Starting phenix.real_space_refine on Wed Aug 5 05:23:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.map" model { file = "/net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pa5_71433/08_2026/9pa5_71433.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 S 64 5.16 5 Cl 1 4.86 5 C 5387 2.51 5 N 1453 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8516 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1684 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 6, 'PHE:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "R" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2048 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 10, 'TRANS': 273} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 5, 'PHE:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2575 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 430 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1763 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.39, per 1000 atoms: 0.16 Number of scatterers: 8516 At special positions: 0 Unit cell: (96.048, 120.06, 129.996, 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) Cl 1 17.00 S 64 16.00 O 1611 8.00 N 1453 7.00 C 5387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 386.2 milliseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 39.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.212A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.654A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.152A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.894A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.165A pdb=" N ALA A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.829A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.726A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.024A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'R' and resid 68 through 97 Processing helix chain 'R' and resid 103 through 132 removed outlier: 3.509A pdb=" N ILE R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.527A pdb=" N HIS R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 4.448A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 Proline residue: R 203 - end of helix removed outlier: 3.532A pdb=" N MET R 207 " --> pdb=" O PRO R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 244 removed outlier: 4.092A pdb=" N LEU R 234 " --> pdb=" O TRP R 230 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS R 235 " --> pdb=" O GLU R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 263 Processing helix chain 'R' and resid 264 through 268 Processing helix chain 'R' and resid 270 through 289 removed outlier: 4.058A pdb=" N VAL R 287 " --> pdb=" O MET R 283 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 340 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 350 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.593A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.558A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.784A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.205A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.529A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.715A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.271A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.875A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.152A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.883A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.562A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.564A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 4.120A pdb=" N ARG E 161 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E 212 " --> pdb=" O SER E 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.381A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2767 1.34 - 1.46: 1647 1.46 - 1.58: 4174 1.58 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 8682 Sorted by residual: bond pdb=" C8 JC9 R 401 " pdb="CL1 JC9 R 401 " ideal model delta sigma weight residual 1.735 1.808 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 JC9 R 401 " pdb=" O1 JC9 R 401 " ideal model delta sigma weight residual 1.217 1.281 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 JC9 R 401 " pdb=" C7 JC9 R 401 " ideal model delta sigma weight residual 1.529 1.589 -0.060 2.00e-02 2.50e+03 9.09e+00 bond pdb=" C1 JC9 R 401 " pdb=" C2 JC9 R 401 " ideal model delta sigma weight residual 1.555 1.594 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C12 JC9 R 401 " pdb=" C9 JC9 R 401 " ideal model delta sigma weight residual 1.398 1.436 -0.038 2.00e-02 2.50e+03 3.53e+00 ... (remaining 8677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 