Starting phenix.real_space_refine on Sat Aug 23 08:43:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqf_38575/08_2025/8xqf_38575.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.030 sd= 1.306 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2113 atoms to isotropic. 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 69 5.16 5 C 5873 2.51 5 N 1564 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9233 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1810 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2450 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 294} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 109 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 9} Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9233 At special positions: 0 Unit cell: (91.52, 122.72, 130, 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 69 16.00 O 1727 8.00 N 1564 7.00 C 5873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 232.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 39.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.545A pdb=" N ASN A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.648A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.682A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.069A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 55 Processing helix chain 'C' and resid 60 through 76 Processing helix chain 'R' and resid 24 through 56 Proline residue: R 32 - end of helix removed outlier: 4.601A pdb=" N THR R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.365A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.599A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 166 removed outlier: 4.103A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 166 " --> pdb=" O MET R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 166' Processing helix chain 'R' and resid 193 through 209 removed outlier: 4.243A pdb=" N GLY R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 removed outlier: 4.007A pdb=" N PHE R 223 " --> pdb=" O THR R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 261 removed outlier: 3.798A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR R 256 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 276 removed outlier: 3.553A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 Processing helix chain 'R' and resid 290 through 309 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 323 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.864A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.946A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.842A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.662A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.738A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.414A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.423A 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: 3.594A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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: 5.896A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.896A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.958A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2967 1.34 - 1.46: 2343 1.46 - 1.58: 4023 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9434 Sorted by residual: bond pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.17e+00 bond pdb=" C TRP R 279 " pdb=" N PRO R 280 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.34e-02 5.57e+03 4.99e+00 bond pdb=" C ASP S 74 " pdb=" N PRO S 75 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.30e-02 5.92e+03 2.71e+00 bond pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 1.233 1.247 -0.014 1.16e-02 7.43e+03 1.55e+00 bond pdb=" CB PRO R 213 " pdb=" CG PRO R 213 " ideal model delta sigma weight residual 1.492 1.430 0.062 5.00e-02 4.00e+02 1.53e+00 ... (remaining 9429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 12664 2.84 - 5.67: 99 5.67 - 8.51: 14 8.51 - 11.35: 5 11.35 - 14.18: 1 Bond angle restraints: 12783 Sorted by residual: angle pdb=" CA CYS R 181 " pdb=" CB CYS R 181 " pdb=" SG CYS R 181 " ideal model delta sigma weight residual 114.40 128.58 -14.18 2.30e+00 1.89e-01 3.80e+01 angle pdb=" CB MET R 162 " pdb=" CG MET R 162 " pdb=" SD MET R 162 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB MET R 288 " pdb=" CG MET R 288 " pdb=" SD MET R 288 " ideal model delta sigma weight residual 112.70 122.53 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA PRO S 75 " pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 121.34 117.84 3.50 1.14e+00 7.69e-01 9.45e+00 angle pdb=" C GLN R 180 " pdb=" N CYS R 181 " pdb=" CA CYS R 181 " ideal model delta sigma weight residual 122.87 118.49 4.38 1.44e+00 4.82e-01 9.25e+00 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4749 16.73 - 33.46: 606 33.46 - 50.19: 179 50.19 - 66.92: 50 66.92 - 83.65: 6 Dihedral angle restraints: 5590 sinusoidal: 2172 harmonic: 3418 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 176.65 -83.65 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 154.44 -61.44 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA PHE R 210 " pdb=" C PHE R 210 " pdb=" N VAL R 211 " pdb=" CA VAL R 211 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1184 0.054 - 0.108: 225 0.108 - 0.162: 27 0.162 - 0.216: 2 0.216 - 0.270: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CG LEU R 259 " pdb=" CB LEU R 259 " pdb=" CD1 LEU R 259 " pdb=" CD2 LEU R 259 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA CYS R 181 " pdb=" N CYS R 181 " pdb=" C CYS R 181 " pdb=" CB CYS R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO R 280 " pdb=" N PRO R 280 " pdb=" C PRO R 280 " pdb=" CB PRO R 280 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1437 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP S 73 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C ASP S 73 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP