Starting phenix.real_space_refine on Thu Jul 2 06:57:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.map" model { file = "/net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0k_61947/07_2026/9k0k_61947.cif" } resolution = 3.14 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= -0.002 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 C 4775 2.51 5 N 1266 2.21 5 O 1346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7441 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1629 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2331 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 321} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'ASP:plan': 14, 'ASN:plan1': 3, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 129 Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 226 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 882 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2344 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 280} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 7} Unresolved non-hydrogen planarities: 35 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.16 Number of scatterers: 7441 At special positions: 0 Unit cell: (76.8575, 97.425, 127.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 3 15.00 O 1346 8.00 N 1266 7.00 C 4775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS I 27 " - pdb=" SG CYS I 278 " distance=2.03 Simple disulfide: pdb=" SG CYS I 108 " - pdb=" SG CYS I 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 391.7 milliseconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 41.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.730A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.013A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.542A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.974A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 16 through 24 removed outlier: 3.762A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'I' and resid 31 through 36 removed outlier: 3.838A pdb=" N ILE I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 53 through 63 removed outlier: 3.881A pdb=" N ILE I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 87 Processing helix chain 'I' and resid 88 through 97 Processing helix chain 'I' and resid 104 through 139 removed outlier: 3.505A pdb=" N CYS I 108 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR I 116 " --> pdb=" O ARG I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 148 through 167 removed outlier: 3.612A pdb=" N ALA I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 174 removed outlier: 3.800A pdb=" N LEU I 171 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE I 172 " --> pdb=" O VAL I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 193 through 229 removed outlier: 3.827A pdb=" N TYR I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) Proline residue: I 212 - end of helix removed outlier: 3.650A pdb=" N GLN I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 275 removed outlier: 3.669A pdb=" N LEU I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) Proline residue: I 260 - end of helix Processing helix chain 'I' and resid 277 through 297 Proline residue: I 293 - end of helix Processing helix chain 'I' and resid 297 through 307 Proline residue: I 303 - end of helix Processing helix chain 'I' and resid 310 through 320 removed outlier: 4.142A pdb=" N ARG I 314 " --> pdb=" O GLY I 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.430A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.514A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.614A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.103A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.526A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.087A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.740A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.521A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.534A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.648A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 176 through 177 375 hydrogen bonds defined for protein. 