11667 2.70 - 5.39: 118 5.39 - 8.09: 25 8.09 - 10.78: 3 10.78 - 13.48: 4 Bond angle restraints: 11817 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" CA LEU A 23 " pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 116.30 129.78 -13.48 3.50e+00 8.16e-02 1.48e+01 angle pdb=" CA LYS A 330 " pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB GLU B 215 " pdb=" CG GLU B 215 " pdb=" CD GLU B 215 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CB LYS A 330 " pdb=" CG LYS A 330 " pdb=" CD LYS A 330 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 ... (remaining 11812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4372 17.66 - 35.32: 524 35.32 - 52.97: 206 52.97 - 70.63: 27 70.63 - 88.29: 14 Dihedral angle restraints: 5143 sinusoidal: 1838 harmonic: 3305 Sorted by residual: dihedral pdb=" CB CYS R 142 " pdb=" SG CYS R 142 " pdb=" SG CYS R 219 " pdb=" CB CYS R 219 " ideal model delta sinusoidal sigma weight residual -86.00 -137.58 51.58 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 54.84 38.16 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1036 0.049 - 0.097: 269 0.097 - 0.146: 76 0.146 - 0.195: 7 0.195 - 0.244: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CB THR R 155 " pdb=" CA THR R 155 " pdb=" OG1 THR R 155 " pdb=" CG2 THR R 155 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE E 139 " pdb=" CA ILE E 139 " pdb=" CG1 ILE E 139 " pdb=" CG2 ILE E 139 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1387 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 202 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO R 203 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 203 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 203 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C THR B 196 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 196 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 197 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.030 5.00e-02 4.00e+02 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 220 2.68 - 3.23: 7856 3.23 - 3.79: 14233 3.79 - 4.34: 18158 4.34 - 4.90: 30779 Nonbonded interactions: 71246 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.121 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP E 90 " pdb=" OH TYR E 94 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.193 3.040 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.258 3.040 ... (remaining 71241 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8684 Z= 0.233 Angle : 0.766 13.478 11821 Z= 0.392 Chirality : 0.048 0.244 1390 Planarity : 0.005 0.064 1501 Dihedral : 18.256 88.290 2999 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.26 % Allowed : 38.50 % Favored : 55.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1125 helix: 0.79 (0.25), residues: 398 sheet: -0.96 (0.33), residues: 251 loop : -1.08 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 181 TYR 0.016 0.002 TYR E 94 PHE 0.015 0.002 PHE B 292 TRP 0.028 0.002 TRP R 295 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 ( 8682) covalent geometry : angle 0.76640 / 0.39 (11817) SS BOND : bond 0.00022 / 0.01 ( 2) SS BOND : angle 0.50052 / 0.27 ( 4) hydrogen bonds : bond 0.16256 / 10.67 ( 447) hydrogen bonds : angle 7.12431 / 4.94 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 39 residues processed: 187 average time/residue: 0.2534 time to fit residues: 52.1224 Evaluate side-chains 177 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 192 CYS Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.223111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.181687 restraints weight = 9306.484| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.73 r_work: 0.3902 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8684 Z= 0.115 Angle : 0.528 8.010 11821 Z= 0.280 Chirality : 0.041 0.144 1390 Planarity : 0.004 0.047 1501 Dihedral : 7.200 59.620 1297 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.38 % Allowed : 35.31 % Favored : 58.