758 (mt) REVERT: D 28 MET cc_start: 0.7147 (tmm) cc_final: 0.6879 (tmm) REVERT: D 33 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6950 (mtm110) REVERT: D 36 LYS cc_start: 0.7882 (mttt) cc_final: 0.7427 (mttp) REVERT: D 39 ASP cc_start: 0.7271 (t0) cc_final: 0.6639 (t0) REVERT: D 72 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 84 GLN cc_start: 0.7234 (tt0) cc_final: 0.6855 (tt0) REVERT: D 117 LYS cc_start: 0.7179 (mttt) cc_final: 0.6816 (mttp) REVERT: D 131 SER cc_start: 0.8437 (m) cc_final: 0.8142 (t) REVERT: D 151 LYS cc_start: 0.7496 (mttp) cc_final: 0.7182 (mtmm) REVERT: D 179 ASP cc_start: 0.7820 (t0) cc_final: 0.7508 (t0) REVERT: D 210 GLU cc_start: 0.7528 (tt0) cc_final: 0.7288 (tt0) REVERT: D 221 ASP cc_start: 0.7057 (t0) cc_final: 0.6678 (t0) REVERT: D 226 GLU cc_start: 0.7985 (tt0) cc_final: 0.7558 (tt0) REVERT: D 271 ASP cc_start: 0.7058 (t70) cc_final: 0.6643 (t0) REVERT: D 312 GLN cc_start: 0.7641 (pm20) cc_final: 0.7402 (pm20) REVERT: D 314 LYS cc_start: 0.7097 (ttmm) cc_final: 0.6885 (ttmm) REVERT: D 327 ASP cc_start: 0.7454 (t70) cc_final: 0.7206 (t0) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1398 time to fit residues: 65.7917 Evaluate side-chains 319 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS C 120 GLN D 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103741 restraints weight = 13748.641| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.94 r_work: 0.3211 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9776 Z= 0.154 Angle : 0.663 15.890 13305 Z= 0.324 Chirality : 0.045 0.177 1541 Planarity : 0.005 0.044 1696 Dihedral : 5.072 24.269 1336 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.76 % Allowed : 9.37 % Favored : 88.88 % 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 aren not related in a simple way. whole: 0.89 (0.24), residues: 1224 helix: 1.24 (0.20), residues: 663 sheet: -0.15 (0.53), residues: 94 loop : -0.06 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 276 TYR 0.012 0.001 TYR B 55 PHE 0.016 0.002 PHE D 303 TRP 0.034 0.002 TRP A 293 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9768) covalent geometry : angle 0.61056 (13281) hydrogen bonds : bond 0.05002 ( 523) hydrogen bonds : angle 4.85913 ( 1515) metal coordination : bond 0.01034 ( 8) metal coordination : angle 6.13880 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 332 time to evaluate : 0.373 Fit side-chains REVERT: A 24 PHE cc_start: 0.8428 (t80) cc_final: 0.8153 (t80) REVERT: A 62 MET cc_start: 0.6840 (mtm) cc_final: 0.6580 (mtm) REVERT: A 96 PHE cc_start: 0.8551 (t80) cc_final: 0.7809 (t80) REVERT: A 151 MET cc_start: 0.8642 (mmm) cc_final: 0.8417 (mmp) REVERT: A 156 VAL cc_start: 0.8319 (t) cc_final: 0.8077 (m) REVERT: A 185 MET cc_start: 0.7830 (tpp) cc_final: 0.7566 (tpp) REVERT: A 247 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7992 (ttp80) REVERT: A 300 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: A 336 ARG cc_start: 0.7555 (mtm180) cc_final: 0.5998 (mmm160) REVERT: B 47 ILE cc_start: 0.8486 (tp) cc_final: 0.8257 (mm) REVERT: B 126 PHE cc_start: 0.8794 (m-80) cc_final: 0.8522 (m-80) REVERT: B 204 MET cc_start: 0.8037 (ppp) cc_final: 0.7831 (ppp) REVERT: B 209 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 248 THR cc_start: 0.9142 (t) cc_final: 0.8934 (p) REVERT: B 286 MET cc_start: 0.7580 (mmp) cc_final: 0.7010 (mmm) REVERT: C 15 ASP cc_start: 0.7745 (t70) cc_final: 0.7409 (t70) REVERT: C 25 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: C 41 GLU cc_start: 0.7463 (pt0) cc_final: 0.7120 (pt0) REVERT: C 50 SER cc_start: 0.8337 (m) cc_final: 0.7874 (p) REVERT: C 80 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6707 (tm-30) REVERT: C 94 ILE cc_start: 0.8397 (mt) cc_final: 0.8186 (mm) REVERT: C 149 VAL cc_start: 0.8444 (t) cc_final: 0.8140 (p) REVERT: C 168 ILE cc_start: 0.8536 (tp) cc_final: 0.8293 (tp) REVERT: C 173 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8147 (ttmm) REVERT: C 198 GLU cc_start: 0.8103 (tp30) cc_final: 0.7869 (tp30) REVERT: C 200 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 213 ASP cc_start: 0.7794 (t0) cc_final: 0.7374 (t0) REVERT: C 234 GLU cc_start: 0.7936 (tt0) cc_final: 0.7560 (tt0) REVERT: D 28 MET cc_start: 0.7021 (tmm) cc_final: 0.6716 (tmm) REVERT: D 36 LYS cc_start: 0.8416 (mttt) cc_final: 0.8138 (mtmp) REVERT: D 39 ASP cc_start: 0.7734 (t0) cc_final: 0.7063 (t0) REVERT: D 54 VAL cc_start: 0.8464 (m) cc_final: 0.8195 (p) REVERT: D 92 GLN cc_start: 0.7472 (pm20) cc_final: 0.7135 (pm20) REVERT: D 116 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8641 (mmtm) REVERT: D 140 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: D 144 MET cc_start: 0.8036 (tpp) cc_final: 0.7609 (mpp) REVERT: D 179 ASP cc_start: 0.8201 (t0) cc_final: 0.7959 (t70) REVERT: D 205 MET cc_start: 0.8115 (mmp) cc_final: 0.7861 (mmp) REVERT: D 210 GLU cc_start: 