Starting phenix.real_space_refine on Mon May 12 18:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6m_36923/05_2025/8k6m_36923.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6m_36923/05_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_36923/05_2025/8k6m_36923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6m_36923/05_2025/8k6m_36923.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6m_36923/05_2025/8k6m_36923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6m_36923/05_2025/8k6m_36923.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.97, per 1000 atoms: 0.64 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.97 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: 2.46 Time building geometry restraints manager: 2.63 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: 1.710 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (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 TRP 0.033 0.001 TRP B 82 HIS 0.010 0.001 HIS B 62 PHE 0.018 0.001 PHE A 190 TYR 0.020 0.001 TYR E 20 ARG 0.009 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.13567 ( 417) hydrogen bonds : angle 4.73364 ( 1200) SS BOND : bond 0.00711 ( 1) SS BOND : angle 0.85398 ( 2) covalent geometry : bond 0.00459 ( 9525) covalent geometry : angle 0.71844 (12896) *********************** 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 : 0.929 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: 0.2161 time to fit residues: 76.7523 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 : 0.980 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.0570 chunk 87 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.143273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115657 restraints weight = 13579.898| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.74 r_work: 0.3379 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9526 Z= 0.108 Angle : 0.543 7.120 12898 Z= 0.282 Chirality : 0.042 0.222 1455 Planarity : 0.004 0.063 1635 Dihedral : 4.088 32.863 1283 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.86 % Allowed : 10.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1164 helix: 2.49 (0.27), residues: 417 sheet: 0.36 (0.32), residues: 265 loop : -1.53 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.001 PHE A 190 TYR 0.012 0.001 TYR E 20 ARG 0.003 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 417) hydrogen bonds : angle 3.99669 ( 1200) SS BOND : bond 0.00608 ( 1) SS BOND : angle 0.83117 ( 2) covalent geometry : bond 0.00227 ( 9525) covalent geometry : angle 0.54303 (12896) *********************** 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 253 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7456 (mtt) REVERT: A 198 LYS cc_start: 0.8089 (mppt) cc_final: 0.7815 (mppt) REVERT: A 241 MET cc_start: 0.7159 (ptp) cc_final: 0.6835 (ptp) REVERT: A 254 ILE cc_start: 0.8047 (tp) cc_final: 0.7841 (tp) REVERT: A 267 LEU cc_start: 0.8294 (tp) cc_final: 0.8001 (tp) REVERT: B 237 ASN cc_start: 0.7815 (t0) cc_final: 0.7510 (t0) REVERT: B 247 ASP cc_start: 0.7469 (t0) cc_final: 0.7142 (t0) REVERT: B 254 ASP cc_start: 0.7520 (p0) cc_final: 0.7130 (p0) REVERT: B 325 MET cc_start: 0.8210 (mmt) cc_final: 0.7907 (tpp) REVERT: D 51 ILE cc_start: 0.8236 (mt) cc_final: 0.7991 (mm) REVERT: D 237 ARG cc_start: 0.7217 (tmt-80) cc_final: 0.6924 (tmt-80) REVERT: D 248 MET cc_start: 0.4308 (mpp) cc_final: 0.3785 (mpp) REVERT: S 93 MET cc_start: 0.8009 (ttp) cc_final: 0.7441 (ttp) REVERT: S 201 ASP cc_start: 0.7633 (t0) cc_final: 0.7416 (t0) REVERT: S 230 MET cc_start: 0.8738 (ttt) cc_final: 0.8321 (ttp) outliers start: 19 outliers final: 11 residues processed: 241 average time/residue: 0.2308 time to fit residues: 75.3496 Evaluate side-chains 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 79 LEU 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 165 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 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.0040 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 7 optimal weight: 0.0050 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115723 restraints weight = 13713.819| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.75 r_work: 0.3375 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1325 