Starting phenix.real_space_refine on Fri Mar 14 06:17:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1v_39737/03_2025/8z1v_39737_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1v_39737/03_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_39737/03_2025/8z1v_39737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1v_39737/03_2025/8z1v_39737.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1v_39737/03_2025/8z1v_39737_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1v_39737/03_2025/8z1v_39737_neut.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.09, per 1000 atoms: 0.64 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.48 Time building geometry restraints manager: 2.86 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: 1.950 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.160 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- 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 : 0.025 0.139 9768 Z= 1.690 Angle : 2.211 10.795 13281 Z= 1.488 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.151 0.018 TRP A 293 HIS 0.016 0.003 HIS C 247 PHE 0.080 0.012 PHE D 162 TYR 0.089 0.016 TYR D 81 ARG 0.009 0.001 ARG C 62 *********************** 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 : 1.038 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: 0.7643 (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: 0.6755 (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: 0.2900 time to fit residues: 136.7311 Evaluate side-chains 320 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 C 160 GLN D 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103120 restraints weight = 13700.323| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.94 r_work: 0.3200 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9768 Z= 0.254 Angle : 0.625 7.049 13281 Z= 0.331 Chirality : 0.046 0.185 1541 Planarity : 0.005 0.047 1696 Dihedral : 5.152 24.757 1336 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.85 % Allowed : 8.98 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1224 helix: 1.18 (0.20), residues: 663 sheet: -0.20 (0.53), residues: 94 loop : -0.11 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 293 HIS 0.005 0.001 HIS C 247 PHE 0.017 0.002 PHE D 303 TYR 0.013 0.001 TYR A 236 ARG 0.007 0.001 ARG D 276 *********************** 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 355 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 336 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 24 PHE cc_start: 0.8442 (t80) cc_final: 0.8111 (t80) REVERT: A 62 MET cc_start: 0.6852 (mtm) cc_final: 0.6585 (mtm) REVERT: A 96 PHE cc_start: 0.8540 (t80) cc_final: 0.7824 (t80) REVERT: A 151 MET cc_start: 0.8651 (mmm) cc_final: 0.8419 (mmp) REVERT: A 156 VAL cc_start: 0.8317 (t) cc_final: 0.8062 (m) REVERT: A 185 MET cc_start: 0.7868 (tpp) cc_final: 0.7592 (tpp) REVERT: A 219 VAL cc_start: 0.8704 (t) cc_final: 0.8391 (p) REVERT: A 247 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7956 (ttp80) REVERT: A 300 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: A 336 ARG cc_start: 0.7570 (mtm180) cc_final: 0.5908 (mmm160) REVERT: B 47 ILE cc_start: 0.8488 (tp) cc_final: 0.8233 (tp) REVERT: B 84 ASP cc_start: 0.8078 (t0) cc_final: 0.7859 (t0) REVERT: B 126 PHE cc_start: 0.8805 (m-80) cc_final: 0.8492 (m-80) REVERT: B 140 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8368 (mt) REVERT: B 185 LEU cc_start: 0.8564 (mt) cc_final: 0.8345 (mm) REVERT: B 204 MET cc_start: 0.8047 (ppp) cc_final: 0.7841 (ppp) REVERT: B 212 PHE cc_start: 0.8418 (t80) cc_final: 0.8216 (t80) REVERT: B 248 THR cc_start: 0.9145 (t) cc_final: 0.8935 (p) REVERT: B 286 MET cc_start: 0.7606 (mmp) cc_final: 0.7005 (mmm) REVERT: C 15 ASP cc_start: 0.7756 (t70) cc_final: 0.7434 (t70) REVERT: C 25 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: C 41 GLU cc_start: 0.7465 (pt0) cc_final: 0.7121 (pt0) REVERT: C 50 SER cc_start: 0.8325 (m) cc_final: 0.7877 (p) REVERT: C 80 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6714 (tm-30) REVERT: C 149 VAL cc_start: 0.8470 (t) cc_final: 0.8203 (p) REVERT: C 168 ILE cc_start: 0.8530 (tp) cc_final: 0.8295 (tp) REVERT: C 173 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8149 (ttmm) REVERT: C 198 GLU cc_start: 0.8094 (tp30) cc_final: 0.7846 (tp30) REVERT: C 200 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 213 ASP cc_start: 0.7806 (t0) cc_final: 0.7361 (t0) REVERT: C 234 GLU cc_start: 0.7939 (tt0) cc_final: 0.7559 (tt0) REVERT: D 28 MET cc_start: 0.6984 (tmm) cc_final: 0.6574 (tmm) REVERT: D 36 LYS cc_start: 0.8410 (mttt) cc_final: 0.8126 (mtmp) REVERT: D 39 ASP cc_start: 0.7742 (t0) cc_final: 0.6918 (t0) REVERT: D 54 VAL cc_start: 0.8450 (m) cc_final: 0.8181 (p) REVERT: D 92 GLN cc_start: 0.7462 (pm20) cc_final: 0.7126 (pm20) REVERT: D 116 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8652 (mmtm) REVERT: D 140 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7974 (ttmm) REVERT: D 144 MET cc_start: 0.8032 (tpp) cc_final: 0.7613 (mpp) REVERT: D 179 ASP cc_start: 0.8198 (t0) cc_final: 0.7948 (t0) REVERT: D 205 MET cc_start: 0.8105 (mmp) cc_final: 0.7865 (mmp) REVERT: D 210 GLU cc_start: 0.8189 (tt0) cc_final: 0.7960 (tt0) REVERT: D 226 GLU cc_start: 0.8167 (tt0) cc_final: 0.7836 (tt0) REVERT: D 252 ASN cc_start: 0.8882 (t0) cc_final: 0.8395 (t0) REVERT: D 271 ASP cc_start: 0.7491 (t70) cc_final: 0.6962 (t0) REVERT: D 309 LEU cc_start: 0.8218 (mt) cc_final: 0.7993 (mm) REVERT: D 314 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8089 (ttmm) REVERT: D 327 ASP cc_start: 0.8430 (t70) cc_final: 0.8039 (t0) outliers start: 19 outliers final: 10 residues processed: 342 average time/residue: 0.2869 time to fit residues: 125.4916 Evaluate side-chains 316 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE 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 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 105 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102872 restraints weight = 13877.497| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.97 r_work: 0.3193 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9768 Z= 0.246 Angle : 0.557 5.766 13281 Z= 0.289 Chirality : 0.043 0.171 1541 Planarity : 0.005 0.037 1696 Dihedral : 4.621 19.852 1336 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.15 % Allowed : 13.56 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1224 helix: 1.63 (0.20), residues: 664 sheet: -0.13 (0.54), residues: 94 loop : -0.29 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 293 HIS 0.003 0.001 HIS A 254 PHE 0.015 0.001 PHE D 303 TYR 0.011 0.001 TYR A 236 ARG 0.006 0.001 ARG A 249 *********************** 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 337 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 1.079 Fit side-chains REVERT: A 62 MET cc_start: 0.6810 (mtm) cc_final: 0.6560 (mtm) REVERT: A 74 MET cc_start: 0.7619 (ppp) cc_final: 0.7127 (ppp) REVERT: A 96 PHE cc_start: 0.8569 (t80) cc_final: 0.7836 (t80) REVERT: A 151 MET cc_start: 0.8671 (mmm) cc_final: 0.8373 (mmp) REVERT: A 156 VAL cc_start: 0.8326 (t) cc_final: 0.8021 (m) REVERT: A 172 MET cc_start: 0.8683 (ppp) cc_final: 0.8198 (ppp) REVERT: A 173 VAL cc_start: 0.8916 (t) cc_final: 0.8694 (p) REVERT: A 185 MET cc_start: 0.7848 (tpp) cc_final: 0.7537 (tpp) REVERT: A 247 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7997 (ttp80) REVERT: A 286 SER cc_start: 0.8923 (t) cc_final: 0.8670 (t) REVERT: A 300 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8038 (mtm-85) REVERT: B 47 ILE cc_start: 0.8529 (tp) cc_final: 0.8284 (tp) REVERT: B 126 PHE cc_start: 0.8768 (m-80) cc_final: 0.8542 (m-80) REVERT: B 196 SER cc_start: 0.8732 (m) cc_final: 0.8496 (t) REVERT: B 204 MET cc_start: 0.8002 (ppp) cc_final: 0.7775 (ppp) REVERT: B 227 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 286 MET cc_start: 0.7805 (mmp) cc_final: 0.7588 (mmm) REVERT: C 15 ASP cc_start: 0.7908 (t70) cc_final: 0.7656 (t70) REVERT: C 16 GLU cc_start: 0.7988 (tp30) cc_final: 0.7711 (tp30) REVERT: C 24 ASP cc_start: 0.8097 (t0) cc_final: 0.7671 (t0) REVERT: C 25 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: C 41 GLU cc_start: 0.7422 (pt0) cc_final: 0.7104 (pt0) REVERT: C 50 SER cc_start: 0.8345 (m) cc_final: 0.7911 (p) REVERT: C 82 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7379 (mm-30) REVERT: C 149 VAL cc_start: 0.8493 (t) cc_final: 0.8145 (p) REVERT: C 171 ARG cc_start: 0.8186 (mmt180) cc_final: 0.7726 (mmt90) REVERT: C 173 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8068 (ttmm) REVERT: C 198 GLU cc_start: 0.8055 (tp30) cc_final: 0.7800 (tp30) REVERT: C 200 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 213 ASP cc_start: 0.7819 (t0) cc_final: 0.7402 (t0) REVERT: C 234 GLU cc_start: 0.7991 (tt0) cc_final: 0.7596 (tt0) REVERT: C 259 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 28 MET cc_start: 0.7052 (tmm) cc_final: 0.6696 (tmm) REVERT: D 36 LYS cc_start: 0.8411 (mttt) cc_final: 0.8074 (mttp) REVERT: D 39 ASP cc_start: 0.7749 (t0) cc_final: 0.6965 (t0) REVERT: D 92 GLN cc_start: 0.7377 (pm20) cc_final: 0.7042 (pm20) REVERT: D 116 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8584 (mmtm) REVERT: D 144 MET cc_start: 0.8054 (tpp) cc_final: 0.7623 (mpp) REVERT: D 177 MET cc_start: 0.8339 (mmm) cc_final: 0.7830 (mmm) REVERT: D 210 GLU cc_start: 0.8168 (tt0) cc_final: 0.7935 (tt0) REVERT: D 226 GLU cc_start: 0.8186 (tt0) cc_final: 0.7819 (tt0) REVERT: D 252 ASN cc_start: 0.8944 (t0) cc_final: 0.8582 (t0) REVERT: D 267 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7723 (ttm-80) REVERT: D 276 ARG cc_start: 0.6499 (ttm110) cc_final: 0.6257 (ttm110) REVERT: D 309 LEU cc_start: 0.8268 (mt) cc_final: 