0.8186 (tt0) cc_final: 0.7959 (tt0) REVERT: D 226 GLU cc_start: 0.8170 (tt0) cc_final: 0.7832 (tt0) REVERT: D 252 ASN cc_start: 0.8878 (t0) cc_final: 0.8347 (t0) REVERT: D 271 ASP cc_start: 0.7494 (t70) cc_final: 0.6958 (t0) REVERT: D 309 LEU cc_start: 0.8210 (mt) cc_final: 0.7990 (mm) REVERT: D 314 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8106 (ttmm) outliers start: 18 outliers final: 10 residues processed: 338 average time/residue: 0.1435 time to fit residues: 62.0708 Evaluate side-chains 312 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 300 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 237 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** C 316 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 = 0.3479 r_free = 0.3479 target = 0.114388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103092 restraints weight = 13792.250| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.96 r_work: 0.3199 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9776 Z= 0.148 Angle : 0.624 15.425 13305 Z= 0.288 Chirality : 0.043 0.170 1541 Planarity : 0.005 0.036 1696 Dihedral : 4.595 19.597 1336 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.05 % Allowed : 14.15 % Favored : 83.80 % 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 aren not related in a simple way. whole: 1.19 (0.24), residues: 1224 helix: 1.67 (0.20), residues: 666 sheet: -0.08 (0.55), residues: 94 loop : -0.25 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 249 TYR 0.011 0.001 TYR A 236 PHE 0.014 0.001 PHE D 303 TRP 0.025 0.001 TRP A 293 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9768) covalent geometry : angle 0.55756 (13281) hydrogen bonds : bond 0.04487 ( 523) hydrogen bonds : angle 4.55572 ( 1515) metal coordination : bond 0.00736 ( 8) metal coordination : angle 6.61823 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.404 Fit side-chains REVERT: A 62 MET cc_start: 0.6806 (mtm) cc_final: 0.6560 (mtm) REVERT: A 74 MET cc_start: 0.7629 (ppp) cc_final: 0.7122 (ppp) REVERT: A 96 PHE cc_start: 0.8564 (t80) cc_final: 0.7831 (t80) REVERT: A 151 MET cc_start: 0.8631 (mmm) cc_final: 0.8347 (mmp) REVERT: A 156 VAL cc_start: 0.8263 (t) cc_final: 0.8000 (m) REVERT: A 172 MET cc_start: 0.8651 (ppp) cc_final: 0.8150 (ppp) REVERT: A 173 VAL cc_start: 0.8890 (t) cc_final: 0.8665 (p) REVERT: A 185 MET cc_start: 0.7852 (tpp) cc_final: 0.7538 (tpp) REVERT: A 247 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7982 (ttp80) REVERT: A 300 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: B 47 ILE cc_start: 0.8539 (tp) cc_final: 0.8299 (tp) REVERT: B 84 ASP cc_start: 0.8091 (t0) cc_final: 0.7736 (t0) REVERT: B 126 PHE cc_start: 0.8767 (m-80) cc_final: 0.8553 (m-80) REVERT: B 196 SER cc_start: 0.8742 (m) cc_final: 0.8449 (t) REVERT: B 204 MET cc_start: 0.7996 (ppp) cc_final: 0.7772 (ppp) REVERT: B 209 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8319 (mm) REVERT: B 227 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7753 (t80) REVERT: B 286 MET cc_start: 0.7769 (mmp) cc_final: 0.7536 (mmm) REVERT: C 15 ASP cc_start: 0.7910 (t70) cc_final: 0.7642 (t70) REVERT: C 16 GLU cc_start: 0.7897 (tp30) cc_final: 0.7633 (tp30) REVERT: C 24 ASP cc_start: 0.8084 (t0) cc_final: 0.7693 (t0) REVERT: C 41 GLU cc_start: 0.7412 (pt0) cc_final: 0.7103 (pt0) REVERT: C 50 SER cc_start: 0.8294 (m) cc_final: 0.7875 (p) REVERT: C 82 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 149 VAL cc_start: 0.8427 (t) cc_final: 0.8065 (p) REVERT: C 168 ILE cc_start: 0.8567 (tp) cc_final: 0.8355 (tp) REVERT: C 171 ARG cc_start: 0.8221 (mmt180) cc_final: 0.7808 (mmt90) REVERT: C 173 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8079 (ttmm) REVERT: C 198 GLU cc_start: 0.8061 (tp30) cc_final: 0.7816 (tp30) REVERT: C 213 ASP cc_start: 0.7834 (t0) cc_final: 0.7403 (t0) REVERT: C 234 GLU cc_start: 0.7988 (tt0) cc_final: 0.7615 (tt0) REVERT: C 259 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 28 MET cc_start: 0.7031 (tmm) cc_final: 0.6679 (tmm) REVERT: D 36 LYS cc_start: 0.8412 (mttt) cc_final: 0.8083 (mttp) REVERT: D 92 GLN cc_start: 0.7453 (pm20) cc_final: 0.7125 (pm20) REVERT: D 116 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8574 (mmtm) REVERT: D 144 MET cc_start: 0.8048 (tpp) cc_final: 0.7618 (mpp) REVERT: D 210 GLU cc_start: 0.8151 (tt0) cc_final: 0.7917 (tt0) REVERT: D 226 GLU cc_start: 0.8183 (tt0) cc_final: 0.7813 (tt0) REVERT: D 252 ASN cc_start: 0.8927 (t0) cc_final: 0.8547 (t0) REVERT: D 267 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7731 (ttm-80) REVERT: D 276 ARG cc_start: 0.6495 (ttm110) cc_final: 0.6241 (ttm110) REVERT: D 309 LEU cc_start: 0.8249 (mt) cc_final: 0.8043 (mt) REVERT: D 314 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8035 (ttmm) REVERT: D 327 ASP cc_start: 0.8307 (t70) cc_final: 0.7945 (t0) outliers start: 21 outliers final: 