Starting phenix.real_space_refine on Sat Aug 23 02:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6m_36923/08_2025/8k6m_36923.cif" } resolution = 3.3 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= 0.028 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5939 2.51 5 N 1588 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1794 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2444 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 250 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain breaks: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9327 At special positions: 0 Unit cell: (103.96, 121.44, 138.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1732 8.00 N 1588 7.00 C 5939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.87 Conformation dependent library (CDL) restraints added in 347.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.558A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.592A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.522A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.584A pdb=" N PHE A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.543A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.768A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.941A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 removed outlier: 3.929A pdb=" N GLN B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.789A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 36 through 68 removed outlier: 3.958A pdb=" N GLN D 68 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 103 Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 109 through 144 removed outlier: 3.591A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Proline residue: D 117 - end of helix removed outlier: 3.587A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 176 Proline residue: D 172 - end of helix removed outlier: 4.091A pdb=" N TYR D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 243 Proline residue: D 223 - end of helix removed outlier: 3.718A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 288 removed outlier: 3.734A pdb=" N SER D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Proline residue: D 278 - end of helix Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 297 through 321 removed outlier: 3.959A pdb=" N ASN D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.113A pdb=" N ARG D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.934A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.567A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.747A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.787A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.951A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.710A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 152 removed outlier: 3.563A pdb=" N CYS B 148 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 157 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 158 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.914A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.580A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.841A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.979A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 111 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG S 98 " --> pdb=" O TRP S 111 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN S 113 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS S 96 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.979A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP S 111 " --> pdb=" O ARG S 98 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG S 98 " --> pdb=" O TRP S 111 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN S 113 " --> pdb=" O CYS S 96 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS S 96 " --> pdb=" O GLN S 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.659A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 157 Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 190 removed outlier: 5.846A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1200 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: 1.22 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1516 1.30 - 1.43: 2587 1.43 - 1.56: 5320 1.56 - 1.69: 1 1.69 - 1.82: 101 Bond restraints: 9525 Sorted by residual: bond pdb=" CA PHE D 173 " pdb=" C PHE D 173 " ideal model delta sigma weight residual 1.523 1.435 0.088 1.34e-02 5.57e+03 4.31e+01 bond pdb=" CA LEU D 174 " pdb=" C LEU D 174 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.34e-02 5.57e+03 3.07e+01 bond pdb=" CA THR B 102 " pdb=" CB THR B 102 " ideal model delta sigma weight residual 1.533 1.450 0.083 1.72e-02 3.38e+03 2.33e+01 bond pdb=" C SER D 312 " pdb=" O SER D 312 " ideal model delta sigma weight residual 1.235 1.176 0.060 1.26e-02 6.30e+03 2.23e+01 bond pdb=" C LEU D 174 " pdb=" O LEU D 174 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.94e+01 ... (remaining 9520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 12724 2.64 - 5.27: 141 5.27 - 7.91: 23 7.91 - 10.54: 4 10.54 - 13.18: 4 Bond angle restraints: 12896 Sorted by residual: angle pdb=" C LEU D 174 " pdb=" N ILE D 175 " pdb=" CA ILE D 175 " ideal model delta sigma weight residual 120.56 109.50 11.06 1.28e+00 6.10e-01 7.47e+01 angle pdb=" N CYS D 198 " pdb=" CA CYS D 198 " pdb=" C CYS D 198 " ideal model delta sigma weight residual 108.34 121.52 -13.18 1.64e+00 3.72e-01 6.46e+01 angle pdb=" N PHE D 173 " pdb=" CA PHE D 173 " pdb=" C PHE D 173 " ideal model delta sigma weight residual 110.80 97.87 12.93 2.13e+00 2.20e-01 3.68e+01 angle pdb=" C ASN E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta sigma weight residual 119.84 127.23 -7.39 1.25e+00 6.40e-01 3.50e+01 angle pdb=" O ASN E 7 " pdb=" C ASN E 7 " pdb=" N PRO E 8 " ideal model delta sigma weight residual 120.48 125.57 -5.09 8.90e-01 1.26e+00 3.27e+01 ... (remaining 12891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 5027 15.19 - 30.37: 490 30.37 - 45.56: 126 45.56 - 60.74: 20 60.74 - 75.93: 2 Dihedral angle restraints: 5665 sinusoidal: 2223 harmonic: 3442 Sorted by residual: dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" N ARG E 35 " pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C ARG E 35 " pdb=" N ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta harmonic sigma weight residual -122.60 -133.83 11.23 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 5662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1350 0.084 - 0.168: 95 0.168 - 0.252: 5 0.252 - 0.336: 3 0.336 - 0.420: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA ARG E 35 " pdb=" N ARG E 35 " pdb=" C ARG E 35 " pdb=" CB ARG E 35 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA THR B 102 " pdb=" N THR B 102 " pdb=" C THR B 102 " pdb=" CB THR B 102 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA TYR E 20 " pdb=" N TYR E 20 " pdb=" C TYR E 20 " pdb=" CB TYR E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1452 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.063 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO B 39 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 312 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 312 " -0.065 2.00e-02 2.50e+03 pdb=" O SER D 312 " 0.025 2.00e-02 2.50e+03 pdb=" N THR D 313 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 94 " -0.060 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO D 95 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.049 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 99 2.65 - 3.21: 8273 3.21 - 3.77: 13266 3.77 - 4.34: 17490 4.34 - 4.90: 29737 Nonbonded interactions: 68865 Sorted by model distance: nonbonded pdb=" CE MET E 17 " pdb=" N ALA E 18 " model vdw 2.085 3.540 nonbonded pdb=" O MET B 101 " pdb=" CG2 THR B 102 " model vdw 2.124 3.460 nonbonded pdb=" O GLN D 201 " pdb=" CD1 PHE D 202 " model vdw 2.170 3.340 nonbonded pdb=" OG1 THR D 75 " pdb=" OE2 GLU D 137 " model vdw 2.217 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.218 3.040 ... (remaining 68860 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 8.