0.7917 (mp) REVERT: D 314 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8097 (ttmm) outliers start: 22 outliers final: 16 residues processed: 321 average time/residue: 0.3169 time to fit residues: 129.8294 Evaluate side-chains 311 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 A residue 269 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 139 ASP 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 329 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102532 restraints weight = 13779.273| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.99 r_work: 0.3186 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9768 Z= 0.238 Angle : 0.547 9.341 13281 Z= 0.278 Chirality : 0.043 0.169 1541 Planarity : 0.005 0.042 1696 Dihedral : 4.397 19.402 1336 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.15 % Allowed : 15.71 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1224 helix: 1.79 (0.20), residues: 667 sheet: -0.21 (0.55), residues: 94 loop : -0.41 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.003 0.001 HIS C 12 PHE 0.015 0.001 PHE D 303 TYR 0.011 0.001 TYR A 236 ARG 0.009 0.001 ARG A 249 *********************** 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 331 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 309 time to evaluate : 1.075 Fit side-chains REVERT: A 62 MET cc_start: 0.6804 (mtm) cc_final: 0.6547 (mtm) REVERT: A 74 MET cc_start: 0.7652 (ppp) cc_final: 0.7122 (ppp) REVERT: A 96 PHE cc_start: 0.8564 (t80) cc_final: 0.7837 (t80) REVERT: A 151 MET cc_start: 0.8639 (mmm) cc_final: 0.8310 (mmp) REVERT: A 156 VAL cc_start: 0.8352 (t) cc_final: 0.8070 (m) REVERT: A 172 MET cc_start: 0.8723 (ppp) cc_final: 0.8181 (ppp) REVERT: A 173 VAL cc_start: 0.8921 (t) cc_final: 0.8690 (p) REVERT: A 185 MET cc_start: 0.7927 (tpp) cc_final: 0.7616 (tpp) REVERT: A 247 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8021 (ttp80) REVERT: A 300 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8041 (mtm-85) REVERT: B 47 ILE cc_start: 0.8557 (tp) cc_final: 0.8324 (tp) REVERT: B 89 ASP cc_start: 0.7291 (t0) cc_final: 0.7078 (t0) REVERT: B 204 MET cc_start: 0.8021 (ppp) cc_final: 0.7793 (ppp) REVERT: B 227 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7844 (t80) REVERT: B 286 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7468 (mtp) REVERT: C 15 ASP cc_start: 0.7970 (t70) cc_final: 0.7734 (t70) REVERT: C 16 GLU cc_start: 0.7956 (tp30) cc_final: 0.7708 (tp30) REVERT: C 24 ASP cc_start: 0.8089 (t0) cc_final: 0.7718 (t0) REVERT: C 50 SER cc_start: 0.8300 (m) cc_final: 0.7888 (p) REVERT: C 82 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 138 VAL cc_start: 0.8457 (m) cc_final: 0.8227 (t) REVERT: C 149 VAL cc_start: 0.8461 (t) cc_final: 0.8140 (p) REVERT: C 168 ILE cc_start: 0.8588 (tp) cc_final: 0.8323 (pt) REVERT: C 171 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7815 (mmt90) REVERT: C 173 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8123 (ttmm) REVERT: C 198 GLU cc_start: 0.8081 (tp30) cc_final: 0.7807 (tp30) REVERT: C 213 ASP cc_start: 0.7839 (t0) cc_final: 0.7444 (t0) REVERT: C 234 GLU cc_start: 0.7985 (tt0) cc_final: 0.7614 (tt0) REVERT: C 259 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 296 ARG cc_start: 0.8634 (ttp-170) cc_final: 0.8406 (ttp80) REVERT: C 320 ASP cc_start: 0.8369 (p0) cc_final: 0.7899 (p0) REVERT: D 28 MET cc_start: 0.7033 (tmm) cc_final: 0.6727 (tmm) REVERT: D 36 LYS cc_start: 0.8436 (mttt) cc_final: 0.8109 (mttp) REVERT: D 39 ASP cc_start: 0.7756 (t0) cc_final: 0.7134 (t0) REVERT: D 92 GLN cc_start: 0.7435 (pm20) cc_final: 0.7087 (pm20) REVERT: D 116 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8565 (mmtm) REVERT: D 144 MET cc_start: 0.8101 (tpp) cc_final: 0.7632 (mpp) REVERT: D 177 MET cc_start: 0.8359 (mmm) cc_final: 0.7899 (mmm) REVERT: D 210 GLU cc_start: 0.8191 (tt0) cc_final: 0.7952 (tt0) REVERT: D 226 GLU cc_start: 0.8165 (tt0) cc_final: 0.7931 (tt0) REVERT: D 252 ASN cc_start: 0.8944 (t0) cc_final: 0.8613 (t0) REVERT: D 267 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7757 (ttm-80) outliers start: 22 outliers final: 16 residues processed: 317 average time/residue: 0.2980 time to fit residues: 120.9086 Evaluate side-chains 321 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 76 SER 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 42 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 95 LYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 233 MET 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 60 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 93 optimal weight: 0.0030 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.113934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102115 restraints weight = 13771.690| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.13 r_work: 0.3185 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9768 Z= 0.208 Angle : 0.540 8.416 13281 Z= 0.271 Chirality : 0.042 0.163 1541 Planarity : 0.004 0.039 1696 Dihedral : 4.222 18.786 1336 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.63 % Allowed : 16.