14 residues processed: 324 average time/residue: 0.1460 time to fit residues: 60.5139 Evaluate side-chains 313 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 297 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.0020 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104029 restraints weight = 13863.567| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.98 r_work: 0.3215 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9776 Z= 0.117 Angle : 0.597 14.785 13305 Z= 0.267 Chirality : 0.041 0.170 1541 Planarity : 0.004 0.043 1696 Dihedral : 4.279 18.417 1336 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.44 % Allowed : 15.80 % Favored : 81.76 % 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 aren not related in a simple way. whole: 1.34 (0.25), residues: 1224 helix: 1.87 (0.20), residues: 668 sheet: -0.04 (0.56), residues: 94 loop : -0.31 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 249 TYR 0.010 0.001 TYR A 236 PHE 0.013 0.001 PHE D 303 TRP 0.020 0.001 TRP A 293 HIS 0.002 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9768) covalent geometry : angle 0.52764 (13281) hydrogen bonds : bond 0.03923 ( 523) hydrogen bonds : angle 4.35487 ( 1515) metal coordination : bond 0.00581 ( 8) metal coordination : angle 6.59790 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 308 time to evaluate : 0.397 Fit side-chains REVERT: A 62 MET cc_start: 0.6776 (mtm) cc_final: 0.6524 (mtm) REVERT: A 74 MET cc_start: 0.7647 (ppp) cc_final: 0.7141 (ppp) REVERT: A 96 PHE cc_start: 0.8556 (t80) cc_final: 0.7801 (t80) REVERT: A 134 VAL cc_start: 0.8219 (t) cc_final: 0.8004 (p) REVERT: A 151 MET cc_start: 0.8632 (mmm) cc_final: 0.8333 (mmp) REVERT: A 156 VAL cc_start: 0.8257 (t) cc_final: 0.7986 (m) REVERT: A 172 MET cc_start: 0.8656 (ppp) cc_final: 0.8288 (ppp) REVERT: A 173 VAL cc_start: 0.8934 (t) cc_final: 0.8724 (p) REVERT: A 185 MET cc_start: 0.7832 (tpp) cc_final: 0.7536 (tpp) REVERT: A 247 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7929 (ttp80) REVERT: A 300 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8092 (mtm-85) REVERT: B 47 ILE cc_start: 0.8508 (tp) cc_final: 0.8271 (tp) REVERT: B 204 MET cc_start: 0.7958 (ppp) cc_final: 0.7717 (ppp) REVERT: B 209 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8262 (mm) REVERT: B 227 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 286 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: C 15 ASP cc_start: 0.7919 (t70) cc_final: 0.7673 (t70) REVERT: C 16 GLU cc_start: 0.7884 (tp30) cc_final: 0.7650 (tp30) REVERT: C 24 ASP cc_start: 0.8092 (t0) cc_final: 0.7663 (t0) REVERT: C 50 SER cc_start: 0.8270 (m) cc_final: 0.7884 (p) REVERT: C 82 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 138 VAL cc_start: 0.8412 (m) cc_final: 0.8117 (t) REVERT: C 149 VAL cc_start: 0.8412 (t) cc_final: 0.8029 (p) REVERT: C 168 ILE cc_start: 0.8618 (tp) cc_final: 0.8348 (tp) REVERT: C 171 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7785 (mmt90) REVERT: C 198 GLU cc_start: 0.8059 (tp30) cc_final: 0.7800 (tp30) REVERT: C 201 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8329 (mm-40) REVERT: C 213 ASP cc_start: 0.7828 (t0) cc_final: 0.7391 (t0) REVERT: C 234 GLU cc_start: 0.7992 (tt0) cc_final: 0.7581 (tt0) REVERT: C 259 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7735 (mt-10) REVERT: C 320 ASP cc_start: 0.8338 (p0) cc_final: 0.7900 (p0) REVERT: D 28 MET cc_start: 0.7024 (tmm) cc_final: 0.6710 (tmm) REVERT: D 36 LYS cc_start: 0.8407 (mttt) cc_final: 0.8065 (mttp) REVERT: D 84 GLN cc_start: 0.8172 (tt0) cc_final: 0.7959 (mt0) REVERT: D 92 GLN cc_start: 0.7431 (pm20) cc_final: 0.7093 (pm20) REVERT: D 116 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8535 (mmtm) REVERT: D 144 MET cc_start: 0.8085 (tpp) cc_final: 0.7616 (mpp) REVERT: D 210 GLU cc_start: 0.8174 (tt0) cc_final: 0.7934 (tt0) REVERT: D 226 GLU cc_start: 0.8190 (tt0) cc_final: 0.7942 (tt0) REVERT: D 252 ASN cc_start: 0.8916 (t0) cc_final: 0.8503 (t0) REVERT: D 267 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7714 (ttm-80) REVERT: D 314 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8082 (ttmm) outliers start: 25 outliers final: 16 residues processed: 316 average time/residue: 0.1448 time to fit residues: 58.6293 Evaluate side-chains 322 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 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 = 0.3482 r_free = 0.3482 target = 0.114723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102922 restraints weight = 13849.255| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.16 r_work: 0.3189 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9776 Z= 0.123 Angle : 0.600 15.057 13305 Z= 0.266 Chirality : 0.041 0.160 1541 Planarity : 0.004 0.042 1696 Dihedral : 4.140 18.173 1336 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.34 % Allowed : 16.88 % Favored : 80.78 % 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 aren not related in a simple way. whole: 1.42 (0.25), residues: 1224 helix: 1.98 (0.20), residues: 668 sheet: -0.05 (0.56), residues: 94 loop : -0.34 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 249 TYR 0.022 0.001 TYR B 55 PHE 0.012 0.001 PHE D 303 TRP 0.019 0.001 TRP A 293 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9768) covalent geometry : angle 0.53068 (13281) hydrogen bonds : bond 0.03866 ( 523) hydrogen bonds : angle 4.28775 ( 1515) metal coordination : bond 0.00522 ( 8) metal coordination : angle 6.59314 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.375 Fit side-chains REVERT: A 24 PHE cc_start: 0.8439 (t80) cc_final: 0.8221 (t80) REVERT: A 62 MET cc_start: 0.6739 (mtm) cc_final: 0.6479 (mtm) REVERT: A 74 MET cc_start: 0.7707 (ppp) cc_final: 0.7157 (ppp) REVERT: A 151 MET cc_start: 0.8636 (mmm) cc_final: 0.8334 (mmp) REVERT: A 156 VAL cc_start: 0.8394 (t) cc_final: 0.8070 (m) REVERT: A 172 MET cc_start: 0.8639 (ppp) cc_final: 0.8222 (ppp) REVERT: A 185 MET cc_start: 0.7966 (tpp) cc_final: 0.7661 (tpp) REVERT: A 247 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8043 (ttp80) REVERT: A 300 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8140 (mtm-85) REVERT: B 204 MET cc_start: 0.7997 (ppp) cc_final: 0.7745 (ppp) REVERT: B 209 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8311 (mm) REVERT: B 227 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 286 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7381 (mtp) REVERT: C 16 GLU cc_start: 0.7902 (tp30) cc_final: 0.7694 (tp30) REVERT: C 24 ASP cc_start: 0.8129 (t0) cc_final: 0.7722 (t0) REVERT: C 50 SER cc_start: 0.8382 (m) cc_final: 0.8028 (p) REVERT: C 82 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7446 (mm-30) REVERT: C 138 VAL cc_start: 0.8468 (m) cc_final: 0.8187 (t) REVERT: C 149 VAL cc_start: 0.8414 (t) cc_final: 0.8051 (p) REVERT: C 168 ILE cc_start: 0.8705 (tp) cc_final: 0.8437 (tp) REVERT: C 171 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7806 (mmt90) REVERT: C 173 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8067 (mtpp) REVERT: C 198 GLU cc_start: 0.8179 (tp30) cc_final: 0.7855 (tp30) REVERT: C 201 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8392 (mm-40) REVERT: C 213 ASP cc_start: 0.7830 (t0) cc_final: 0.7412 (t0) REVERT: C 234 GLU cc_start: 0.8007 (tt0) cc_final: 0.7407 (tt0) REVERT: D 28 MET cc_start: 0.7079 (tmm) cc_final: 0.6770 (tmm) REVERT: D 36 LYS cc_start: 0.8413 (mttt) cc_final: 0.8126 (mtmm) REVERT: D 67 LEU cc_start: 0.8216 (mt) cc_final: 0.7836 (mp) REVERT: D 92 GLN cc_start: 0.7494 (pm20) cc_final: 0.7146 (pm20) REVERT: D 116 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8539 (mmtm) REVERT: D 137 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: D 144 MET cc_start: 0.8200 (tpp) cc_final: 0.7762 (mpp) REVERT: D 192 LEU cc_start: 0.8697 (mt) cc_final: 0.8438 (mp) REVERT: D 210 GLU cc_start: 0.8206 (tt0) cc_final: 0.7984 (tt0) REVERT: D 226 GLU cc_start: 0.8242 (tt0) cc_final: 0.8020 (tt0) REVERT: D 252 ASN cc_start: 0.8957 (t0) cc_final: 0.8685 (t0) REVERT: D 267 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7789 (ttm-80) outliers start: 24 outliers final: 16 residues processed: 316 average time/residue: 0.1417 time to fit residues: 57.7819 Evaluate side-chains 320 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 121 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 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 = 0.3478 r_free = 0.3478 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102741 restraints weight = 13937.240| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.15 r_work: 0.3183 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9776 Z= 0.130 Angle : 0.603 15.673 13305 Z= 0.268 Chirality : 0.041 0.157 1541 Planarity : 0.004 0.043 1696 Dihedral : 4.102 18.119 1336 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.44 % Allowed : 18.24 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1224 helix: 2.05 (0.20), residues: 668 sheet: -0.12 (0.56), residues: 94 loop : -0.41 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 249 TYR 0.016 0.001 TYR B 55 PHE 0.011 0.001 PHE D 303 TRP 0.017 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9768) covalent geometry : angle 0.53540 (13281) hydrogen bonds : bond 0.03860 ( 523) hydrogen bonds : angle 4.24068 ( 1515) metal coordination : bond 0.00554 ( 8) metal coordination : angle 6.57348 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 304 time to evaluate : 0.378 Fit side-chains REVERT: A 62 MET cc_start: 0.6773 (mtm) cc_final: 0.6514 (mtm) REVERT: A 74 MET cc_start: 0.7722 (ppp) cc_final: 0.7134 (ppp) REVERT: A 151 MET cc_start: 0.8608 (mmm) cc_final: 0.8296 (mmp) REVERT: A 156 VAL cc_start: 0.8404 (t) cc_final: 0.8071 (m) REVERT: A 172 MET cc_start: 