1083 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: 0.92 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1169 1.31 - 1.45: 2205 1.45 - 1.58: 4171 1.58 - 1.71: 5 1.71 - 1.84: 67 Bond restraints: 7617 Sorted by residual: bond pdb=" O3B UTP I 401 " pdb=" PG UTP I 401 " ideal model delta sigma weight residual 1.726 1.643 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O3A UTP I 401 " pdb=" PB UTP I 401 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4 UTP I 401 " pdb=" C5 UTP I 401 " ideal model delta sigma weight residual 1.439 1.367 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4 UTP I 401 " pdb=" N3 UTP I 401 " ideal model delta sigma weight residual 1.390 1.320 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O3A UTP I 401 " pdb=" PA UTP I 401 " ideal model delta sigma weight residual 1.632 1.584 0.048 2.00e-02 2.50e+03 5.77e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 10283 2.63 - 5.26: 98 5.26 - 7.89: 22 7.89 - 10.52: 4 10.52 - 13.15: 3 Bond angle restraints: 10410 Sorted by residual: angle pdb=" O1A UTP I 401 " pdb=" PA UTP I 401 " pdb=" O2A UTP I 401 " ideal model delta sigma weight residual 121.55 108.40 13.15 3.00e+00 1.11e-01 1.92e+01 angle pdb=" PA UTP I 401 " pdb=" O3A UTP I 401 " pdb=" PB UTP I 401 " ideal model delta sigma weight residual 133.62 121.31 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N PHE A 246 " pdb=" CA PHE A 246 " pdb=" C PHE A 246 " ideal model delta sigma weight residual 109.76 103.63 6.13 1.59e+00 3.96e-01 1.49e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.12 109.06 3.06 8.40e-01 1.42e+00 1.33e+01 angle pdb=" O3A UTP I 401 " pdb=" PB UTP I 401 " pdb=" O3B UTP I 401 " ideal model delta sigma weight residual 98.89 109.60 -10.71 3.00e+00 1.11e-01 1.27e+01 ... (remaining 10405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3847 17.62 - 35.24: 450 35.24 - 52.86: 118 52.86 - 70.48: 18 70.48 - 88.10: 2 Dihedral angle restraints: 4435 sinusoidal: 1532 harmonic: 2903 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.12 59.88 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS I 27 " pdb=" SG CYS I 27 " pdb=" SG CYS I 278 " pdb=" CB CYS I 278 " ideal model delta sinusoidal sigma weight residual -86.00 -139.51 53.51 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 4432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1028 0.060 - 0.119: 175 0.119 - 0.179: 13 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 1217 Sorted by residual: chirality pdb=" CA PHE A 246 " pdb=" N PHE A 246 " pdb=" C PHE A 246 " pdb=" CB PHE A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C4' UTP I 401 " pdb=" C3' UTP I 401 " pdb=" C5' UTP I 401 " pdb=" O4' UTP I 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CB ILE N 70 " pdb=" CA ILE N 70 " pdb=" CG1 ILE N 70 " pdb=" CG2 ILE N 70 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1214 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 211 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO I 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO I 212 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 212 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 340 " -0.012 2.00e-02 2.50e+03 1.83e-02 5.89e+00 pdb=" CG PHE A 340 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 340 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 340 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 340 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 340 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C THR B 164 " 0.037 2.00e-02 2.50e+03 pdb=" O THR B 164 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B 165 " -0.013 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1273 2.76 - 3.30: 6901 3.30 - 3.83: 12850 3.83 - 4.37: 14605 4.37 - 4.90: 26179 Nonbonded interactions: 61808 Sorted by model distance: nonbonded pdb=" OG1 THR B 164 " pdb=" O GLY B 185 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.233 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR I 95 " pdb=" O2G UTP I 401 " model vdw 2.266 3.040 nonbonded pdb=" O ASN I 118 " pdb=" OG SER I 122 " model vdw 2.283 3.040 ... (remaining 61803 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: 0.760 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.400 Find NCS groups from input model: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.004 0.083 7621 Z= 0.188 Angle : 0.709 13.150 10418 Z= 0.348 Chirality : 0.044 0.299 1217 Planarity : 0.005 0.073 1309 Dihedral : 16.158 88.099 2549 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 29.99 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 980 helix: 1.29 (0.27), residues: 362 sheet: -0.71 (0.35), residues: 212 loop : -1.53 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 19 TYR 0.016 0.002 TYR I 94 PHE 0.041 0.002 PHE A 340 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 ( 7617) covalent geometry : angle 0.70700 / 0.35 (10410) SS BOND : bond 0.00436 / 0.21 ( 4) SS BOND : angle 1.82801 / 1.12 ( 8) hydrogen bonds : bond 0.16585 / 11.42 ( 375) hydrogen bonds : angle 6.61824 / 4.73 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0786 time to fit residues: 9.1772 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 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 = 0.4008 r_free = 0.4008 target = 0.184599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.148315 restraints weight = 8056.117| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.09 r_work: 0.3480 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7621 Z= 0.289 Angle : 0.678 9.358 10418 Z= 0.353 Chirality : 0.046 0.168 1217 Planarity : 0.005 0.077 1309 Dihedral : 6.214 52.079 1110 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.81 % Allowed : 27.92 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 980 helix: 1.05 (0.27), residues: 368 sheet: -0.91 (0.36), residues: 208 loop : -1.57 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 118 TYR 0.016 0.002 TYR N 60 PHE 0.020 0.003 PHE N 108 TRP 0.018 0.002 TRP B 82 HIS 0.006 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.29 ( 7617) covalent geometry : angle 0.67580 / 0.35 (10410) SS BOND : bond 0.00340 / 0.17 ( 4) SS BOND : angle 2.20271 / 1.32 ( 8) hydrogen bonds : bond 0.04972 / 3.40 ( 375) hydrogen bonds : angle 5.51275 / 3.96 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.171 Fit side-chains REVERT: A 220 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6461 (t-90) REVERT: B 275 SER cc_start: 0.8315 (m) cc_final: 0.8086 (m) REVERT: N 83 MET cc_start: 0.4821 (ttm) cc_final: 0.4437 (ttt) REVERT: I 193 GLU cc_start: 0.6246 (tt0) cc_final: 0.5997 (tt0) outliers start: 35 outliers final: 19 residues processed: 116 average time/residue: 0.0578 time to fit residues: 9.7847 Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 205 MET Chi-restraints excluded: chain I residue 229 GLN Chi-restraints excluded: chain I residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 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 = 0.4065 r_free = 0.4065 target = 0.190773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154293 restraints weight = 8041.781| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.15 r_work: 0.3542 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7621 Z= 0.139 Angle : 0.541 9.697 10418 Z= 0.281 Chirality : 0.041 0.132 1217 Planarity : 0.004 0.069 1309 Dihedral : 5.769 48.738 1110 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.85 % Allowed : 28.61 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 980 helix: 1.53 (0.28), residues: 367 sheet: -0.85 (0.38), residues: 191 loop : -1.50 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 272 TYR 0.012 0.001 TYR I 197 PHE 0.015 0.001 PHE I 62 TRP 0.016 0.002 TRP I 146 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7617) covalent geometry : angle 0.53953 / 0.28 (10410) SS BOND : bond 0.00413 / 0.20 ( 4) SS BOND : angle 1.48068 / 0.89 ( 8) hydrogen bonds : bond 0.03959 / 2.75 ( 375) hydrogen bonds : angle 5.05848 / 3.62 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.244 Fit side-chains REVERT: A 220 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6379 (t-90) REVERT: B 183 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6385 (t-90) REVERT: B 205 ASP cc_start: 0.6947 (p0) cc_final: 0.6646 (p0) REVERT: B 234 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 275 SER cc_start: 0.8343 (m) cc_final: 0.8112 (m) REVERT: N 18 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5666 (pt) REVERT: N 67 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4017 (ptm160) REVERT: N 83 MET cc_start: 0.4635 (ttm) cc_final: 0.4192 (ttt) REVERT: I 193 GLU cc_start: 0.6124 (tt0) cc_final: 0.5856 (tt0) outliers start: 28 outliers final: 14 residues processed: 123 average time/residue: 0.0584 time to fit residues: 10.4414 Evaluate side-chains 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 229 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 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 = 0.4075 r_free = 0.4075 target = 0.191633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155324 restraints weight = 8117.174| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.15 r_work: 0.3572 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7621 Z= 0.132 Angle : 0.528 9.396 10418 Z= 0.274 Chirality : 0.041 0.129 1217 Planarity : 0.004 0.066 1309 Dihedral : 5.734 50.403 1110 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.36 % Allowed : 28.20 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 980 helix: 