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1224 helix: 1.92 (0.20), residues: 668 sheet: -0.18 (0.56), residues: 94 loop : -0.43 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 PHE 0.014 0.001 PHE C 70 TYR 0.010 0.001 TYR A 236 ARG 0.009 0.000 ARG A 249 *********************** 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 331 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.151 Fit side-chains REVERT: A 24 PHE cc_start: 0.8470 (t80) cc_final: 0.8215 (t80) REVERT: A 62 MET cc_start: 0.6800 (mtm) cc_final: 0.6543 (mtm) REVERT: A 74 MET cc_start: 0.7683 (ppp) cc_final: 0.7164 (ppp) REVERT: A 96 PHE cc_start: 0.8574 (t80) cc_final: 0.7844 (t80) REVERT: A 151 MET cc_start: 0.8612 (mmm) cc_final: 0.8285 (mmp) REVERT: A 156 VAL cc_start: 0.8417 (t) cc_final: 0.8095 (m) REVERT: A 172 MET cc_start: 0.8700 (ppp) cc_final: 0.8124 (ppp) REVERT: A 185 MET cc_start: 0.7968 (tpp) cc_final: 0.7660 (tpp) REVERT: A 247 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8081 (ttp80) REVERT: A 300 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8092 (mtm-85) REVERT: B 47 ILE cc_start: 0.8604 (tp) cc_final: 0.8397 (tp) REVERT: B 204 MET cc_start: 0.8027 (ppp) cc_final: 0.7793 (ppp) REVERT: B 227 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 286 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: C 16 GLU cc_start: 0.7963 (tp30) cc_final: 0.7700 (tp30) REVERT: C 24 ASP cc_start: 0.8112 (t0) cc_final: 0.7737 (t0) REVERT: C 50 SER cc_start: 0.8351 (m) cc_final: 0.7987 (p) REVERT: C 70 PHE cc_start: 0.8607 (t80) cc_final: 0.8385 (t80) REVERT: C 82 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 138 VAL cc_start: 0.8489 (m) cc_final: 0.8205 (t) REVERT: C 149 VAL cc_start: 0.8461 (t) cc_final: 0.8096 (p) REVERT: C 168 ILE cc_start: 0.8698 (tp) cc_final: 0.8399 (pt) REVERT: C 171 ARG cc_start: 0.8309 (mmt180) cc_final: 0.7850 (mmt90) REVERT: C 198 GLU cc_start: 0.8182 (tp30) cc_final: 0.7841 (tp30) REVERT: C 201 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8386 (mm-40) REVERT: C 213 ASP cc_start: 0.7824 (t0) cc_final: 0.7401 (t0) REVERT: C 234 GLU cc_start: 0.7997 (tt0) cc_final: 0.7410 (tt0) REVERT: C 296 ARG cc_start: 0.8673 (ttp-170) cc_final: 0.8407 (ttp80) REVERT: D 28 MET cc_start: 0.7109 (tmm) cc_final: 0.6808 (tmm) REVERT: D 36 LYS cc_start: 0.8423 (mttt) cc_final: 0.8151 (mtmp) REVERT: D 84 GLN cc_start: 0.8292 (tt0) cc_final: 0.8076 (mt0) REVERT: D 116 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8574 (mmtm) REVERT: D 144 MET cc_start: 0.8160 (tpp) cc_final: 0.7721 (mpp) REVERT: D 177 MET cc_start: 0.8320 (mmm) cc_final: 0.7886 (mmm) REVERT: D 192 LEU cc_start: 0.8761 (mt) cc_final: 0.8508 (mp) REVERT: D 210 GLU cc_start: 0.8228 (tt0) cc_final: 0.8001 (tt0) REVERT: D 226 GLU cc_start: 0.8209 (tt0) cc_final: 0.7991 (tt0) REVERT: D 252 ASN cc_start: 0.8954 (t0) cc_final: 0.8649 (t0) REVERT: D 267 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7816 (ttm-80) REVERT: D 276 ARG cc_start: 0.6397 (ttm110) cc_final: 0.6122 (ttm110) REVERT: D 314 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8164 (mtmm) outliers start: 27 outliers final: 19 residues processed: 314 average time/residue: 0.3204 time to fit residues: 128.7877 Evaluate side-chains 321 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 300 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG 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 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 78 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 233 MET 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 68 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.113085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101279 restraints weight = 13774.145| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9768 Z= 0.231 Angle : 0.538 7.745 13281 Z= 0.271 Chirality : 0.042 0.160 1541 Planarity : 0.004 0.038 1696 Dihedral : 4.190 18.629 1336 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.05 % Allowed : 18.34 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1224 helix: 1.98 (0.20), residues: 668 sheet: -0.23 (0.56), residues: 94 loop : -0.51 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 PHE 0.013 0.001 PHE D 303 TYR 0.010 0.001 TYR A 236 ARG 0.004 0.000 ARG C 266 *********************** 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 322 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 301 time to evaluate : 1.170 Fit side-chains REVERT: A 24 PHE cc_start: 0.8459 (t80) cc_final: 0.8229 (t80) REVERT: A 62 MET cc_start: 0.6814 (mtm) cc_final: 0.6551 (mtm) REVERT: A 74 MET cc_start: 