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1125 helix: 1.38 (0.26), residues: 405 sheet: -0.75 (0.33), residues: 246 loop : -0.90 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.012 0.001 TYR E 174 PHE 0.011 0.001 PHE A 323 TRP 0.014 0.001 TRP R 295 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8682) covalent geometry : angle 0.52762 / 0.28 (11817) SS BOND : bond 0.00312 / 0.16 ( 2) SS BOND : angle 0.77000 / 0.44 ( 4) hydrogen bonds : bond 0.03457 / 2.35 ( 447) hydrogen bonds : angle 4.99955 / 3.45 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.5499 (mpt) cc_final: 0.5254 (mmm) REVERT: R 129 ASN cc_start: 0.6613 (m110) cc_final: 0.6276 (m110) REVERT: R 262 LYS cc_start: 0.4820 (ptpp) cc_final: 0.4440 (ptpp) REVERT: R 283 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.4826 (tmm) REVERT: C 47 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6001 (tm-30) REVERT: E 106 SER cc_start: 0.6984 (p) cc_final: 0.6702 (t) REVERT: E 187 GLN cc_start: 0.7488 (mm110) cc_final: 0.7067 (pt0) REVERT: E 192 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8120 (mtt90) outliers start: 56 outliers final: 17 residues processed: 196 average time/residue: 0.3103 time to fit residues: 66.2768 Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 215 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.216999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178449 restraints weight = 9277.103| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.26 r_work: 0.3764 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8684 Z= 0.217 Angle : 0.608 10.457 11821 Z= 0.318 Chirality : 0.044 0.156 1390 Planarity : 0.004 0.053 1501 Dihedral : 6.050 57.697 1253 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 8.31 % Allowed : 34.17 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1125 helix: 1.49 (0.26), residues: 404 sheet: -0.97 (0.33), residues: 243 loop : -1.03 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 129 TYR 0.016 0.002 TYR E 174 PHE 0.018 0.002 PHE B 253 TRP 0.015 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 ( 8682) covalent geometry : angle 0.60834 / 0.32 (11817) SS BOND : bond 0.00324 / 0.16 ( 2) SS BOND : angle 0.76457 / 0.39 ( 4) hydrogen bonds : bond 0.03786 / 2.58 ( 447) hydrogen bonds : angle 5.04968 / 3.47 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 146 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7339 (tp) cc_final: 0.7106 (tp) REVERT: A 243 MET cc_start: 0.5493 (mpt) cc_final: 0.5228 (mmm) REVERT: R 129 ASN cc_start: 0.6897 (m110) cc_final: 0.6488 (m110) REVERT: R 187 LYS cc_start: 0.7176 (mppt) cc_final: 0.6710 (mmmm) REVERT: R 262 LYS cc_start: 0.4671 (ptpp) cc_final: 0.4426 (ptpp) REVERT: B 54 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7577 (t-90) REVERT: B 280 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6946 (mmtm) REVERT: B 318 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7938 (tm) REVERT: C 19 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6020 (mm) REVERT: C 21 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4876 (ptt) REVERT: E 192 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8226 (mtt180) outliers start: 73 outliers final: 35 residues processed: 196 average time/residue: 0.3156 time to fit residues: 67.4782 Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 296 THR Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.215259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.176550 restraints weight = 9479.709| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.32 r_work: 0.3733 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8684 Z= 0.258 Angle : 0.645 10.632 11821 Z= 0.338 Chirality : 0.045 0.159 1390 Planarity : 0.004 0.058 1501 Dihedral : 6.139 57.995 1252 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 8.09 % Allowed : 35.19 % Favored : 56.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.25), residues: 1125 helix: 1.36 (0.26), residues: 407 sheet: -1.21 (0.32), residues: 248 loop : -1.12 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.016 0.002 TYR E 103 PHE 0.020 0.002 PHE E 240 TRP 0.014 0.002 TRP B 211 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 ( 8682) covalent geometry : angle 0.64448 / 0.34 (11817) SS BOND : bond 0.00308 / 0.15 ( 2) SS BOND : angle 0.95757 / 0.49 ( 4) hydrogen bonds : bond 0.03852 / 2.62 ( 447) hydrogen bonds : angle 5.13272 / 3.54 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 141 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.4942 (tm-30) REVERT: R 129 ASN cc_start: 0.7044 (m110) cc_final: 0.6595 (m110) REVERT: R 187 LYS cc_start: 0.7152 (mppt) cc_final: 0.6743 (mmmm) REVERT: B 54 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7562 (t-90) REVERT: B 57 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7284 (ttpp) REVERT: B 215 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 280 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6971 (mmtm) REVERT: C 19 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6109 (mm) REVERT: C 21 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.4953 (ptt) REVERT: E 187 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: E 192 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8289 (mtt180) REVERT: E 234 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5440 (tp) outliers start: 71 outliers final: 36 residues processed: 191 average time/residue: 0.3311 time to fit residues: 68.9890 Evaluate side-chains 177 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 296 THR Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 50.0000 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS E 143 GLN E 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.218985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.180677 restraints weight = 9444.346| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.21 r_work: 0.3794 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8684 Z= 0.142 Angle : 0.556 10.498 11821 Z= 0.290 Chirality : 0.042 0.133 1390 Planarity : 0.004 0.054 1501 Dihedral : 5.750 58.790 1252 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.69 % Allowed : 38.15 % Favored : 56.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 1125 helix: 1.56 (0.26), residues: 407 sheet: -1.15 (0.32), residues: 246 loop : -0.99 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.010 0.002 TYR R 108 PHE 0.014 0.001 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8682) covalent geometry : angle 0.55554 / 0.29 (11817) SS BOND : bond 0.00483 / 0.25 ( 2) SS BOND : angle 0.52001 / 0.28 ( 4) hydrogen bonds : bond 0.03290 / 2.24 ( 447) hydrogen bonds : angle 4.82696 / 3.32 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 129 ASN cc_start: 0.7019 (m110) cc_final: 0.6570 (m-40) REVERT: R 154 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: R 187 LYS cc_start: 0.7185 (mppt) cc_final: 0.6835 (mmmm) REVERT: R 249 ILE cc_start: 0.5623 (pp) cc_final: 0.5373 (pt) REVERT: R 324 ILE cc_start: 0.8813 (pp) cc_final: 0.8462 (mp) REVERT: B 215 GLU cc_start: 0.7743 (mp0) cc_final: 0.7147 (mp0) REVERT: C 21 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.4748 (ptt) REVERT: E 161 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6845 (ptm160) REVERT: E 192 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8189 (mpt-90) REVERT: E 234 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5471 (tp) outliers start: 50 outliers final: 22 residues processed: 178 average time/residue: 0.3195 time to fit residues: 62.0159 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.218396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178924 restraints weight = 9326.471| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.04 r_work: 0.3786 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8684 Z= 0.157 Angle : 0.570 10.860 11821 Z= 0.297 Chirality : 0.042 0.134 1390 Planarity : 0.004 0.053 1501 Dihedral : 5.751 59.106 1252 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.72 % Allowed : 37.36 % Favored : 55.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1125 helix: 1.64 (0.26), residues: 407 sheet: -1.15 (0.32), residues: 248 loop : -0.95 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.016 0.002 TYR E 59 PHE 0.015 0.002 PHE B 199 TRP 0.018 0.002 TRP R 194 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 8682) covalent geometry : angle 0.57008 / 0.30 (11817) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 0.87422 / 0.45 ( 4) hydrogen bonds : bond 0.03316 / 2.26 ( 447) hydrogen bonds : angle 4.80012 / 3.31 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.4776 (tm-30) REVERT: R 129 ASN cc_start: 0.7168 (m110) cc_final: 0.6752 (m-40) REVERT: R 154 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: R 187 LYS cc_start: 0.7000 (mppt) cc_final: 0.6732 (mmmm) REVERT: R 324 ILE cc_start: 0.8825 (pp) cc_final: 0.8492 (mp) REVERT: B 215 GLU cc_start: 0.7758 (mp0) cc_final: 0.7231 (mp0) REVERT: B 318 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7848 (tm) REVERT: C 19 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5931 (mm) REVERT: C 21 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4763 (ptt) REVERT: E 161 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7135 (ttp-110) REVERT: E 192 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8212 (mpt-90) REVERT: E 234 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5409 (tp) outliers start: 59 outliers final: 31 residues processed: 182 average time/residue: 0.3155 time to fit residues: 62.4576 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.218600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.178983 restraints weight = 9412.694| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.98 r_work: 0.3807 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8684 Z= 0.154 Angle : 0.570 11.175 11821 Z= 0.296 Chirality : 0.042 0.163 1390 Planarity : 0.004 0.052 1501 Dihedral : 5.717 59.414 1252 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.72 % Allowed : 37.24 % Favored : 56.