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= 0.105 Angle : 0.525 7.328 12898 Z= 0.271 Chirality : 0.041 0.170 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.837 25.903 1280 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 2.15 % Allowed : 13.96 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1164 helix: 2.48 (0.26), residues: 423 sheet: 0.52 (0.32), residues: 264 loop : -1.59 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.017 0.001 PHE D 282 TYR 0.011 0.001 TYR E 20 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 417) hydrogen bonds : angle 3.90504 ( 1200) SS BOND : bond 0.00613 ( 1) SS BOND : angle 0.86645 ( 2) covalent geometry : bond 0.00222 ( 9525) covalent geometry : angle 0.52537 (12896) *********************** 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 255 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 1.043 Fit side-chains REVERT: A 23 LEU cc_start: 0.7382 (mp) cc_final: 0.7112 (mp) REVERT: A 198 LYS cc_start: 0.8099 (mppt) cc_final: 0.7857 (mppt) REVERT: A 241 MET cc_start: 0.7100 (ptp) cc_final: 0.6773 (ptp) REVERT: A 254 ILE cc_start: 0.8100 (tp) cc_final: 0.7868 (tp) REVERT: A 267 LEU cc_start: 0.8303 (tp) cc_final: 0.8001 (tp) REVERT: A 346 LYS cc_start: 0.8478 (tmtt) cc_final: 0.7950 (tmtt) REVERT: B 176 GLN cc_start: 0.8462 (mt0) cc_final: 0.8210 (mt0) REVERT: B 237 ASN cc_start: 0.7870 (t0) cc_final: 0.7531 (t0) REVERT: B 247 ASP cc_start: 0.7455 (t0) cc_final: 0.7099 (t0) REVERT: B 254 ASP cc_start: 0.7511 (p0) cc_final: 0.7125 (p0) REVERT: B 275 SER cc_start: 0.8457 (m) cc_final: 0.8236 (m) REVERT: B 325 MET cc_start: 0.8192 (mmt) cc_final: 0.7894 (tpp) REVERT: D 199 PHE cc_start: 0.7867 (p90) cc_final: 0.7642 (p90) REVERT: D 237 ARG cc_start: 0.7220 (tmt-80) cc_final: 0.6951 (tmt-80) REVERT: D 310 MET cc_start: 0.8045 (mmm) cc_final: 0.7741 (mmm) REVERT: S 65 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8080 (ttmm) REVERT: S 93 MET cc_start: 0.8028 (ttp) cc_final: 0.7473 (ttp) REVERT: S 201 ASP cc_start: 0.7610 (t0) cc_final: 0.7399 (t0) REVERT: S 230 MET cc_start: 0.8726 (ttt) cc_final: 0.8297 (ttp) REVERT: E 27 TYR cc_start: 0.7522 (t80) cc_final: 0.7124 (t80) outliers start: 22 outliers final: 17 residues processed: 239 average time/residue: 0.2305 time to fit residues: 74.1235 Evaluate side-chains 247 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 THR 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 D residue 66 LEU Chi-restraints excluded: chain D residue 112 MET 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 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.139599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112003 restraints weight = 13671.396| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.72 r_work: 0.3316 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9526 Z= 0.149 Angle : 0.567 6.937 12898 Z= 0.297 Chirality : 0.043 0.253 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.043 22.595 1280 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.22 % Allowed : 15.72 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1164 helix: 2.50 (0.26), residues: 422 sheet: 0.57 (0.31), residues: 274 loop : -1.72 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.015 0.002 PHE A 190 TYR 0.016 0.001 TYR B 105 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05449 ( 417) hydrogen bonds : angle 4.01953 ( 1200) SS BOND : bond 0.01078 ( 1) SS BOND : angle 1.05327 ( 2) covalent geometry : bond 0.00338 ( 9525) covalent geometry : angle 0.56682 (12896) *********************** 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 268 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.027 Fit side-chains REVERT: A 33 GLU cc_start: 0.7583 (pt0) cc_final: 0.7337 (pt0) REVERT: A 198 LYS cc_start: 0.8093 (mppt) cc_final: 0.7772 (mppt) REVERT: A 241 MET cc_start: 0.7027 (ptp) cc_final: 0.6695 (ptp) REVERT: A 254 ILE cc_start: 0.8140 (tp) cc_final: 0.7832 (tp) REVERT: A 267 LEU cc_start: 0.8318 (tp) cc_final: 0.8015 (tp) REVERT: A 305 GLN cc_start: 0.7449 (tp-100) cc_final: 0.7226 (tp-100) REVERT: A 346 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7926 (tmtt) REVERT: B 237 ASN cc_start: 0.7964 (t0) cc_final: 0.7593 (t0) REVERT: B 247 ASP