0.8548 (ppp) cc_final: 0.7922 (ppp) REVERT: A 185 MET cc_start: 0.7952 (tpp) cc_final: 0.7672 (tpp) REVERT: A 247 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8075 (ttp80) REVERT: A 300 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8084 (mtm-85) REVERT: B 204 MET cc_start: 0.8009 (ppp) cc_final: 0.7769 (ppp) REVERT: B 227 PHE cc_start: 0.8282 (m-80) cc_final: 0.7838 (t80) REVERT: C 16 GLU cc_start: 0.7868 (tp30) cc_final: 0.7556 (tp30) REVERT: C 24 ASP cc_start: 0.8136 (t0) cc_final: 0.7727 (t0) REVERT: C 50 SER cc_start: 0.8393 (m) cc_final: 0.8045 (p) REVERT: C 82 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 138 VAL cc_start: 0.8472 (m) cc_final: 0.8194 (t) REVERT: C 149 VAL cc_start: 0.8421 (t) cc_final: 0.8049 (p) REVERT: C 168 ILE cc_start: 0.8702 (tp) cc_final: 0.8428 (tp) REVERT: C 171 ARG cc_start: 0.8251 (mmt180) cc_final: 0.7802 (mmt90) REVERT: C 173 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: C 198 GLU cc_start: 0.8178 (tp30) cc_final: 0.7841 (tp30) REVERT: C 201 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8396 (mm-40) REVERT: C 213 ASP cc_start: 0.7834 (t0) cc_final: 0.7422 (t0) REVERT: C 234 GLU cc_start: 0.7962 (tt0) cc_final: 0.7395 (tt0) REVERT: C 320 ASP cc_start: 0.8519 (p0) cc_final: 0.7984 (p0) REVERT: D 28 MET cc_start: 0.7095 (tmm) cc_final: 0.6761 (tmm) REVERT: D 36 LYS cc_start: 0.8419 (mttt) cc_final: 0.8135 (mtmm) REVERT: D 67 LEU cc_start: 0.8191 (mt) cc_final: 0.7877 (mp) REVERT: D 92 GLN cc_start: 0.7529 (pm20) cc_final: 0.7203 (pm20) REVERT: D 116 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8529 (mmtm) REVERT: D 137 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: D 144 MET cc_start: 0.8212 (tpp) cc_final: 0.7776 (mpp) REVERT: D 157 ARG cc_start: 0.8601 (mmt90) cc_final: 0.8247 (mmt90) REVERT: D 192 LEU cc_start: 0.8716 (mt) cc_final: 0.8470 (mp) REVERT: D 210 GLU cc_start: 0.8189 (tt0) cc_final: 0.7960 (tt0) REVERT: D 226 GLU cc_start: 0.8219 (tt0) cc_final: 0.8008 (tt0) REVERT: D 252 ASN cc_start: 0.8929 (t0) cc_final: 0.8657 (t0) REVERT: D 314 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8160 (mtmm) outliers start: 25 outliers final: 18 residues processed: 315 average time/residue: 0.1411 time to fit residues: 57.1730 Evaluate side-chains 323 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 103 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 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 = 0.3477 r_free = 0.3477 target = 0.114427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102624 restraints weight = 13921.887| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.13 r_work: 0.3181 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9776 Z= 0.138 Angle : 0.601 16.039 13305 Z= 0.268 Chirality : 0.042 0.159 1541 Planarity : 0.004 0.045 1696 Dihedral : 4.095 18.302 1336 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.44 % Allowed : 19.12 % Favored : 78.44 % 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 aren not related in a simple way. whole: 1.46 (0.25), residues: 1224 helix: 2.09 (0.20), residues: 668 sheet: -0.19 (0.56), residues: 94 loop : -0.43 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 249 TYR 0.023 0.001 TYR B 55 PHE 0.012 0.001 PHE B 44 TRP 0.016 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9768) covalent geometry : angle 0.53240 (13281) hydrogen bonds : bond 0.03903 ( 523) hydrogen bonds : angle 4.20899 ( 1515) metal coordination : bond 0.00595 ( 8) metal coordination : angle 6.59088 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 0.366 Fit side-chains REVERT: A 62 MET cc_start: 0.6770 (mtm) cc_final: 0.6504 (mtm) REVERT: A 74 MET cc_start: 0.7753 (ppp) cc_final: 0.7166 (ppp) REVERT: A 95 ARG cc_start: 0.8591 (mtt90) cc_final: 0.8256 (mtt90) REVERT: A 151 MET cc_start: 0.8598 (mmm) cc_final: 0.8296 (mmp) REVERT: A 172 MET cc_start: 0.8552 (ppp) cc_final: 0.7890 (ppp) REVERT: A 185 MET cc_start: 0.7967 (tpp) cc_final: 0.7696 (tpp) REVERT: A 247 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8066 (ttp80) REVERT: A 300 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8032 (mtm-85) REVERT: B 166 LEU cc_start: 0.8484 (mt) cc_final: 0.8280 (mm) REVERT: B 204 MET cc_start: 0.8014 (ppp) cc_final: 0.7776 (ppp) REVERT: B 227 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 16 GLU cc_start: 0.7880 (tp30) cc_final: 0.7540 (tp30) REVERT: C 24 ASP cc_start: 0.8124 (t0) cc_final: 0.7719 (t0) REVERT: C 50 SER cc_start: 0.8377 (m) cc_final: 0.8031 (p) REVERT: C 82 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 138 VAL cc_start: 0.8469 (m) cc_final: 0.8205 (t) REVERT: C 149 VAL cc_start: 0.8471 (t) cc_final: 0.8105 (p) REVERT: C 168 ILE cc_start: 0.8710 (tp) cc_final: 0.8365 (pt) REVERT: C 171 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7804 (mmt90) REVERT: C 173 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8074 (mtpp) REVERT: C 198 GLU cc_start: 0.8142 (tp30) cc_final: 0.7811 (tp30) REVERT: C 201 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8404 (mm-40) REVERT: C 213 ASP cc_start: 0.7845 (t0) cc_final: 0.7466 (t0) REVERT: C 234 GLU cc_start: 0.7941 (tt0) cc_final: 0.7374 (tt0) REVERT: C 320 ASP cc_start: 0.8503 (p0) cc_final: 0.8024 (p0) REVERT: D 28 MET cc_start: 0.7082 (tmm) cc_final: 0.6759 (tmm) REVERT: D 36 LYS cc_start: 0.8424 (mttt) cc_final: 0.8131 (mtmm) REVERT: D 67 LEU cc_start: 0.8189 (mt) cc_final: 0.7895 (mp) REVERT: D 92 GLN cc_start: 0.7630 (pm20) cc_final: 0.7329 (pm20) REVERT: D 116 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8537 (mmtm) REVERT: D 144 MET cc_start: 0.8210 (tpp) cc_final: 0.7769 (mpp) REVERT: D 157 ARG cc_start: 0.8604 (mmt90) cc_final: 0.8262 (mmt90) REVERT: D 177 MET cc_start: 0.8300 (mmm) cc_final: 0.7928 (mmm) REVERT: D 192 LEU cc_start: 0.8753 (mt) cc_final: 0.8504 (mp) REVERT: D 210 GLU cc_start: 0.8174 (tt0) cc_final: 0.7953 (tt0) REVERT: D 252 ASN cc_start: 0.8906 (t0) cc_final: 0.8632 (t0) REVERT: D 276 ARG cc_start: 0.6378 (ttm110) cc_final: 0.6111 (ttm110) REVERT: D 314 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8170 (mtmm) outliers start: 25 outliers final: 17 residues processed: 322 average time/residue: 0.1462 time to fit residues: 60.2556 Evaluate side-chains 328 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 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 = 0.3473 r_free = 0.3473 target = 0.114006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102181 restraints weight = 13924.086| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.14 r_work: 0.3185 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9776 Z= 0.132 Angle : 0.605 16.214 13305 Z= 0.268 Chirality : 0.041 0.160 1541 Planarity : 0.004 0.045 1696 Dihedral : 4.044 18.362 1336 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 19.80 % Favored : 77.27 % 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 aren not related in a simple way. whole: 1.52 (0.25), residues: 1224 helix: 2.18 (0.20), residues: 662 sheet: -0.23 (0.56), residues: 94 loop : -0.43 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 249 TYR 0.020 0.001 TYR B 55 PHE 0.024 0.001 PHE A 96 TRP 0.016 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9768) covalent geometry : angle 0.53377 (13281) hydrogen bonds : bond 0.03842 ( 523) hydrogen bonds : angle 4.19329 ( 1515) metal coordination : bond 0.00583 ( 8) metal coordination : angle 6.70551 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.365 Fit side-chains REVERT: A 62 MET cc_start: 0.6703 (mtm) cc_final: 0.6445 (mtm) REVERT: A 74 MET cc_start: 0.7746 (ppp) cc_final: 0.7170 (ppp) REVERT: A 95 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8280 (mtt90) REVERT: A 96 PHE cc_start: 0.8507 (t80) cc_final: 0.8281 (t80) REVERT: A 151 MET cc_start: 0.8577 (mmm) cc_final: 0.8275 (mmp) REVERT: A 172 MET cc_start: 0.8552 (ppp) cc_final: 0.7898 (ppp) REVERT: A 185 MET cc_start: 0.7955 (tpp) cc_final: 0.7698 (tpp) REVERT: A 247 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8059 (ttp80) REVERT: A 300 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8070 (mtm-85) REVERT: B 166 LEU cc_start: 0.8488 (mt) cc_final: 0.8286 (mm) REVERT: B 204 MET cc_start: 0.8008 (ppp) cc_final: 0.7766 (ppp) REVERT: B 227 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7795 (t80) REVERT: C 16 GLU cc_start: 0.7838 (tp30) cc_final: 0.7487 (tp30) REVERT: C 24 ASP cc_start: 0.8119 (t0) cc_final: 0.7712 (t0) REVERT: C 50 SER cc_start: 0.8353 (m) cc_final: 0.8003 (p) REVERT: C 82 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7469 (mm-30) REVERT: C 138 VAL cc_start: 0.8453 (m) cc_final: 0.8202 (t) REVERT: C 149 VAL cc_start: 0.8470 (t) cc_final: 0.8092 (p) REVERT: C 168 ILE cc_start: 0.8700 (tp) cc_final: 0.8349 (pt) REVERT: C 171 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7777 (mmt90) REVERT: C 173 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8187 (mttp) REVERT: C 198 GLU cc_start: 0.8163 (tp30) cc_final: 0.7831 (tp30) REVERT: C 201 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8397 (mm-40) REVERT: C 213 ASP cc_start: 0.7852 (t0) cc_final: 0.7481 (t0) REVERT: C 234 GLU cc_start: 0.7942 (tt0) cc_final: 0.7363 (tt0) REVERT: D 28 MET cc_start: 0.7104 (tmm) cc_final: 0.6799 (tmm) REVERT: D 36 LYS cc_start: 0.8429 (mttt) cc_final: 0.8131 (mtmm) REVERT: D 67 LEU cc_start: 0.8230 (mt) cc_final: 0.7813 (mp) REVERT: D 92 GLN cc_start: 0.7644 (pm20) cc_final: 0.7326 (pm20) REVERT: D 116 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8543 (mmtm) REVERT: D 144 MET cc_start: 0.8201 (tpp) cc_final: 0.7755 (mpp) REVERT: D 157 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8280 (mmt90) REVERT: D 177 MET cc_start: 0.8289 (mmm) cc_final: 0.7933 (mmm) REVERT: D 192 LEU cc_start: 0.8731 (mt) cc_final: 