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 0.088 9526 Z= 0.285 Angle : 0.718 13.177 12898 Z= 0.421 Chirality : 0.048 0.420 1455 Planarity : 0.006 0.095 1635 Dihedral : 12.804 75.925 3438 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.41 % Favored : 94.24 % Rotamer: Outliers : 0.29 % Allowed : 0.49 % Favored : 99.22 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1164 helix: 2.45 (0.27), residues: 407 sheet: 0.22 (0.32), residues: 261 loop : -1.58 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 18 TYR 0.020 0.001 TYR E 20 PHE 0.018 0.001 PHE A 190 TRP 0.033 0.001 TRP B 82 HIS 0.010 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9525) covalent geometry : angle 0.71844 (12896) SS BOND : bond 0.00711 ( 1) SS BOND : angle 0.85398 ( 2) hydrogen bonds : bond 0.13567 ( 417) hydrogen bonds : angle 4.73364 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.350 Fit side-chains REVERT: A 198 LYS cc_start: 0.7736 (mppt) cc_final: 0.7407 (mppt) REVERT: A 241 MET cc_start: 0.6595 (ptp) cc_final: 0.6375 (ptp) REVERT: A 254 ILE cc_start: 0.8083 (tp) cc_final: 0.7862 (tp) REVERT: A 318 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7800 (ttmt) REVERT: B 237 ASN cc_start: 0.7642 (t0) cc_final: 0.7338 (t0) REVERT: B 247 ASP cc_start: 0.7312 (t0) cc_final: 0.7097 (t0) REVERT: D 106 TRP cc_start: 0.7154 (t-100) cc_final: 0.6582 (t-100) REVERT: D 248 MET cc_start: 0.4059 (mpp) cc_final: 0.3445 (mpp) REVERT: D 282 PHE cc_start: 0.7939 (t80) cc_final: 0.7728 (t80) REVERT: D 310 MET cc_start: 0.7361 (mmm) cc_final: 0.7141 (mmm) REVERT: S 230 MET cc_start: 0.8687 (ttt) cc_final: 0.8251 (ttp) REVERT: E 31 ILE cc_start: 0.8198 (tt) cc_final: 0.7948 (tt) outliers start: 3 outliers final: 1 residues processed: 261 average time/residue: 0.1030 time to fit residues: 36.6392 Evaluate side-chains 238 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 7 ASN ** 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 = 0.3870 r_free = 0.3870 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115025 restraints weight = 13679.462| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.74 r_work: 0.3338 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9526 Z= 0.113 Angle : 0.548 7.146 12898 Z= 0.286 Chirality : 0.042 0.233 1455 Planarity : 0.004 0.063 1635 Dihedral : 4.127 32.523 1283 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 1.66 % Allowed : 11.04 % Favored : 87.30 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1164 helix: 2.49 (0.27), residues: 417 sheet: 0.37 (0.32), residues: 266 loop : -1.52 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 18 TYR 0.011 0.001 TYR B 289 PHE 0.015 0.001 PHE A 190 TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9525) covalent geometry : angle 0.54839 (12896) SS BOND : bond 0.00672 ( 1) SS BOND : angle 0.95225 ( 2) hydrogen bonds : bond 0.04701 ( 417) hydrogen bonds : angle 4.01805 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8084 (mppt) cc_final: 0.7783 (mppt) REVERT: A 241 MET cc_start: 0.7162 (ptp) cc_final: 0.6822 (ptp) REVERT: A 254 ILE cc_start: 0.8021 (tp) cc_final: 0.7820 (tp) REVERT: A 267 LEU cc_start: 0.8259 (tp) cc_final: 0.7977 (tp) REVERT: B 119 ASN cc_start: 0.7492 (m-40) cc_final: 0.7202 (m110) REVERT: B 237 ASN cc_start: 0.7826 (t0) cc_final: 0.7496 (t0) REVERT: B 