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1125 helix: 1.67 (0.26), residues: 407 sheet: -1.20 (0.32), residues: 253 loop : -0.88 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.011 0.002 TYR E 103 PHE 0.016 0.002 PHE A 336 TRP 0.015 0.002 TRP B 332 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8682) covalent geometry : angle 0.56947 / 0.30 (11817) SS BOND : bond 0.00331 / 0.17 ( 2) SS BOND : angle 0.70132 / 0.37 ( 4) hydrogen bonds : bond 0.03266 / 2.22 ( 447) hydrogen bonds : angle 4.76959 / 3.29 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.4862 (tm-30) REVERT: R 129 ASN cc_start: 0.7223 (m110) cc_final: 0.6822 (m-40) REVERT: R 154 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: R 187 LYS cc_start: 0.7005 (mppt) cc_final: 0.6752 (mmmm) REVERT: R 324 ILE cc_start: 0.8769 (pp) cc_final: 0.8438 (mp) REVERT: B 215 GLU cc_start: 0.7756 (mp0) cc_final: 0.7208 (mp0) REVERT: C 19 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5964 (mm) REVERT: C 21 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4804 (ptt) REVERT: E 143 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6247 (mt0) REVERT: E 192 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8213 (mpt-90) REVERT: E 234 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5457 (tp) outliers start: 59 outliers final: 34 residues processed: 182 average time/residue: 0.3169 time to fit residues: 62.8147 Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 0.0170 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.220877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.182507 restraints weight = 9345.710| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.04 r_work: 0.3838 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8684 Z= 0.119 Angle : 0.551 11.491 11821 Z= 0.288 Chirality : 0.042 0.163 1390 Planarity : 0.003 0.051 1501 Dihedral : 5.541 59.872 1252 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.58 % Allowed : 38.15 % Favored : 56.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1125 helix: 1.78 (0.26), residues: 406 sheet: -1.04 (0.32), residues: 245 loop : -0.86 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.015 0.001 TYR E 59 PHE 0.012 0.001 PHE B 199 TRP 0.016 0.001 TRP B 332 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8682) covalent geometry : angle 0.55151 / 0.29 (11817) SS BOND : bond 0.00283 / 0.15 ( 2) SS BOND : angle 0.38550 / 0.19 ( 4) hydrogen bonds : bond 0.03100 / 2.11 ( 447) hydrogen bonds : angle 4.60874 / 3.18 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.6430 (t80) cc_final: 0.6219 (t80) REVERT: R 129 ASN cc_start: 0.7222 (m110) cc_final: 0.6807 (m110) REVERT: R 154 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: R 187 LYS cc_start: 0.6985 (mppt) cc_final: 0.6754 (mmmm) REVERT: R 283 MET cc_start: 0.5896 (OUTLIER) cc_final: 0.5060 (tmm) REVERT: R 324 ILE cc_start: 0.8750 (pp) cc_final: 0.8434 (mp) REVERT: B 215 GLU cc_start: 0.7681 (mp0) cc_final: 0.7086 (mp0) REVERT: B 217 MET cc_start: 0.6785 (pmm) cc_final: 0.6478 (ppp) REVERT: C 21 MET cc_start: 0.4977 (OUTLIER) cc_final: 0.4758 (ptt) REVERT: C 47 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6209 (tm-30) REVERT: E 161 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6819 (mmm160) REVERT: E 192 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8132 (mpt-90) REVERT: E 234 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5436 (tp) outliers start: 49 outliers final: 25 residues processed: 181 average time/residue: 0.3034 time to fit residues: 59.9764 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 254 TYR Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.221169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.181547 restraints weight = 9303.342| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.97 r_work: 0.3848 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8684 Z= 0.122 Angle : 0.556 11.858 11821 Z= 0.289 Chirality : 0.042 0.167 1390 Planarity : 0.003 0.051 1501 Dihedral : 5.299 59.790 1249 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.47 % Allowed : 38.04 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1125 helix: 1.85 (0.26), residues: 406 sheet: -1.01 (0.32), residues: 245 loop : -0.84 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.009 0.001 TYR E 191 PHE 0.012 0.001 PHE B 199 TRP 0.018 0.001 TRP B 332 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8682) covalent geometry : angle 0.55640 / 0.29 (11817) SS BOND : bond 0.00134 / 0.07 ( 2) SS BOND : angle 0.35810 / 