0.8472 (mp) REVERT: D 210 GLU cc_start: 0.8196 (tt0) cc_final: 0.7963 (tt0) REVERT: D 226 GLU cc_start: 0.8229 (tt0) cc_final: 0.7971 (tt0) REVERT: D 252 ASN cc_start: 0.8909 (t0) cc_final: 0.8642 (t0) REVERT: D 314 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8157 (mtmm) outliers start: 30 outliers final: 21 residues processed: 321 average time/residue: 0.1426 time to fit residues: 58.8186 Evaluate side-chains 326 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102063 restraints weight = 13856.134| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.92 r_work: 0.3172 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9776 Z= 0.211 Angle : 0.653 17.757 13305 Z= 0.295 Chirality : 0.044 0.162 1541 Planarity : 0.004 0.040 1696 Dihedral : 4.188 19.336 1336 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.54 % Allowed : 20.39 % Favored : 77.07 % 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 aren not related in a simple way. whole: 1.32 (0.25), residues: 1224 helix: 2.03 (0.20), residues: 667 sheet: -0.35 (0.56), residues: 94 loop : -0.55 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 138 TYR 0.019 0.001 TYR B 55 PHE 0.027 0.002 PHE A 109 TRP 0.017 0.001 TRP A 293 HIS 0.008 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9768) covalent geometry : angle 0.58541 (13281) hydrogen bonds : bond 0.04501 ( 523) hydrogen bonds : angle 4.29584 ( 1515) metal coordination : bond 0.00819 ( 8) metal coordination : angle 6.84326 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6644 (mtm) cc_final: 0.6404 (mtm) REVERT: A 74 MET cc_start: 0.7714 (ppp) cc_final: 0.7168 (ppp) REVERT: A 86 ILE cc_start: 0.8703 (mp) cc_final: 0.8497 (mm) REVERT: A 95 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8330 (mtt90) REVERT: A 151 MET cc_start: 0.8554 (mmm) cc_final: 0.8231 (mmp) REVERT: A 172 MET cc_start: 0.8641 (ppp) cc_final: 0.7964 (ppp) REVERT: A 185 MET cc_start: 0.7953 (tpp) cc_final: 0.7681 (tpp) REVERT: A 247 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8025 (ttp80) REVERT: A 286 SER cc_start: 0.9028 (t) cc_final: 0.8751 (t) REVERT: A 300 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8046 (mtm-85) REVERT: B 166 LEU cc_start: 0.8459 (mt) cc_final: 0.8252 (mm) REVERT: B 204 MET cc_start: 0.8089 (ppp) cc_final: 0.7852 (ppp) REVERT: B 227 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7845 (t80) REVERT: C 16 GLU cc_start: 0.7915 (tp30) cc_final: 0.7618 (tp30) REVERT: C 24 ASP cc_start: 0.8078 (t0) cc_final: 0.7636 (t0) REVERT: C 50 SER cc_start: 0.8271 (m) cc_final: 0.7900 (p) REVERT: C 70 PHE cc_start: 0.8595 (t80) cc_final: 0.8362 (t80) REVERT: C 82 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 138 VAL cc_start: 0.8443 (m) cc_final: 0.8144 (t) REVERT: C 149 VAL cc_start: 0.8475 (t) cc_final: 0.8112 (p) REVERT: C 158 MET cc_start: 0.8300 (mmm) cc_final: 0.7799 (mmm) REVERT: C 168 ILE cc_start: 0.8675 (tp) cc_final: 0.8312 (pt) REVERT: C 171 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7823 (mmt90) REVERT: C 173 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8015 (mtpp) REVERT: C 198 GLU cc_start: 0.8046 (tp30) cc_final: 0.7717 (tp30) REVERT: C 201 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8388 (mm-40) REVERT: C 213 ASP cc_start: 0.7875 (t0) cc_final: 0.7481 (t0) REVERT: C 234 GLU cc_start: 0.7874 (tt0) cc_final: 0.7219 (tt0) REVERT: D 28 MET cc_start: 0.7031 (tmm) cc_final: 0.6748 (tmm) REVERT: D 36 LYS cc_start: 0.8380 (mttt) cc_final: 0.8077 (mtmm) REVERT: D 70 MET cc_start: 0.8125 (tpp) cc_final: 0.7913 (mpp) REVERT: D 92 GLN cc_start: 0.7523 (pm20) cc_final: 0.7206 (pm20) REVERT: D 116 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8484 (mmtm) REVERT: D 129 ASN cc_start: 0.8444 (m-40) cc_final: 0.8093 (m110) REVERT: D 144 MET cc_start: 0.8072 (tpp) cc_final: 0.7616 (mpp) REVERT: D 192 LEU cc_start: 0.8781 (mt) cc_final: 0.8519 (mp) REVERT: D 210 GLU cc_start: 0.8153 (tt0) cc_final: 0.7929 (tt0) REVERT: D 226 GLU cc_start: 0.8134 (tt0) cc_final: 0.7831 (tt0) REVERT: D 252 ASN cc_start: 0.8897 (t0) cc_final: 0.8571 (t0) REVERT: D 302 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7650 (mtp-110) outliers start: 26 outliers final: 21 residues processed: 326 average time/residue: 0.1445 time to fit residues: 60.4407 Evaluate side-chains 337 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 329 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.0000 chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 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 = 0.3471 r_free = 0.3471 target = 0.113818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102767 restraints weight = 13615.192| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.91 r_work: 0.3185 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9776 Z= 0.170 Angle : 0.637 17.662 13305 Z= 0.285 Chirality : 0.043 0.161 1541 