247 ASP cc_start: 0.7486 (t0) cc_final: 0.7144 (t0) REVERT: B 254 ASP cc_start: 0.7485 (p0) cc_final: 0.7070 (p0) REVERT: B 275 SER cc_start: 0.8458 (m) cc_final: 0.8235 (m) REVERT: D 51 ILE cc_start: 0.8248 (mt) cc_final: 0.8011 (mm) REVERT: D 173 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7630 (t80) REVERT: D 181 ASP cc_start: 0.7155 (m-30) cc_final: 0.6947 (m-30) REVERT: D 237 ARG cc_start: 0.7218 (tmt-80) cc_final: 0.6905 (tmt-80) REVERT: S 93 MET cc_start: 0.7989 (ttp) cc_final: 0.7458 (ttp) REVERT: S 201 ASP cc_start: 0.7650 (t0) cc_final: 0.7431 (t0) REVERT: S 230 MET cc_start: 0.8716 (ttt) cc_final: 0.8274 (ttp) outliers start: 17 outliers final: 10 residues processed: 236 average time/residue: 0.1143 time to fit residues: 36.1032 Evaluate side-chains 238 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** 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 = 0.3845 r_free = 0.3845 target = 0.140485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112940 restraints weight = 13589.259| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.72 r_work: 0.3329 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9526 Z= 0.134 Angle : 0.552 6.914 12898 Z= 0.289 Chirality : 0.042 0.168 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.018 25.355 1280 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 2.83 % Allowed : 13.87 % Favored : 83.30 % 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 aren not related in a simple way. whole: 0.60 (0.25), residues: 1164 helix: 2.49 (0.26), residues: 421 sheet: 0.49 (0.32), residues: 272 loop : -1.71 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR B 105 PHE 0.019 0.001 PHE D 282 TRP 0.029 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9525) covalent geometry : angle 0.55161 (12896) SS BOND : bond 0.00842 ( 1) SS BOND : angle 1.26382 ( 2) hydrogen bonds : bond 0.05204 ( 417) hydrogen bonds : angle 4.05099 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7460 (mp) cc_final: 0.7223 (mp) REVERT: A 198 LYS cc_start: 0.8091 (mppt) cc_final: 0.7818 (mppt) REVERT: A 241 MET cc_start: 0.7120 (ptp) cc_final: 0.6789 (ptp) REVERT: A 254 ILE cc_start: 0.8159 (tp) cc_final: 0.7930 (tp) REVERT: A 346 LYS cc_start: 0.8477 (tmtt) cc_final: 0.7970 (tmtt) REVERT: B 237 ASN cc_start: 0.7935 (t0) cc_final: 0.7583 (t0) REVERT: B 247 ASP cc_start: 0.7492 (t0) cc_final: 0.7149 (t0) REVERT: B 254 ASP cc_start: 0.7405 (p0) cc_final: 0.7013 (p0) REVERT: B 275 SER cc_start: 0.8456 (m) cc_final: 0.8209 (m) REVERT: B 325 MET cc_start: 0.8230 (mmt) cc_final: 0.7946 (tpp) REVERT: D 51 ILE cc_start: 0.8275 (mt) cc_final: 0.8035 (mm) REVERT: D 199 PHE cc_start: 0.7980 (p90) cc_final: 0.7753 (p90) REVERT: D 282 PHE cc_start: 0.7978 (t80) cc_final: 0.7776 (t80) REVERT: D 310 MET cc_start: 0.8090 (mmm) cc_final: 0.7795 (mmm) REVERT: S 93 MET cc_start: 0.8017 (ttp) cc_final: 0.7462 (ttp) REVERT: S 230 MET cc_start: 0.8744 (ttt) cc_final: 0.8328 (ttp) REVERT: E 27 TYR cc_start: 0.7568 (t80) cc_final: 0.7167 (t80) outliers start: 29 outliers final: 20 residues processed: 244 average time/residue: 0.1086 time to fit residues: 35.9659 Evaluate side-chains 254 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113387 restraints weight = 13787.368| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.74 r_work: 0.3337 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9526 Z= 0.120 Angle : 0.536 6.978 12898 Z= 0.279 Chirality : 0.042 0.239 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.922 24.417 1280 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 2.93 % Allowed : 16.60 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1164 helix: 2.53 (0.26), residues: 422 sheet: 0.53 (0.31), residues: 277 loop : -1.66 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.014 0.001 TYR D 100 PHE 