cc_start: 0.7500 (t0) cc_final: 0.7172 (t0) REVERT: B 254 ASP cc_start: 0.7441 (p0) cc_final: 0.7042 (p0) REVERT: B 275 SER cc_start: 0.8445 (m) cc_final: 0.8201 (m) REVERT: D 282 PHE cc_start: 0.8050 (t80) cc_final: 0.7832 (t80) REVERT: D 310 MET cc_start: 0.8118 (mmm) cc_final: 0.7656 (mmm) REVERT: S 172 THR cc_start: 0.8306 (p) cc_final: 0.8042 (p) REVERT: S 201 ASP cc_start: 0.7643 (t0) cc_final: 0.7427 (t0) REVERT: E 27 TYR cc_start: 0.7579 (t80) cc_final: 0.7182 (t80) outliers start: 33 outliers final: 27 residues processed: 243 average time/residue: 0.2359 time to fit residues: 78.4263 Evaluate side-chains 258 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 322 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 B residue 318 LEU 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 D residue 303 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain S residue 69 THR 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 243 THR 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 75 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 0.0000 chunk 43 optimal weight: 0.2980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112389 restraints weight = 13724.363| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.74 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: 0.7424 moved from start: 0.1645 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= 0.127 Angle : 0.541 7.736 12898 Z= 0.282 Chirality : 0.042 0.193 1455 Planarity : 0.004 0.053 1635 Dihedral : 3.956 24.199 1280 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.22 % Allowed : 17.58 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1164 helix: 2.53 (0.26), residues: 422 sheet: 0.46 (0.31), residues: 281 loop : -1.64 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.024 0.001 PHE D 286 TYR 0.014 0.001 TYR E 20 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 417) hydrogen bonds : angle 3.94801 ( 1200) SS BOND : bond 0.00750 ( 1) SS BOND : angle 0.72741 ( 2) covalent geometry : bond 0.00283 ( 9525) covalent geometry : angle 0.54102 (12896) *********************** 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 267 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8093 (mppt) cc_final: 0.7738 (mppt) REVERT: A 241 MET cc_start: 0.6993 (ptp) cc_final: 0.6650 (ptp) REVERT: A 254 ILE cc_start: 0.8048 (tp) cc_final: 0.7798 (tp) REVERT: A 267 LEU cc_start: 0.8245 (tp) cc_final: 0.7950 (tp) REVERT: A 305 GLN cc_start: 0.7395 (tp-100) cc_final: 0.7189 (tp-100) REVERT: A 318 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7509 (ttmm) REVERT: B 237 ASN cc_start: 0.8001 (t0) cc_final: 0.7677 (t0) REVERT: B 247 ASP cc_start: 0.7480 (t0) cc_final: 0.7132 (t0) REVERT: B 254 ASP cc_start: 0.7371 (p0) cc_final: 0.7010 (p0) REVERT: B 275 SER cc_start: 0.8466 (m) cc_final: 0.8211 (m) REVERT: D 282 PHE cc_start: 0.8164 (t80) cc_final: 0.7938 (t80) REVERT: D 310 MET cc_start: 0.8112 (mmm) cc_final: 0.7628 (mmm) REVERT: S 192 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7573 (mpp) REVERT: S 201 ASP cc_start: 0.7602 (t0) cc_final: 0.7401 (t0) REVERT: E 27 TYR cc_start: 0.7577 (t80) cc_final: 0.7174 (t80) outliers start: 33 outliers final: 27 residues processed: 244 average time/residue: 0.2166 time to fit residues: 71.6267 Evaluate side-chains 261 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 322 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 B residue 278 PHE 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 69 THR 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 192 MET Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109444 restraints weight = 13742.681| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.71 r_work: 0.3275 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1879 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= 0.194 Angle : 0.604 6.616 12898 Z= 0.320 Chirality : 0.045 0.291 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.281 24.022 1280 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.91 % Allowed : 18.07 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1164 helix: 2.44 (0.26), residues: 416 sheet: 0.63 (0.32), residues: 269 loop : -1.73 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE D 286 TYR 0.016 0.002 