0.7713 (ppp) cc_final: 0.7149 (ppp) REVERT: A 96 PHE cc_start: 0.8584 (t80) cc_final: 0.7850 (t80) REVERT: A 151 MET cc_start: 0.8591 (mmm) cc_final: 0.8287 (mmp) REVERT: A 172 MET cc_start: 0.8625 (ppp) cc_final: 0.8002 (ppp) REVERT: A 185 MET cc_start: 0.7936 (tpp) cc_final: 0.7575 (tpp) REVERT: A 247 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8081 (ttp80) REVERT: A 286 SER cc_start: 0.8991 (t) cc_final: 0.8706 (t) REVERT: A 300 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8033 (mtm-85) REVERT: B 204 MET cc_start: 0.8035 (ppp) cc_final: 0.7802 (ppp) REVERT: B 227 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7831 (t80) REVERT: C 16 GLU cc_start: 0.8013 (tp30) cc_final: 0.7701 (tp30) REVERT: C 24 ASP cc_start: 0.8119 (t0) cc_final: 0.7737 (t0) REVERT: C 50 SER cc_start: 0.8338 (m) cc_final: 0.7984 (p) REVERT: C 70 PHE cc_start: 0.8624 (t80) cc_final: 0.8421 (t80) REVERT: C 82 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 138 VAL cc_start: 0.8499 (m) cc_final: 0.8218 (t) REVERT: C 149 VAL cc_start: 0.8470 (t) cc_final: 0.8094 (p) REVERT: C 158 MET cc_start: 0.8315 (mmm) cc_final: 0.7845 (mmm) REVERT: C 168 ILE cc_start: 0.8727 (tp) cc_final: 0.8400 (pt) REVERT: C 171 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7911 (mmt180) REVERT: C 173 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8079 (mtpp) REVERT: C 198 GLU cc_start: 0.8196 (tp30) cc_final: 0.7843 (tp30) REVERT: C 201 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8377 (mm-40) REVERT: C 213 ASP cc_start: 0.7800 (t0) cc_final: 0.7402 (t0) REVERT: C 234 GLU cc_start: 0.7976 (tt0) cc_final: 0.7406 (tt0) REVERT: D 28 MET cc_start: 0.7097 (tmm) cc_final: 0.6787 (tmm) REVERT: D 36 LYS cc_start: 0.8432 (mttt) cc_final: 0.8149 (mtmp) REVERT: D 92 GLN cc_start: 0.7480 (pm20) cc_final: 0.7135 (pm20) REVERT: D 116 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8522 (mmtm) REVERT: D 144 MET cc_start: 0.8183 (tpp) cc_final: 0.7738 (mpp) REVERT: D 192 LEU cc_start: 0.8776 (mt) cc_final: 0.8531 (mp) REVERT: D 210 GLU cc_start: 0.8186 (tt0) cc_final: 0.7957 (tt0) REVERT: D 226 GLU cc_start: 0.8160 (tt0) cc_final: 0.7959 (tt0) REVERT: D 252 ASN cc_start: 0.8934 (t0) cc_final: 0.8626 (t0) REVERT: D 267 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7708 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 308 average time/residue: 0.3165 time to fit residues: 124.3657 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 : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 139 ASP 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 233 MET Chi-restraints excluded: chain D residue 237 LEU 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 34 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.113516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102337 restraints weight = 13712.368| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.94 r_work: 0.3178 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9768 Z= 0.287 Angle : 0.560 8.186 13281 Z= 0.282 Chirality : 0.043 0.161 1541 Planarity : 0.004 0.045 1696 Dihedral : 4.202 19.049 1336 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.24 % Allowed : 20.10 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1224 helix: 2.00 (0.20), residues: 667 sheet: -0.34 (0.56), residues: 94 loop : -0.57 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.007 0.001 HIS C 12 PHE 0.012 0.001 PHE D 303 TYR 0.011 0.001 TYR A 236 ARG 0.010 0.001 ARG A 249 *********************** 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 337 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 1.040 Fit side-chains REVERT: A 24 PHE cc_start: 0.8425 (t80) cc_final: 0.8184 (t80) REVERT: A 62 MET cc_start: 0.6755 (mtm) cc_final: 0.6510 (mtm) REVERT: A 74 MET cc_start: 0.7682 (ppp) cc_final: 0.7128 (ppp) REVERT: A 95 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8276 (mtt90) REVERT: A 96 PHE cc_start: 0.8589 (t80) cc_final: 0.7857 (t80) REVERT: A 151 MET cc_start: 0.8477 (mmm) cc_final: 0.8169 (mmp) REVERT: A 172 MET cc_start: 0.8691 (ppp) cc_final: 0.8049 (ppp) REVERT: A 185 MET cc_start: 0.7924 (tpp) cc_final: 0.7535 (tpp) REVERT: A 247 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8025 (ttp80) REVERT: A 286 SER cc_start: 0.9004 (t) cc_final: 0.8726 (t) REVERT: A 300 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8029 (mtm-85) REVERT: B 60 GLN cc_start: 0.8825 (mt0) cc_final: 0.8510 (mt0) REVERT: B 204 MET cc_start: 0.8087 (ppp) cc_final: 0.7860 (ppp) REVERT: B 227 PHE cc_start: 0.8267 (m-80) cc_final: 0.7816 (t80) REVERT: C 16 GLU cc_start: 0.8012 (tp30) cc_final: 0.7662 (tp30) REVERT: C 24 ASP cc_start: 0.8063 (t0) cc_final: 0.7656 (t0) REVERT: C 50 SER cc_start: 0.8275 (m) cc_final: 0.7898 (p) REVERT: C 82 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7440 (mm-30) REVERT: C 138 VAL cc_start: 