0.023 0.001 PHE D 286 TRP 0.025 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9525) covalent geometry : angle 0.53591 (12896) SS BOND : bond 0.00742 ( 1) SS BOND : angle 1.13830 ( 2) hydrogen bonds : bond 0.04767 ( 417) hydrogen bonds : angle 3.94681 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7525 (pt0) cc_final: 0.7316 (pt0) REVERT: A 198 LYS cc_start: 0.8113 (mppt) cc_final: 0.7793 (mppt) REVERT: A 241 MET cc_start: 0.7045 (ptp) cc_final: 0.6713 (ptp) REVERT: A 254 ILE cc_start: 0.8122 (tp) cc_final: 0.7888 (tp) REVERT: A 267 LEU cc_start: 0.8328 (tp) cc_final: 0.8011 (tp) REVERT: B 176 GLN cc_start: 0.8484 (mt0) cc_final: 0.8222 (mt0) REVERT: B 237 ASN cc_start: 0.7949 (t0) cc_final: 0.7616 (t0) REVERT: B 247 ASP cc_start: 0.7467 (t0) cc_final: 0.7121 (t0) REVERT: B 254 ASP cc_start: 0.7485 (p0) cc_final: 0.7100 (p0) REVERT: B 275 SER cc_start: 0.8454 (m) cc_final: 0.8197 (m) REVERT: B 325 MET cc_start: 0.8241 (mmt) cc_final: 0.7957 (tpp) REVERT: D 237 ARG cc_start: 0.7201 (tmt-80) cc_final: 0.6994 (tmt-80) REVERT: D 310 MET cc_start: 0.8075 (mmm) cc_final: 0.7509 (mmm) REVERT: S 93 MET cc_start: 0.8021 (ttp) cc_final: 0.7817 (ttm) REVERT: S 201 ASP cc_start: 0.7622 (t0) cc_final: 0.7408 (t0) REVERT: S 230 MET cc_start: 0.8734 (ttt) cc_final: 0.8393 (ttp) REVERT: E 27 TYR cc_start: 0.7569 (t80) cc_final: 0.7183 (t80) outliers start: 30 outliers final: 25 residues processed: 242 average time/residue: 0.1029 time to fit residues: 33.5766 Evaluate side-chains 257 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 98 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111973 restraints weight = 13774.538| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.73 r_work: 0.3294 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9526 Z= 0.133 Angle : 0.545 6.863 12898 Z= 0.285 Chirality : 0.042 0.192 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.975 23.704 1280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.71 % Allowed : 16.80 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1164 helix: 2.54 (0.26), residues: 422 sheet: 0.49 (0.32), residues: 281 loop : -1.64 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.018 0.001 TYR D 100 PHE 0.021 0.001 PHE D 282 TRP 0.025 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9525) covalent geometry : angle 0.54462 (12896) SS BOND : bond 0.00796 ( 1) SS BOND : angle 0.95667 ( 2) hydrogen bonds : bond 0.05067 ( 417) hydrogen bonds : angle 3.94731 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8063 (mppt) cc_final: 0.7739 (mppt) REVERT: A 241 MET cc_start: 0.6972 (ptp) cc_final: 0.6644 (ptp) REVERT: A 254 ILE cc_start: 0.8169 (tp) cc_final: 0.7919 (tp) REVERT: A 267 LEU cc_start: 0.8324 (tp) cc_final: 0.8009 (tp) REVERT: B 221 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8137 (t) REVERT: B 237 ASN cc_start: 0.7985 (t0) cc_final: 0.7671 (t0) REVERT: B 246 ASP cc_start: 0.8261 (t0) cc_final: 0.8046 (t0) REVERT: B 247 ASP cc_start: 0.7463 (t0) cc_final: 0.7145 (t0) REVERT: B 254 ASP cc_start: 0.7413 (p0) cc_final: 0.6969 (p0) REVERT: B 275 SER cc_start: 0.8525 (m) cc_final: 0.8222 (m) REVERT: B 325 MET cc_start: 0.8233 (mmt) cc_final: 0.7956 (tpp) REVERT: D 310 MET cc_start: 0.8109 (mmm) cc_final: 0.7644 (mmm) REVERT: S 59 TYR cc_start: 0.7684 (m-10) cc_final: 0.7456 (m-10) REVERT: S 93 MET cc_start: 0.8040 (ttp) cc_final: 0.7821 (ttm) REVERT: E 27 TYR cc_start: 0.7586 (t80) cc_final: 0.7212 (t80) outliers start: 38 outliers final: 30 residues processed: 252 average time/residue: 0.1020 time to fit residues: 35.3256 Evaluate side-chains 266 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 chunk 104 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109286 restraints weight = 13912.765| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.74 r_work: 