TYR B 105 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.06210 ( 417) hydrogen bonds : angle 4.19471 ( 1200) SS BOND : bond 0.01029 ( 1) SS BOND : angle 1.42281 ( 2) covalent geometry : bond 0.00445 ( 9525) covalent geometry : angle 0.60345 (12896) *********************** 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 282 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8167 (mppt) cc_final: 0.7826 (mppt) REVERT: A 241 MET cc_start: 0.7034 (ptp) cc_final: 0.6705 (ptp) REVERT: A 254 ILE cc_start: 0.8200 (tp) cc_final: 0.7930 (tp) REVERT: A 346 LYS cc_start: 0.8417 (tmtt) cc_final: 0.7969 (tmtt) REVERT: B 82 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.7204 (p90) REVERT: B 237 ASN cc_start: 0.8066 (t0) cc_final: 0.7631 (t0) REVERT: B 247 ASP cc_start: 0.7529 (t0) cc_final: 0.7162 (t0) REVERT: B 254 ASP cc_start: 0.7361 (p0) cc_final: 0.6917 (p0) REVERT: B 275 SER cc_start: 0.8517 (m) cc_final: 0.8216 (m) REVERT: D 310 MET cc_start: 0.8156 (mmm) cc_final: 0.7704 (mmm) REVERT: S 201 ASP cc_start: 0.7625 (t0) cc_final: 0.7414 (t0) REVERT: E 27 TYR cc_start: 0.7613 (t80) cc_final: 0.7245 (t80) outliers start: 40 outliers final: 34 residues processed: 253 average time/residue: 0.2220 time to fit residues: 76.3374 Evaluate side-chains 277 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111065 restraints weight = 13815.994| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.76 r_work: 0.3294 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1875 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= 0.137 Angle : 0.560 7.342 12898 Z= 0.294 Chirality : 0.043 0.195 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.079 24.471 1280 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.71 % Allowed : 19.63 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1164 helix: 2.50 (0.26), residues: 416 sheet: 0.50 (0.32), residues: 276 loop : -1.63 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE D 286 TYR 0.013 0.001 TYR E 20 ARG 0.007 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 417) hydrogen bonds : angle 4.03656 ( 1200) SS BOND : bond 0.00856 ( 1) SS BOND : angle 1.17182 ( 2) covalent geometry : bond 0.00308 ( 9525) covalent geometry : angle 0.56007 (12896) *********************** 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 283 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8160 (mppt) cc_final: 0.7785 (mppt) REVERT: A 241 MET cc_start: 0.6963 (ptp) cc_final: 0.6638 (ptp) REVERT: A 254 ILE cc_start: 0.8171 (tp) cc_final: 0.7909 (tp) REVERT: A 346 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7956 (tmtt) REVERT: B 237 ASN cc_start: 0.8103 (t0) cc_final: 0.7738 (t0) REVERT: B 246 ASP cc_start: 0.8220 (t0) cc_final: 0.8009 (t0) REVERT: B 247 ASP cc_start: 0.7492 (t0) cc_final: 0.7171 (t0) REVERT: B 254 ASP cc_start: 0.7375 (p0) cc_final: 0.7009 (p0) REVERT: B 275 SER cc_start: 0.8501 (m) cc_final: 0.8201 (m) REVERT: B 325 MET cc_start: 0.8273 (mmt) cc_final: 0.7998 (tpp) REVERT: D 282 PHE cc_start: 0.8155 (t80) cc_final: 0.7914 (t80) REVERT: D 310 MET cc_start: 0.8132 (mmm) cc_final: 0.7663 (mmm) REVERT: S 201 ASP cc_start: 0.7618 (t0) cc_final: 0.7415 (t0) REVERT: S 220 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7496 (mm-30) REVERT: E 27 TYR cc_start: 0.7600 (t80) cc_final: 0.7238 (t80) outliers start: 38 outliers final: 35 residues processed: 254 average time/residue: 0.2327 time to fit residues: 80.0667 Evaluate side-chains 273 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 267 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 82 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL 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 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 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 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 86 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111167 restraints weight = 13918.212| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.77 r_work: 0.3301 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1933 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= 0.141 Angle : 0.564 6.960 12898 Z= 0.294 Chirality : 0.043 0.176 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.064 25.683 