1.62 (0.28), residues: 368 sheet: -0.81 (0.38), residues: 191 loop : -1.48 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 272 TYR 0.013 0.001 TYR I 197 PHE 0.013 0.001 PHE I 62 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7617) covalent geometry : angle 0.52653 / 0.27 (10410) SS BOND : bond 0.00319 / 0.15 ( 4) SS BOND : angle 1.64134 / 1.00 ( 8) hydrogen bonds : bond 0.03782 / 2.61 ( 375) hydrogen bonds : angle 4.85726 / 3.48 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 95 time to evaluate : 0.258 Fit side-chains REVERT: A 220 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6402 (t-90) REVERT: B 183 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6416 (t-90) REVERT: B 205 ASP cc_start: 0.7001 (p0) cc_final: 0.6701 (p0) REVERT: B 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: B 245 SER cc_start: 0.7057 (OUTLIER) cc_final: 0.6296 (t) REVERT: B 275 SER cc_start: 0.8370 (m) cc_final: 0.8148 (m) REVERT: N 18 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5786 (pt) REVERT: N 67 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4431 (ptm160) REVERT: N 83 MET cc_start: 0.4686 (ttm) cc_final: 0.4268 (ttp) REVERT: I 193 GLU cc_start: 0.6131 (tt0) cc_final: 0.5809 (tt0) outliers start: 39 outliers final: 21 residues processed: 130 average time/residue: 0.0614 time to fit residues: 11.4675 Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 229 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155534 restraints weight = 8098.610| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.15 r_work: 0.3592 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7621 Z= 0.129 Angle : 0.528 10.430 10418 Z= 0.273 Chirality : 0.041 0.127 1217 Planarity : 0.004 0.063 1309 Dihedral : 5.736 51.024 1110 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.36 % Allowed : 28.20 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 980 helix: 1.64 (0.28), residues: 369 sheet: -0.81 (0.38), residues: 191 loop : -1.47 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 272 TYR 0.017 0.001 TYR I 313 PHE 0.014 0.001 PHE I 62 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7617) covalent geometry : angle 0.52656 / 0.27 (10410) SS BOND : bond 0.00366 / 0.17 ( 4) SS BOND : angle 1.62094 / 0.97 ( 8) hydrogen bonds : bond 0.03720 / 2.58 ( 375) hydrogen bonds : angle 4.79076 / 3.43 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.332 Fit side-chains REVERT: A 220 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6454 (t-90) REVERT: B 183 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6550 (t-90) REVERT: B 205 ASP cc_start: 0.7022 (p0) cc_final: 0.6725 (p0) REVERT: B 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: B 245 SER cc_start: 0.7580 (OUTLIER) cc_final: 0.6870 (t) REVERT: B 275 SER cc_start: 0.8292 (m) cc_final: 0.8045 (m) REVERT: N 18 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5812 (pt) REVERT: N 67 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5031 (ptm160) REVERT: N 83 MET cc_start: 0.4836 (ttm) cc_final: 0.4430 (ttp) REVERT: I 193 GLU cc_start: 0.6452 (tt0) cc_final: 0.5941 (tt0) REVERT: I 307 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7696 (mm) outliers start: 39 outliers final: 27 residues processed: 125 average time/residue: 0.0716 time to fit residues: 12.9591 Evaluate side-chains 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 53 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.194500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.158950 restraints weight = 8015.633| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.09 r_work: 0.3631 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7621 Z= 0.100 Angle : 0.493 9.835 10418 Z= 0.256 Chirality : 0.040 0.125 1217 Planarity : 0.004 0.059 1309 Dihedral : 5.624 51.892 1110 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.54 % Allowed : 29.16 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.28), residues: 980 helix: 1.81 (0.28), residues: 369 sheet: -0.62 (0.38), residues: 198 loop : -1.48 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 272 TYR 0.018 0.001 TYR I 313 PHE 0.023 0.001 PHE A 340 TRP 0.015 0.001 TRP I 146 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7617) covalent geometry : angle 0.49180 / 0.26 (10410) SS BOND : bond 0.00326 / 0.15 ( 4) SS BOND : angle 1.40799 / 0.85 ( 8) hydrogen bonds : bond 0.03384 / 2.36 ( 375) hydrogen bonds : angle 4.58465 / 3.27 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.169 Fit side-chains REVERT: A 220 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6307 (t-90) REVERT: A 378 ASP cc_start: 0.7668 (m-30) cc_final: 0.6614 (m-30) REVERT: B 183 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6308 (t-90) REVERT: B 234 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 245 SER cc_start: 0.7427 (OUTLIER) cc_final: 0.6723 (t) REVERT: B 275 SER cc_start: 0.8267 (m) cc_final: 0.8013 (m) REVERT: N 67 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5259 (ptm160) REVERT: N 83 MET cc_start: 0.4711 (ttm) cc_final: 0.4384 (ttp) REVERT: I 193 GLU cc_start: 0.6281 (tt0) cc_final: 0.5875 (tt0) REVERT: I 307 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7595 (mm) outliers start: 33 outliers final: 21 residues processed: 126 average time/residue: 0.0720 time to fit residues: 12.6137 Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 0.0020 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.194663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158556 restraints weight = 8038.875| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.14 r_work: 0.3625 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7621 Z= 0.115 Angle : 0.511 11.613 10418 Z= 0.263 Chirality : 0.040 0.126 1217 Planarity : 0.004 0.057 1309 Dihedral : 5.665 52.560 1110 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.26 % Allowed : 29.57 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 980 helix: 1.79 (0.28), residues: 370 sheet: -0.62 (0.38), residues: 198 loop : -1.46 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 272 TYR 0.017 0.001 TYR I 313 PHE 0.014 0.001 PHE A 340 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7617) covalent geometry : angle 0.50955 / 0.26 (10410) SS BOND : bond 0.00311 / 0.15 ( 4) SS BOND : angle 1.45941 / 0.88 ( 8) hydrogen bonds : bond 0.03520 / 2.44 ( 375) hydrogen bonds : angle 4.59636 / 3.28 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.167 Fit side-chains REVERT: A 220 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6400 (t-90) REVERT: B 183 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6494 (t-90) REVERT: B 234 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: B 245 SER cc_start: 0.7491 (OUTLIER) cc_final: 0.6801 (t) REVERT: B 275 SER cc_start: 0.8300 (m) cc_final: 0.8042 (m) REVERT: N 83 MET cc_start: 0.4745 (ttm) cc_final: 0.4531 (ttp) REVERT: I 193 GLU cc_start: 0.6286 (tt0) cc_final: 0.5927 (tt0) REVERT: I 307 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7808 (mm) outliers start: 31 outliers final: 22 residues processed: 118 average time/residue: 0.0554 time to fit residues: 9.5060 Evaluate side-chains 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 307 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 82 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.0170 chunk 91 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161289 restraints weight = 8131.599| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.16 r_work: 0.3655 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7621 Z= 0.098 Angle : 0.500 11.109 10418 Z= 0.255 Chirality : 0.040 0.131 1217 Planarity : 0.003 0.055 1309 Dihedral : 5.667 54.112 1110 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.13 % Allowed : 29.71 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 980 helix: 1.83 (0.28), residues: 373 sheet: -0.57 (0.38), residues: 198 loop : -1.47 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.015 0.001 TYR I 313 PHE 0.014 0.001 PHE I 62 TRP 0.014 0.001 TRP I 146 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 7617) covalent geometry : angle 0.49872 / 0.25 (10410) SS BOND : bond 0.00305 / 0.14 ( 4) SS BOND : angle 1.34267 / 0.81 ( 8) hydrogen bonds : bond 0.03313 / 2.30 ( 375) hydrogen bonds : angle 4.48367 / 3.20 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.225 Fit side-chains REVERT: A 220 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6376 (t-90) REVERT: A 378 ASP cc_start: 0.7673 (m-30) cc_final: 0.6972 (m-30) REVERT: B 183 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6342 (t-90) REVERT: B 234 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 245 SER cc_start: 0.7446 (OUTLIER) cc_final: 0.6765 (t) REVERT: B 275 SER cc_start: 0.8266 (m) cc_final: 0.8008 (m) REVERT: N 83 MET cc_start: 0.5102 (ttm) cc_final: 0.4895 (ttp) REVERT: I 193 GLU cc_start: 0.6116 (tt0) cc_final: 0.5914 (tt0) outliers start: 30 outliers final: 20 residues processed: 119 average time/residue: 0.0734 time to fit residues: 12.4043 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 37 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 