0.3254 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9526 Z= 0.191 Angle : 0.598 6.629 12898 Z= 0.318 Chirality : 0.045 0.320 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.252 24.169 1280 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.91 % Allowed : 17.68 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.25), residues: 1164 helix: 2.49 (0.26), residues: 416 sheet: 0.51 (0.31), residues: 277 loop : -1.67 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.021 0.002 TYR D 100 PHE 0.017 0.002 PHE B 234 TRP 0.030 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9525) covalent geometry : angle 0.59777 (12896) SS BOND : bond 0.01005 ( 1) SS BOND : angle 1.13094 ( 2) hydrogen bonds : bond 0.06101 ( 417) hydrogen bonds : angle 4.18531 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8144 (mppt) cc_final: 0.7847 (mppt) REVERT: A 241 MET cc_start: 0.6957 (ptp) cc_final: 0.6648 (ptp) REVERT: A 254 ILE cc_start: 0.8267 (tp) cc_final: 0.8000 (tp) REVERT: A 346 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7970 (tmtt) REVERT: B 237 ASN cc_start: 0.8125 (t0) cc_final: 0.7749 (t0) REVERT: B 247 ASP cc_start: 0.7541 (t0) cc_final: 0.7202 (t0) REVERT: B 254 ASP cc_start: 0.7366 (p0) cc_final: 0.6949 (p0) REVERT: B 275 SER cc_start: 0.8550 (m) cc_final: 0.8245 (m) REVERT: D 310 MET cc_start: 0.8148 (mmm) cc_final: 0.7696 (mmm) REVERT: S 93 MET cc_start: 0.8083 (ttp) cc_final: 0.7861 (ttm) REVERT: S 192 MET cc_start: 0.8253 (mtt) cc_final: 0.8030 (mtt) REVERT: E 27 TYR cc_start: 0.7625 (t80) cc_final: 0.7248 (t80) outliers start: 40 outliers final: 38 residues processed: 253 average time/residue: 0.0980 time to fit residues: 33.8520 Evaluate side-chains 274 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.0370 chunk 5 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114510 restraints weight = 13748.786| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.76 r_work: 0.3348 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9526 Z= 0.102 Angle : 0.525 9.150 12898 Z= 0.271 Chirality : 0.041 0.197 1455 Planarity : 0.004 0.053 1635 Dihedral : 3.812 24.345 1280 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.12 % Allowed : 20.02 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1164 helix: 2.57 (0.26), residues: 422 sheet: 0.44 (0.32), residues: 271 loop : -1.55 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 18 TYR 0.013 0.001 TYR D 100 PHE 0.015 0.001 PHE D 286 TRP 0.011 0.001 TRP B 332 HIS 0.002 0.000 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9525) covalent geometry : angle 0.52451 (12896) SS BOND : bond 0.00667 ( 1) SS BOND : angle 0.53501 ( 2) hydrogen bonds : bond 0.04081 ( 417) hydrogen bonds : angle 3.86268 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8124 (mppt) cc_final: 0.7813 (mppt) REVERT: A 241 MET cc_start: 0.6988 (ptp) cc_final: 0.6661 (ptp) REVERT: A 254 ILE cc_start: 0.8175 (tp) cc_final: 0.7907 (tp) REVERT: A 314 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7794 (mtt90) REVERT: A 318 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7551 (ttmm) REVERT: B 237 ASN cc_start: 0.7966 (t0) cc_final: 0.7656 (t0) REVERT: B 247 ASP cc_start: 0.7401 (t0) cc_final: 0.6959 (t0) REVERT: B 254 ASP cc_start: 0.7440 (p0) cc_final: 0.7056 (p0) REVERT: B 275 SER cc_start: 0.8466 (m) cc_final: 0.8207 (m) REVERT: B 325 MET cc_start: 0.8226 (mmt) cc_final: 0.7954 (tpp) REVERT: D 310 MET cc_start: 0.8057 (mmm) cc_final: 0.7587 (mmm) REVERT: S 93 MET cc_start: 0.8065 (ttp) cc_final: 0.7856 (ttm) REVERT: S 119 VAL cc_start: 0.8333 (t) cc_final: 0.8044 (m) REVERT: S 192 MET cc_start: 0.7975 (mtt) cc_final: 0.7772 (mtt) REVERT: S 220 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 27 TYR cc_start: 0.7574 (t80) cc_final: 0.7240 (t80) outliers start: 32 outliers final: 22 