1280 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.10 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1164 helix: 2.51 (0.26), residues: 416 sheet: 0.56 (0.32), residues: 274 loop : -1.64 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.001 PHE D 286 TYR 0.013 0.001 TYR E 20 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 417) hydrogen bonds : angle 4.03801 ( 1200) SS BOND : bond 0.00909 ( 1) SS BOND : angle 1.30166 ( 2) covalent geometry : bond 0.00318 ( 9525) covalent geometry : angle 0.56411 (12896) *********************** 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 289 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8179 (mppt) cc_final: 0.7832 (mppt) REVERT: A 241 MET cc_start: 0.6953 (ptp) cc_final: 0.6639 (ptp) REVERT: A 254 ILE cc_start: 0.8165 (tp) cc_final: 0.7897 (tp) REVERT: A 318 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7780 (ttmm) REVERT: B 237 ASN cc_start: 0.8099 (t0) cc_final: 0.7752 (t0) REVERT: B 246 ASP cc_start: 0.8232 (t0) cc_final: 0.8018 (t0) REVERT: B 247 ASP cc_start: 0.7467 (t0) cc_final: 0.7121 (t0) REVERT: B 254 ASP cc_start: 0.7366 (p0) cc_final: 0.6978 (p0) REVERT: B 275 SER cc_start: 0.8511 (m) cc_final: 0.8210 (m) REVERT: B 325 MET cc_start: 0.8257 (mmt) cc_final: 0.7983 (tpp) REVERT: D 282 PHE cc_start: 0.8141 (t80) cc_final: 0.7888 (t80) REVERT: D 310 MET cc_start: 0.8119 (mmm) cc_final: 0.7664 (mmm) REVERT: S 118 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7875 (t) REVERT: S 220 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7510 (mm-30) REVERT: E 27 TYR cc_start: 0.7610 (t80) cc_final: 0.7190 (t80) REVERT: E 31 ILE cc_start: 0.8297 (tt) cc_final: 0.7932 (tt) outliers start: 42 outliers final: 36 residues processed: 258 average time/residue: 0.2234 time to fit residues: 78.1144 Evaluate side-chains 281 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 267 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 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL 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 290 ASP 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 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 Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111752 restraints weight = 13688.845| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.74 r_work: 0.3311 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1985 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 : 0.565 7.356 12898 Z= 0.293 Chirality : 0.042 0.168 1455 Planarity : 0.004 0.053 1635 Dihedral : 4.024 26.307 1280 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.81 % Allowed : 20.41 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1164 helix: 2.52 (0.26), residues: 416 sheet: 0.46 (0.32), residues: 278 loop : -1.59 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 332 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.001 PHE D 286 TYR 0.012 0.001 TYR E 20 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 417) hydrogen bonds : angle 3.94849 ( 1200) SS BOND : bond 0.00883 ( 1) SS BOND : angle 1.23056 ( 2) covalent geometry : bond 0.00294 ( 9525) covalent geometry : angle 0.56439 (12896) *********************** 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 286 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8158 (mppt) cc_final: 0.7767 (mppt) REVERT: A 241 MET cc_start: 0.6922 (ptp) cc_final: 0.6616 (ptp) REVERT: A 254 ILE cc_start: 0.8156 (tp) cc_final: 0.7892 (tp) REVERT: A 318 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7787 (ttmm) REVERT: B 237 ASN cc_start: 0.8003 (t0) cc_final: 0.7671 (t0) REVERT: B 246 ASP cc_start: 0.8203 (t0) cc_final: 0.7987 (t0) REVERT: B 247 ASP cc_start: 0.7440 (t0) cc_final: 0.7086 (t0) REVERT: B 254 ASP cc_start: 0.7388 (p0) cc_final: 0.6951 (p0) REVERT: B 275 SER cc_start: 0.8491 (m) cc_final: 0.8196 (m) REVERT: B 325 MET cc_start: 0.8244 (mmt) cc_final: 0.7977 (tpp) REVERT: D 282 PHE cc_start: 0.8102 (t80) cc_final: 0.7868 (t80) REVERT: D 310 MET cc_start: 0.8118 (mmm) cc_final: 0.7644 (mmm) REVERT: S 220 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7525 (mm-30) REVERT: E 27 TYR cc_start: 0.7581 (t80) cc_final: 0.7167 (t80) REVERT: E 31 ILE cc_start: 0.8283 (tt) cc_final: 0.7920 (tt) outliers