0.8446 (m) cc_final: 0.8171 (t) REVERT: C 149 VAL cc_start: 0.8460 (t) cc_final: 0.8085 (p) REVERT: C 158 MET cc_start: 0.8296 (mmm) cc_final: 0.7789 (mmm) REVERT: C 168 ILE cc_start: 0.8679 (tp) cc_final: 0.8335 (pt) REVERT: C 171 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7911 (mmt180) REVERT: C 173 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8053 (mtpp) REVERT: C 198 GLU cc_start: 0.8071 (tp30) cc_final: 0.7719 (tp30) REVERT: C 213 ASP cc_start: 0.7843 (t0) cc_final: 0.7443 (t0) REVERT: C 234 GLU cc_start: 0.7880 (tt0) cc_final: 0.7242 (tt0) REVERT: D 28 MET cc_start: 0.7091 (tmm) cc_final: 0.6785 (tmm) REVERT: D 36 LYS cc_start: 0.8409 (mttt) cc_final: 0.8113 (mtmp) REVERT: D 92 GLN cc_start: 0.7494 (pm20) cc_final: 0.7145 (pm20) REVERT: D 116 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8480 (mmtm) REVERT: D 129 ASN cc_start: 0.8455 (m-40) cc_final: 0.8136 (m110) REVERT: D 144 MET cc_start: 0.8106 (tpp) cc_final: 0.7652 (mpp) REVERT: D 192 LEU cc_start: 0.8785 (mt) cc_final: 0.8530 (mp) REVERT: D 210 GLU cc_start: 0.8181 (tt0) cc_final: 0.7956 (tt0) REVERT: D 252 ASN cc_start: 0.8920 (t0) cc_final: 0.8606 (t0) REVERT: D 267 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7687 (ttm-80) outliers start: 23 outliers final: 19 residues processed: 322 average time/residue: 0.3076 time to fit residues: 126.4261 Evaluate side-chains 327 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 139 ASP Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 160 SER 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 128 ILE Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 152 THR 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 329 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3474 r_free = 0.3474 target = 0.113980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102798 restraints weight = 13802.723| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.96 r_work: 0.3195 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9768 Z= 0.228 Angle : 0.542 7.166 13281 Z= 0.273 Chirality : 0.042 0.159 1541 Planarity : 0.004 0.040 1696 Dihedral : 4.126 18.401 1336 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.54 % Allowed : 19.71 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1224 helix: 2.07 (0.20), residues: 667 sheet: -0.30 (0.57), residues: 94 loop : -0.55 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 PHE 0.012 0.001 PHE D 303 TYR 0.009 0.001 TYR A 236 ARG 0.009 0.000 ARG A 249 *********************** 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 333 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 0.945 Fit side-chains REVERT: A 24 PHE cc_start: 0.8351 (t80) cc_final: 0.8135 (t80) REVERT: A 62 MET cc_start: 0.6649 (mtm) cc_final: 0.6402 (mtm) REVERT: A 74 MET cc_start: 0.7648 (ppp) cc_final: 0.7120 (ppp) REVERT: A 95 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8240 (mtt90) REVERT: A 96 PHE cc_start: 0.8575 (t80) cc_final: 0.7839 (t80) REVERT: A 151 MET cc_start: 0.8470 (mmm) cc_final: 0.8148 (mmp) REVERT: A 172 MET cc_start: 0.8669 (ppp) cc_final: 0.8032 (ppp) REVERT: A 185 MET cc_start: 0.7898 (tpp) cc_final: 0.7475 (tpp) REVERT: A 247 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7948 (ttp80) REVERT: A 286 SER cc_start: 0.8993 (t) cc_final: 0.8699 (t) REVERT: A 300 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7998 (mtm-85) REVERT: B 60 GLN cc_start: 0.8837 (mt0) cc_final: 0.8503 (mt0) REVERT: B 204 MET cc_start: 0.8005 (ppp) cc_final: 0.7761 (ppp) REVERT: B 227 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7752 (t80) REVERT: C 16 GLU cc_start: 0.7934 (tp30) cc_final: 0.7547 (tp30) REVERT: C 24 ASP cc_start: 0.8073 (t0) cc_final: 0.7615 (t0) REVERT: C 50 SER cc_start: 0.8204 (m) cc_final: 0.7828 (p) REVERT: C 82 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 138 VAL cc_start: 0.8391 (m) cc_final: 0.8151 (t) REVERT: C 149 VAL cc_start: 0.8432 (t) cc_final: 0.8035 (p) REVERT: C 158 MET cc_start: 0.8257 (mmm) cc_final: 0.7746 (mmm) REVERT: C 168 ILE cc_start: 0.8649 (tp) cc_final: 0.8289 (pt) REVERT: C 171 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7878 (mmt180) REVERT: C 173 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7989 (mtpp) REVERT: C 198 GLU cc_start: 0.8055 (tp30) cc_final: 0.7720 (tp30) REVERT: C 213 ASP cc_start: 0.7841 (t0) cc_final: 0.7424 (t0) REVERT: C 234 GLU cc_start: 0.7898 (tt0) cc_final: 0.7241 (tt0) REVERT: D 28 MET cc_start: 0.7066 (tmm) cc_final: 0.6774 (tmm) REVERT: D 36 LYS cc_start: 0.8392 (mttt) cc_final: 0.8078 (mtmp) REVERT: D 92 GLN cc_start: 0.7483 (pm20) cc_final: 0.7151 (pm20) REVERT: D 116 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8483 (mmtm) REVERT: D 144 MET cc_start: 0.8103 (tpp) cc_final: 0.7646 (mpp) REVERT: D 192 LEU cc_start: 0.8751 (mt) cc_final: 0.8495 (mp) REVERT: D 210 GLU cc_start: 