residues processed: 252 average time/residue: 0.1061 time to fit residues: 35.7732 Evaluate side-chains 268 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111890 restraints weight = 13655.726| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.75 r_work: 0.3291 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9526 Z= 0.139 Angle : 0.571 9.202 12898 Z= 0.296 Chirality : 0.043 0.188 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.954 25.409 1280 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.71 % Allowed : 20.02 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1164 helix: 2.49 (0.26), residues: 422 sheet: 0.49 (0.32), residues: 280 loop : -1.58 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.019 0.001 TYR D 100 PHE 0.015 0.001 PHE A 190 TRP 0.015 0.001 TRP B 332 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9525) covalent geometry : angle 0.57130 (12896) SS BOND : bond 0.00859 ( 1) SS BOND : angle 1.05366 ( 2) hydrogen bonds : bond 0.05034 ( 417) hydrogen bonds : angle 3.99954 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8126 (mppt) cc_final: 0.7781 (mppt) REVERT: A 241 MET cc_start: 0.6955 (ptp) cc_final: 0.6632 (ptp) REVERT: A 254 ILE cc_start: 0.8239 (tp) cc_final: 0.7964 (tp) REVERT: B 237 ASN cc_start: 0.8002 (t0) cc_final: 0.7672 (t0) REVERT: B 246 ASP cc_start: 0.8252 (t0) cc_final: 0.8032 (t0) REVERT: B 247 ASP cc_start: 0.7441 (t0) cc_final: 0.7119 (t0) REVERT: B 254 ASP cc_start: 0.7408 (p0) cc_final: 0.7012 (p0) REVERT: B 275 SER cc_start: 0.8532 (m) cc_final: 0.8224 (m) REVERT: B 325 MET cc_start: 0.8250 (mmt) cc_final: 0.7962 (tpp) REVERT: D 310 MET cc_start: 0.8119 (mmm) cc_final: 0.7652 (mmm) REVERT: S 93 MET cc_start: 0.8084 (ttp) cc_final: 0.7874 (ttm) REVERT: S 116 THR cc_start: 0.8644 (p) cc_final: 0.8204 (t) REVERT: S 118 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7821 (t) REVERT: S 192 MET cc_start: 0.8039 (mtt) cc_final: 0.7822 (mtt) REVERT: E 27 TYR cc_start: 0.7590 (t80) cc_final: 0.7202 (t80) REVERT: E 31 ILE cc_start: 0.8262 (tt) cc_final: 0.7899 (tt) outliers start: 38 outliers final: 31 residues processed: 256 average time/residue: 0.1024 time to fit residues: 35.7421 Evaluate side-chains 273 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 305 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112479 restraints weight = 13686.140| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.75 r_work: 0.3318 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9526 Z= 0.131 Angle : 0.570 8.669 12898 Z= 0.295 Chirality : 0.043 0.230 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.965 25.411 1280 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.42 % Allowed : 21.39 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1164 helix: 2.50 (0.26), residues: 422 sheet: 0.47 (0.32), residues: 280 loop : -1.56 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.012 0.001 TYR E 20 PHE 0.015 0.001 PHE A 190 TRP 0.019 0.001 TRP B 332 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9525) covalent geometry : angle 0.56991 (12896) SS BOND : bond 0.00894 ( 1) SS BOND : angle 1.06299 ( 2) hydrogen bonds : bond 0.04903 ( 417) hydrogen bonds : angle 3.98974 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8145 (mppt) cc_final: 0.7831 (mppt) REVERT: A 241 MET cc_start: 0.6918 (ptp) cc_final: 0.6617 (ptp) REVERT: A 254 ILE cc_start: 0.8239 (tp) cc_final: 0.7980 (tp) REVERT: A 318 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7803 (ttmt) REVERT: B 237 ASN cc_start: 0.7985 (t0) cc_final: 0.7656 (t0) REVERT: B 246 ASP cc_start: 0.8239 (t0) cc_final: 0.8017 (t0) REVERT: B 247 ASP cc_start: 0.7423 (t0) cc_final: 0.7084 (t0) REVERT: B 254 ASP cc_start: 0.7386 (p0) cc_final: 0.7018 (p0) REVERT: B 275 SER cc_start: 0.8516 (m) cc_final: 0.8207 (m) REVERT: B 