Planarity : 0.004 0.041 1696 Dihedral : 4.146 18.975 1336 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.54 % Allowed : 20.39 % Favored : 77.07 % 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 aren not related in a simple way. whole: 1.40 (0.25), residues: 1224 helix: 2.12 (0.20), residues: 662 sheet: -0.36 (0.56), residues: 94 loop : -0.51 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 249 TYR 0.019 0.001 TYR B 55 PHE 0.022 0.001 PHE A 109 TRP 0.017 0.001 TRP A 293 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9768) covalent geometry : angle 0.56655 (13281) hydrogen bonds : bond 0.04201 ( 523) hydrogen bonds : angle 4.25054 ( 1515) metal coordination : bond 0.00649 ( 8) metal coordination : angle 6.86002 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8347 (mt) cc_final: 0.8119 (mp) REVERT: A 62 MET cc_start: 0.6643 (mtm) cc_final: 0.6396 (mtm) REVERT: A 74 MET cc_start: 0.7685 (ppp) cc_final: 0.7420 (ppp) REVERT: A 95 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8301 (mtt90) REVERT: A 151 MET cc_start: 0.8544 (mmm) cc_final: 0.8229 (mmp) REVERT: A 172 MET cc_start: 0.8657 (ppp) cc_final: 0.7966 (ppp) REVERT: A 185 MET cc_start: 0.7923 (tpp) cc_final: 0.7655 (tpp) REVERT: A 247 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7945 (ttp80) REVERT: A 286 SER cc_start: 0.9013 (t) cc_final: 0.8725 (t) REVERT: A 300 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8016 (mtm-85) REVERT: B 204 MET cc_start: 0.8022 (ppp) cc_final: 0.7781 (ppp) REVERT: B 227 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 16 GLU cc_start: 0.7836 (tp30) cc_final: 0.7396 (tp30) REVERT: C 24 ASP cc_start: 0.8068 (t0) cc_final: 0.7634 (t0) REVERT: C 50 SER cc_start: 0.8214 (m) cc_final: 0.7839 (p) REVERT: C 70 PHE cc_start: 0.8571 (t80) cc_final: 0.8327 (t80) REVERT: C 82 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 138 VAL cc_start: 0.8397 (m) cc_final: 0.8136 (t) REVERT: C 149 VAL cc_start: 0.8439 (t) cc_final: 0.8069 (p) REVERT: C 158 MET cc_start: 0.8265 (mmm) cc_final: 0.7749 (mmm) REVERT: C 171 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7786 (mmt90) REVERT: C 173 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7993 (mtpp) REVERT: C 198 GLU cc_start: 0.8021 (tp30) cc_final: 0.7684 (tp30) REVERT: C 201 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8442 (tp40) REVERT: C 213 ASP cc_start: 0.7883 (t0) cc_final: 0.7468 (t0) REVERT: C 234 GLU cc_start: 0.7872 (tt0) cc_final: 0.7204 (tt0) REVERT: C 320 ASP cc_start: 0.8536 (p0) cc_final: 0.7963 (p0) REVERT: D 28 MET cc_start: 0.7044 (tmm) cc_final: 0.6782 (tmm) REVERT: D 36 LYS cc_start: 0.8398 (mttt) cc_final: 0.8082 (mtmm) REVERT: D 70 MET cc_start: 0.8093 (tpp) cc_final: 0.7853 (mpp) REVERT: D 92 GLN cc_start: 0.7530 (pm20) cc_final: 0.7193 (pm20) REVERT: D 116 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8473 (mmtm) REVERT: D 129 ASN cc_start: 0.8392 (m-40) cc_final: 0.8060 (m110) REVERT: D 144 MET cc_start: 0.8056 (tpp) cc_final: 0.7595 (mpp) REVERT: D 192 LEU cc_start: 0.8751 (mt) cc_final: 0.8506 (mp) REVERT: D 210 GLU cc_start: 0.8133 (tt0) cc_final: 0.7921 (tt0) REVERT: D 226 GLU cc_start: 0.8128 (tt0) cc_final: 0.7807 (tt0) REVERT: D 252 ASN cc_start: 0.8898 (t0) cc_final: 0.8566 (t0) REVERT: D 254 ARG cc_start: 0.8537 (mtp180) cc_final: 0.8244 (mtp180) REVERT: D 302 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7644 (mtp-110) REVERT: D 314 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8058 (mtmm) outliers start: 26 outliers final: 20 residues processed: 323 average time/residue: 0.1485 time to fit residues: 61.2079 Evaluate side-chains 333 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain D residue 314 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102410 restraints weight = 13776.787| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.99 r_work: 0.3188 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9776 Z= 0.167 Angle : 0.644 17.625 13305 Z= 0.288 Chirality : 0.043 0.161 1541 Planarity : 0.004 0.044 1696 Dihedral : 4.135 18.765 1336 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.15 % Allowed : 21.17 % Favored : 76.68 % 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 aren not related in a simple way. whole: 1.40 (0.25), residues: 1224 helix: 2.13 (0.20), residues: 661 sheet: -0.35 (0.56), residues: 94 loop : -0.55 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 249 TYR 0.019 0.001 TYR B 55 PHE 0.024 0.002 PHE A 96 TRP 0.017 0.001 TRP A 293 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9768) covalent geometry : angle 0.57456 (13281) hydrogen bonds : bond 0.04172 ( 523) hydrogen bonds : angle 4.22798 ( 1515) metal coordination : bond 0.00653 ( 8) metal coordination : angle 6.88922 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.53 seconds wall clock time: 49 minutes 3.11 seconds (2943.11 seconds total)