0.8172 (tt0) cc_final: 0.7947 (tt0) REVERT: D 226 GLU cc_start: 0.8133 (tt0) cc_final: 0.7843 (tt0) REVERT: D 252 ASN cc_start: 0.8905 (t0) cc_final: 0.8572 (t0) REVERT: D 267 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7645 (ttm-80) REVERT: D 276 ARG cc_start: 0.6405 (ttm110) cc_final: 0.6139 (ttm110) outliers start: 26 outliers final: 20 residues processed: 317 average time/residue: 0.2922 time to fit residues: 118.5669 Evaluate side-chains 326 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 141 MET 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 151 LYS Chi-restraints excluded: chain D residue 152 THR 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 329 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 116 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.115330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104182 restraints weight = 13691.971| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.95 r_work: 0.3212 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9768 Z= 0.182 Angle : 0.539 11.156 13281 Z= 0.268 Chirality : 0.041 0.222 1541 Planarity : 0.004 0.041 1696 Dihedral : 3.986 17.862 1336 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.15 % Allowed : 20.00 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1224 helix: 2.16 (0.20), residues: 667 sheet: -0.37 (0.52), residues: 104 loop : -0.53 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.004 0.001 HIS C 12 PHE 0.012 0.001 PHE B 44 TYR 0.009 0.001 TYR A 236 ARG 0.009 0.000 ARG C 77 *********************** 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 327 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 1.695 Fit side-chains REVERT: A 9 LEU cc_start: 0.8346 (mt) cc_final: 0.8124 (mp) REVERT: A 62 MET cc_start: 0.6620 (mtm) cc_final: 0.6380 (mtm) REVERT: A 74 MET cc_start: 0.7661 (ppp) cc_final: 0.7395 (ppp) REVERT: A 95 ARG cc_start: 0.8563 (mtt90) cc_final: 0.8246 (mtt90) REVERT: A 151 MET cc_start: 0.8446 (mmm) cc_final: 0.8127 (mmp) REVERT: A 172 MET cc_start: 0.8638 (ppp) cc_final: 0.7996 (ppp) REVERT: A 185 MET cc_start: 0.7875 (tpp) cc_final: 0.7432 (tpp) REVERT: A 247 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7925 (ttp80) REVERT: A 286 SER cc_start: 0.8990 (t) cc_final: 0.8695 (t) REVERT: A 300 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: B 60 GLN cc_start: 0.8815 (mt0) cc_final: 0.8464 (mt0) REVERT: B 204 MET cc_start: 0.7980 (ppp) cc_final: 0.7675 (ppp) REVERT: B 227 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 16 GLU cc_start: 0.7899 (tp30) cc_final: 0.7491 (tp30) REVERT: C 24 ASP cc_start: 0.8031 (t0) cc_final: 0.7594 (t0) REVERT: C 50 SER cc_start: 0.8234 (m) cc_final: 0.7863 (p) REVERT: C 82 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 138 VAL cc_start: 0.8323 (m) cc_final: 0.8123 (t) REVERT: C 149 VAL cc_start: 0.8373 (t) cc_final: 0.7974 (p) REVERT: C 158 MET cc_start: 0.8241 (mmm) cc_final: 0.7724 (mmm) REVERT: C 168 ILE cc_start: 0.8647 (tp) cc_final: 0.8286 (pt) REVERT: C 171 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7850 (mmt180) REVERT: C 173 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7940 (mtpp) REVERT: C 198 GLU cc_start: 0.8035 (tp30) cc_final: 0.7699 (tp30) REVERT: C 213 ASP cc_start: 0.7832 (t0) cc_final: 0.7418 (t0) REVERT: C 234 GLU cc_start: 0.7853 (tt0) cc_final: 0.7188 (tt0) REVERT: C 320 ASP cc_start: 0.8393 (p0) cc_final: 0.7933 (p0) REVERT: D 28 MET cc_start: 0.7042 (tmm) cc_final: 0.6766 (tmm) REVERT: D 36 LYS cc_start: 0.8376 (mttt) cc_final: 0.8065 (mtmp) REVERT: D 67 LEU cc_start: 0.8179 (mt) cc_final: 0.7833 (mp) REVERT: D 92 GLN cc_start: 0.7438 (pm20) cc_final: 0.7134 (pm20) REVERT: D 116 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8478 (mmtm) REVERT: D 144 MET cc_start: 0.8073 (tpp) cc_final: 0.7594 (mpp) REVERT: D 177 MET cc_start: 0.8270 (mmm) cc_final: 0.7937 (mmm) REVERT: D 192 LEU cc_start: 0.8730 (mt) cc_final: 0.8477 (mp) REVERT: D 210 GLU cc_start: 0.8134 (tt0) cc_final: 0.7913 (tt0) REVERT: D 226 GLU cc_start: 0.8137 (tt0) cc_final: 0.7837 (tp30) REVERT: D 252 ASN cc_start: 0.8892 (t0) cc_final: 0.8586 (t0) REVERT: D 267 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7651 (ttm-80) REVERT: D 302 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7763 (mtp85) outliers start: 22 outliers final: 17 residues processed: 312 average time/residue: 0.2923 time to fit residues: 116.5711 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 : 1.092 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 227 PHE 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 223 SER 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 329 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** C 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103540 restraints weight = 13762.289| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.95 