0.18 ( 4) hydrogen bonds : bond 0.03087 / 2.10 ( 447) hydrogen bonds : angle 4.54897 / 3.14 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 129 ASN cc_start: 0.7263 (m110) cc_final: 0.6829 (m110) REVERT: R 154 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: R 187 LYS cc_start: 0.7050 (mppt) cc_final: 0.6836 (mmmm) REVERT: R 283 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5072 (tmm) REVERT: R 324 ILE cc_start: 0.8743 (pp) cc_final: 0.8447 (mp) REVERT: B 215 GLU cc_start: 0.7664 (mp0) cc_final: 0.7123 (mp0) REVERT: C 21 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.4671 (ptt) REVERT: C 47 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: E 143 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.4724 (mp10) REVERT: E 161 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6805 (ptm160) REVERT: E 192 ARG cc_start: 0.8393 (tpp80) cc_final: 0.8120 (mpt-90) REVERT: E 234 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5394 (tp) outliers start: 48 outliers final: 28 residues processed: 176 average time/residue: 0.3122 time to fit residues: 59.7679 Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 15 optimal weight: 20.0000 chunk 58 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS E 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.224289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.184414 restraints weight = 9326.178| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.71 r_work: 0.3917 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8684 Z= 0.104 Angle : 0.549 11.795 11821 Z= 0.284 Chirality : 0.041 0.151 1390 Planarity : 0.003 0.051 1501 Dihedral : 4.954 58.991 1249 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.30 % Allowed : 40.21 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1125 helix: 1.99 (0.26), residues: 406 sheet: -0.81 (0.32), residues: 243 loop : -0.77 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.014 0.001 TYR E 59 PHE 0.010 0.001 PHE B 199 TRP 0.018 0.001 TRP B 332 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 8682) covalent geometry : angle 0.54865 / 0.28 (11817) SS BOND : bond 0.00087 / 0.04 ( 2) SS BOND : angle 0.26756 / 0.13 ( 4) hydrogen bonds : bond 0.02988 / 2.04 ( 447) hydrogen bonds : angle 4.35176 / 3.00 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: R 129 ASN cc_start: 0.7260 (m110) cc_final: 0.6832 (m110) REVERT: R 154 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: R 262 LYS cc_start: 0.5019 (mtpm) cc_final: 0.4677 (ptpp) REVERT: R 283 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5079 (tmm) REVERT: R 324 ILE cc_start: 0.8741 (pp) cc_final: 0.8469 (mp) REVERT: B 215 GLU cc_start: 0.7521 (mp0) cc_final: 0.6990 (mp0) REVERT: B 217 MET cc_start: 0.6723 (pmm) cc_final: 0.6483 (ppp) REVERT: B 234 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8486 (t80) REVERT: E 161 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7012 (mmm160) REVERT: E 184 GLN cc_start: 0.7052 (tt0) cc_final: 0.6697 (tt0) REVERT: E 187 GLN cc_start: 0.7287 (mm-40) cc_final: 0.7017 (pt0) REVERT: E 234 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5310 (tp) outliers start: 29 outliers final: 16 residues processed: 171 average time/residue: 0.2994 time to fit residues: 55.7544 Evaluate side-chains 162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 154 PHE Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 253 CYS Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 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 = 0.4484 r_free = 0.4484 target = 0.221073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181985 restraints weight = 9311.147| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.14 r_work: 0.3819 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8684 Z= 0.141 Angle : 0.597 11.802 11821 Z= 0.305 Chirality : 0.043 0.199 1390 Planarity : 0.003 0.050 1501 Dihedral : 5.021 59.350 1245 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.30 % Allowed : 40.32 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1125 helix: 1.96 (0.26), residues: 406 sheet: -1.08 (0.31), residues: 255 loop : -0.71 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.011 0.001 TYR E 103 PHE 0.014 0.001 PHE B 199 TRP 0.021 0.002 TRP B 332 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8682) covalent geometry : angle 0.59714 / 0.31 (11817) SS BOND : bond 0.00438 / 0.23 ( 2) SS BOND : angle 0.56753 / 0.27 ( 4) hydrogen bonds : bond 0.03145 / 2.15 ( 447) hydrogen bonds : angle 4.51880 / 3.10 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2881.58 seconds wall clock time: 49 minutes 45.14 seconds (2985.14 seconds total)