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 = 0.4101 r_free = 0.4101 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158263 restraints weight = 7953.209| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.13 r_work: 0.3617 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7621 Z= 0.125 Angle : 0.518 10.931 10418 Z= 0.266 Chirality : 0.041 0.133 1217 Planarity : 0.003 0.055 1309 Dihedral : 5.786 55.314 1110 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 29.57 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.28), residues: 980 helix: 1.82 (0.28), residues: 371 sheet: -0.66 (0.36), residues: 214 loop : -1.49 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.021 0.001 TYR I 313 PHE 0.014 0.001 PHE I 62 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 7617) covalent geometry : angle 0.51643 / 0.27 (10410) SS BOND : bond 0.00303 / 0.14 ( 4) SS BOND : angle 1.42811 / 0.86 ( 8) hydrogen bonds : bond 0.03556 / 2.46 ( 375) hydrogen bonds : angle 4.56875 / 3.27 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.261 Fit side-chains REVERT: A 220 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6401 (t-90) REVERT: B 183 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6505 (t-90) REVERT: B 234 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 245 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.6825 (t) REVERT: B 275 SER cc_start: 0.8309 (m) cc_final: 0.8055 (m) REVERT: N 83 MET cc_start: 0.5141 (ttm) cc_final: 0.4934 (ttp) REVERT: I 307 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (mm) outliers start: 29 outliers final: 20 residues processed: 113 average time/residue: 0.0699 time to fit residues: 11.4116 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.0050 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 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 = 0.4097 r_free = 0.4097 target = 0.194106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157727 restraints weight = 7974.042| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.14 r_work: 0.3615 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7621 Z= 0.125 Angle : 0.527 10.805 10418 Z= 0.271 Chirality : 0.041 0.138 1217 Planarity : 0.004 0.055 1309 Dihedral : 5.945 59.159 1110 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.44 % Allowed : 30.26 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 980 helix: 1.80 (0.28), residues: 371 sheet: -0.66 (0.35), residues: 214 loop : -1.49 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.021 0.001 TYR I 313 PHE 0.014 0.001 PHE I 62 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7617) covalent geometry : angle 0.52567 / 0.27 (10410) SS BOND : bond 0.00328 / 0.15 ( 4) SS BOND : angle 1.46789 / 0.88 ( 8) hydrogen bonds : bond 0.03573 / 2.49 ( 375) hydrogen bonds : angle 4.58490 / 3.28 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.193 Fit side-chains REVERT: A 220 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6379 (t-90) REVERT: B 183 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6519 (t-90) REVERT: B 234 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: B 245 SER cc_start: 0.7507 (OUTLIER) cc_final: 0.6807 (t) REVERT: B 275 SER cc_start: 0.8299 (m) cc_final: 0.8042 (m) REVERT: N 83 MET cc_start: 0.5012 (ttm) cc_final: 0.4802 (ttp) outliers start: 25 outliers final: 21 residues processed: 108 average time/residue: 0.0656 time to fit residues: 10.1903 Evaluate side-chains 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.195019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158763 restraints weight = 7947.029| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.13 r_work: 0.3645 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7621 Z= 0.114 Angle : 0.518 10.706 10418 Z= 0.266 Chirality : 0.040 0.136 1217 Planarity : 0.003 0.055 1309 Dihedral : 5.901 58.324 1110 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 29.71 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 980 helix: 1.80 (0.28), residues: 370 sheet: -0.57 (0.37), residues: 198 loop : -1.43 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 19 TYR 0.019 0.001 TYR I 313 PHE 0.014 0.001 PHE I 62 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 7617) covalent geometry : angle 0.51637 / 0.27 (10410) SS BOND : bond 0.00315 / 0.15 ( 4) SS BOND : angle 1.42022 / 0.86 ( 8) hydrogen bonds : bond 0.03489 / 2.43 ( 375) hydrogen bonds : angle 4.54671 / 3.25 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.13 seconds wall clock time: 33 minutes 34.75 seconds (2014.75 seconds total)