r_work: 0.3204 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9768 Z= 0.218 Angle : 0.557 9.165 13281 Z= 0.278 Chirality : 0.042 0.160 1541 Planarity : 0.004 0.049 1696 Dihedral : 3.989 17.808 1336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.05 % Allowed : 20.98 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1224 helix: 2.17 (0.20), residues: 667 sheet: -0.43 (0.52), residues: 104 loop : -0.52 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.006 0.001 HIS C 12 PHE 0.013 0.001 PHE A 24 TYR 0.010 0.001 TYR A 236 ARG 0.010 0.001 ARG A 249 ********************** 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 324 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 303 time to evaluate : 1.016 Fit side-chains REVERT: A 9 LEU cc_start: 0.8350 (mt) cc_final: 0.8127 (mp) REVERT: A 62 MET cc_start: 0.6621 (mtm) cc_final: 0.6373 (mtm) REVERT: A 74 MET cc_start: 0.7665 (ppp) cc_final: 0.7400 (ppp) REVERT: A 95 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8258 (mtt90) REVERT: A 151 MET cc_start: 0.8441 (mmm) cc_final: 0.8118 (mmp) REVERT: A 172 MET cc_start: 0.8589 (ppp) cc_final: 0.8002 (ppp) REVERT: A 185 MET cc_start: 0.7881 (tpp) cc_final: 0.7414 (tpp) REVERT: A 247 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7903 (ttp80) REVERT: A 286 SER cc_start: 0.8990 (t) cc_final: 0.8696 (t) REVERT: A 300 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8013 (mtm-85) REVERT: B 60 GLN cc_start: 0.8840 (mt0) cc_final: 0.8494 (mt0) REVERT: B 204 MET cc_start: 0.7987 (ppp) cc_final: 0.7692 (ppp) REVERT: B 227 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7700 (t80) REVERT: C 16 GLU cc_start: 0.7914 (tp30) cc_final: 0.7479 (tp30) REVERT: C 24 ASP cc_start: 0.8019 (t0) cc_final: 0.7589 (t0) REVERT: C 50 SER cc_start: 0.8198 (m) cc_final: 0.7834 (p) REVERT: C 82 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 138 VAL cc_start: 0.8351 (m) cc_final: 0.8132 (t) REVERT: C 149 VAL cc_start: 0.8402 (t) cc_final: 0.8033 (p) REVERT: C 158 MET cc_start: 0.8258 (mmm) cc_final: 0.7763 (mmm) REVERT: C 168 ILE cc_start: 0.8663 (tp) cc_final: 0.8302 (pt) REVERT: C 171 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7875 (mmt180) REVERT: C 173 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: C 198 GLU cc_start: 0.8034 (tp30) cc_final: 0.7695 (tp30) REVERT: C 213 ASP cc_start: 0.7843 (t0) cc_final: 0.7437 (t0) REVERT: C 234 GLU cc_start: 0.7867 (tt0) cc_final: 0.7211 (tt0) REVERT: C 320 ASP cc_start: 0.8407 (p0) cc_final: 0.7968 (p0) REVERT: D 28 MET cc_start: 0.7085 (tmm) cc_final: 0.6829 (tmm) REVERT: D 36 LYS cc_start: 0.8377 (mttt) cc_final: 0.8072 (mtmp) REVERT: D 67 LEU cc_start: 0.8197 (mt) cc_final: 0.7852 (mp) REVERT: D 92 GLN cc_start: 0.7435 (pm20) cc_final: 0.7133 (pm20) REVERT: D 116 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8469 (mmtm) REVERT: D 144 MET cc_start: 0.8089 (tpp) cc_final: 0.7618 (mpp) REVERT: D 177 MET cc_start: 0.8289 (mmm) cc_final: 0.7948 (mmm) REVERT: D 192 LEU cc_start: 0.8733 (mt) cc_final: 0.8482 (mp) REVERT: D 205 MET cc_start: 0.8016 (mmp) cc_final: 0.7777 (mtm) REVERT: D 210 GLU cc_start: 0.8110 (tt0) cc_final: 0.7880 (tt0) REVERT: D 226 GLU cc_start: 0.8148 (tt0) cc_final: 0.7795 (tt0) REVERT: D 250 PHE cc_start: 0.8771 (m-80) cc_final: 0.8527 (m-80) REVERT: D 252 ASN cc_start: 0.8874 (t0) cc_final: 0.8594 (t0) REVERT: D 267 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7640 (ttm-80) REVERT: D 302 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7692 (mtp-110) outliers start: 21 outliers final: 18 residues processed: 310 average time/residue: 0.2920 time to fit residues: 115.2496 Evaluate side-chains 321 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 246 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 227 PHE 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 262 GLN Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 223 SER 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 329 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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** C 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103782 restraints weight = 13688.266| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9768 Z= 0.194 Angle : 0.553 9.777 13281 Z= 0.273 Chirality : 0.041 0.159 1541 Planarity : 0.004 0.041 1696 Dihedral : 3.947 17.738 1336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.34 % Allowed : 20.68 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1224 helix: 2.20 (0.20), residues: 667 sheet: -0.41 (0.52), residues: 104 loop : -0.52 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 293 HIS 0.005 0.001 HIS C 12 PHE 0.020 0.001 PHE A 96 TYR 0.010 0.001 TYR A 236 ARG 0.008 0.000 ARG C 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.57 seconds wall clock time: 92 minutes 5.64 seconds (5525.64 seconds total)