325 MET cc_start: 0.8251 (mmt) cc_final: 0.7968 (tpp) REVERT: D 310 MET cc_start: 0.8118 (mmm) cc_final: 0.7661 (mmm) REVERT: S 93 MET cc_start: 0.8091 (ttp) cc_final: 0.7871 (ttm) REVERT: S 192 MET cc_start: 0.8053 (mtt) cc_final: 0.7850 (mtt) REVERT: S 220 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7563 (mm-30) REVERT: E 27 TYR cc_start: 0.7584 (t80) cc_final: 0.7204 (t80) REVERT: E 31 ILE cc_start: 0.8267 (tt) cc_final: 0.7899 (tt) outliers start: 35 outliers final: 34 residues processed: 256 average time/residue: 0.0998 time to fit residues: 34.5580 Evaluate side-chains 282 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 305 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112359 restraints weight = 13742.115| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.64 r_work: 0.3306 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9526 Z= 0.135 Angle : 0.579 8.564 12898 Z= 0.300 Chirality : 0.043 0.196 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.969 25.724 1280 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.52 % Allowed : 20.61 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1164 helix: 2.54 (0.26), residues: 416 sheet: 0.46 (0.32), residues: 280 loop : -1.55 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.012 0.001 TYR E 20 PHE 0.015 0.001 PHE A 190 TRP 0.022 0.001 TRP B 332 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9525) covalent geometry : angle 0.57868 (12896) SS BOND : bond 0.00919 ( 1) SS BOND : angle 1.10904 ( 2) hydrogen bonds : bond 0.04959 ( 417) hydrogen bonds : angle 4.00029 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8117 (mppt) cc_final: 0.7755 (mppt) REVERT: A 241 MET cc_start: 0.6907 (ptp) cc_final: 0.6609 (ptp) REVERT: A 254 ILE cc_start: 0.8233 (tp) cc_final: 0.7965 (tp) REVERT: A 318 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7794 (ttmt) REVERT: B 237 ASN cc_start: 0.7985 (t0) cc_final: 0.7647 (t0) REVERT: B 246 ASP cc_start: 0.8233 (t0) cc_final: 0.8011 (t0) REVERT: B 247 ASP cc_start: 0.7428 (t0) cc_final: 0.7085 (t0) REVERT: B 254 ASP cc_start: 0.7391 (p0) cc_final: 0.6997 (p0) REVERT: B 275 SER cc_start: 0.8515 (m) cc_final: 0.8205 (m) REVERT: B 325 MET cc_start: 0.8248 (mmt) cc_final: 0.7963 (tpp) REVERT: D 310 MET cc_start: 0.8108 (mmm) cc_final: 0.7647 (mmm) REVERT: S 93 MET cc_start: 0.8102 (ttp) cc_final: 0.7884 (ttm) REVERT: S 220 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 27 TYR cc_start: 0.7558 (t80) cc_final: 0.7180 (t80) REVERT: E 31 ILE cc_start: 0.8257 (tt) cc_final: 0.7886 (tt) outliers start: 36 outliers final: 33 residues processed: 258 average time/residue: 0.1000 time to fit residues: 35.2315 Evaluate side-chains 282 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 305 GLN D 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112754 restraints weight = 13615.325| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.75 r_work: 0.3307 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9526 Z= 0.122 Angle : 0.564 8.910 12898 Z= 0.292 Chirality : 0.042 0.178 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.947 26.038 1280 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.93 % Allowed : 21.09 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1164 helix: 2.51 (0.26), residues: 422 sheet: 0.46 (0.32), residues: 280 loop : -1.57 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.012 0.001 TYR E 20 PHE 0.015 0.001 PHE A 190 TRP 0.022 0.001 TRP B 332 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9525) covalent geometry : angle 0.56361 (12896) SS BOND : bond 0.00812 ( 1) SS BOND : angle 0.94604 ( 2) hydrogen bonds : bond 0.04720 ( 417) hydrogen bonds : angle 3.96018 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.38 seconds wall clock time: 37 minutes 28.20 seconds (2248.20 seconds total)