start: 39 outliers final: 34 residues processed: 257 average time/residue: 0.2167 time to fit residues: 75.8367 Evaluate side-chains 281 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU 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 267 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 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL 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 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 308 THR 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 S residue 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 81 optimal weight: 0.0370 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114683 restraints weight = 13813.768| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.61 r_work: 0.3356 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9526 Z= 0.103 Angle : 0.534 7.697 12898 Z= 0.274 Chirality : 0.041 0.167 1455 Planarity : 0.004 0.053 1635 Dihedral : 3.796 27.021 1280 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.64 % Allowed : 21.68 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1164 helix: 2.54 (0.26), residues: 423 sheet: 0.47 (0.33), residues: 265 loop : -1.57 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 332 HIS 0.002 0.000 HIS A 189 PHE 0.015 0.001 PHE D 286 TYR 0.011 0.001 TYR E 20 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 417) hydrogen bonds : angle 3.79732 ( 1200) SS BOND : bond 0.00684 ( 1) SS BOND : angle 0.78995 ( 2) covalent geometry : bond 0.00224 ( 9525) covalent geometry : angle 0.53417 (12896) ********************** 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 281 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8153 (mppt) cc_final: 0.7825 (mppt) REVERT: A 241 MET cc_start: 0.6873 (ptp) cc_final: 0.6563 (ptp) REVERT: A 254 ILE cc_start: 0.8095 (tp) cc_final: 0.7844 (tp) REVERT: A 310 ASP cc_start: 0.7851 (t0) cc_final: 0.7611 (t0) REVERT: B 176 GLN cc_start: 0.8512 (mt0) cc_final: 0.8275 (mt0) REVERT: B 237 ASN cc_start: 0.7944 (t0) cc_final: 0.7629 (t0) REVERT: B 246 ASP cc_start: 0.8143 (t0) cc_final: 0.7923 (t0) REVERT: B 247 ASP cc_start: 0.7353 (t0) cc_final: 0.6999 (t0) REVERT: B 254 ASP cc_start: 0.7430 (p0) cc_final: 0.7076 (p0) REVERT: B 275 SER cc_start: 0.8534 (m) cc_final: 0.8246 (m) REVERT: B 325 MET cc_start: 0.8201 (mmt) cc_final: 0.7922 (tpp) REVERT: D 310 MET cc_start: 0.8110 (mmm) cc_final: 0.7689 (mmp) REVERT: S 220 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7550 (mm-30) REVERT: E 27 TYR cc_start: 0.7537 (t80) cc_final: 0.7147 (t80) REVERT: E 31 ILE cc_start: 0.8212 (tt) cc_final: 0.7857 (tt) outliers start: 27 outliers final: 24 residues processed: 262 average time/residue: 0.2282 time to fit residues: 81.5167 Evaluate side-chains 275 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 267 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 187 VAL 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 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 308 THR 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 243 THR Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.0030 chunk 101 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN D 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114118 restraints weight = 13695.021| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.74 r_work: 0.3340 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9526 Z= 0.117 Angle : 0.561 10.290 12898 Z= 0.288 Chirality : 0.043 0.164 1455 Planarity : 0.004 0.052 1635 Dihedral : 3.838 26.979 1280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.83 % Allowed : 21.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1164 helix: 2.52 (0.26), residues: 423 sheet: 0.51 (0.32), residues: 283 loop : -1.55 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 332 HIS 0.002 0.001 HIS A 214 PHE 0.025 0.001 PHE D 282 TYR 0.011 0.001 TYR B 105 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 417) hydrogen bonds : angle 3.86058 ( 1200) SS BOND : bond 0.00779 ( 1) SS BOND : angle 0.96655 ( 2) covalent geometry : bond 0.00259 ( 9525) covalent geometry : angle 0.56074 (12896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4683.43 seconds wall clock time: 81 minutes 53.93 seconds (4913.93 seconds total)