S 73 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP S 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 108 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C LEU R 108 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU R 108 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 109 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 236 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.029 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 242 2.68 - 3.24: 9161 3.24 - 3.79: 15306 3.79 - 4.35: 20014 4.35 - 4.90: 32811 Nonbonded interactions: 77534 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.129 3.040 nonbonded pdb=" ND2 ASN B 237 " pdb=" OD1 ASN B 239 " model vdw 2.165 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.180 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.210 3.120 ... (remaining 77529 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9437 Z= 0.167 Angle : 0.680 14.184 12789 Z= 0.350 Chirality : 0.043 0.270 1440 Planarity : 0.004 0.052 1617 Dihedral : 16.727 81.208 3377 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 30.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.26), residues: 1161 helix: 1.26 (0.27), residues: 403 sheet: -0.88 (0.33), residues: 263 loop : -1.57 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.025 0.002 TYR R 88 PHE 0.018 0.002 PHE A 250 TRP 0.012 0.001 TRP R 85 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9434) covalent geometry : angle 0.67706 (12783) SS BOND : bond 0.00859 ( 3) SS BOND : angle 2.90314 ( 6) hydrogen bonds : bond 0.17175 ( 433) hydrogen bonds : angle 6.83035 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6719 (ttmm) cc_final: 0.6474 (ttmm) REVERT: C 44 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: R 50 LEU cc_start: 0.6044 (mp) cc_final: 0.5772 (mm) REVERT: R 154 TRP cc_start: 0.6868 (m100) cc_final: 0.4924 (m100) REVERT: S 83 MET cc_start: 0.6604 (mpp) cc_final: 0.6311 (mtm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1016 time to fit residues: 34.7769 Evaluate side-chains 258 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN C 55 ASN R 46 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.180792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158638 restraints weight = 14305.476| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.38 r_work: 0.3908 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9437 Z= 0.136 Angle : 0.619 12.930 12789 Z= 0.320 Chirality : 0.042 0.189 1440 Planarity : 0.004 0.052 1617 Dihedral : 4.846 37.451 1280 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 25.15 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.26), residues: 1161 helix: 1.38 (0.26), residues: 406 sheet: -0.96 (0.31), residues: 276 loop : -1.55 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 2 TYR 0.016 0.001 TYR R 88 PHE 0.018 0.002 PHE R 283 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9434) covalent geometry : angle 0.61772 (12783) SS BOND : bond 0.00638 ( 3) SS BOND : angle 2.21335 ( 6) hydrogen bonds : bond 0.04411 ( 433) hydrogen bonds : angle 5.21575 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6325 (tm-30) REVERT: A 243 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6846 (mmm) REVERT: A 308 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6251 (mt-10) REVERT: A 337 ASP cc_start: 0.6878 (m-30) cc_final: 0.6578 (m-30) REVERT: B 36 ASN cc_start: 0.7754 (m-40) cc_final: 0.7501 (m-40) REVERT: B 45 MET cc_start: 0.8045 (mtm) cc_final: 0.7778 (mtt) REVERT: B 123 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (mm) REVERT: B 156 GLN cc_start: 0.7939 (mt0) cc_final: 0.7730 (mt0) REVERT: C 44 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7473 (tpp-160) REVERT: R 65 ASP cc_start: 0.5973 (m-30) cc_final: 0.5658 (m-30) REVERT: R 108 LEU cc_start: 0.5641 (mt) cc_final: 0.5325 (mp) REVERT: R 182 TYR cc_start: 0.7501 (p90) cc_final: 0.6986 (p90) REVERT: S 83 MET cc_start: 0.6502 (mpp) cc_final: 0.6145 (mtm) REVERT: S 93 MET cc_start: 0.7551 (tpp) cc_final: 0.7142 (tpp) REVERT: S 99 SER cc_start: 0.7796 (m) cc_final: 0.7524 (p) outliers start: 51 outliers final: 28 residues processed: 284 average time/residue: 0.1010 time to fit residues: 38.1989 Evaluate side-chains 281 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 67 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.157496 restraints weight = 14276.372| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.37 r_work: 0.3892 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9437 Z= 0.155 Angle : 0.634 13.468 12789 Z= 0.323 Chirality : 0.042 0.171 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.868 32.106 1280 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 5.17 % Allowed : 25.55 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1161 helix: 1.30 (0.26), residues: 408 sheet: -0.97 (0.31), residues: 273 loop : -1.54 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.017 0.002 TYR S 95 PHE 0.016 0.002 PHE R 257 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9434) covalent geometry : angle 0.63271 (12783) SS BOND : bond 0.00648 ( 3) SS BOND : angle 1.96126 ( 6) hydrogen bonds : bond 0.04196 ( 433) hydrogen bonds : angle 5.05372 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6258 (tm-30) REVERT: A 308 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6200 (mt-10) REVERT: A 337 ASP cc_start: 0.6900 (m-30) cc_final: 0.6586 (m-30) REVERT: B 36 ASN cc_start: 0.7756 (m-40) cc_final: 0.7511 (m-40) REVERT: B 45 MET cc_start: 0.8171 (mtm) cc_final: 0.7967 (mtt) REVERT: B 123 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8332 (mm) REVERT: B 156 GLN cc_start: 0.7937 (mt0) cc_final: 0.7723 (mt0) REVERT: B 186 ASP cc_start: 0.7091 (m-30) cc_final: 0.6882 (m-30) REVERT: C 44 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7473 (tpp-160) REVERT: C 61 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7705 (t) REVERT: R 65 ASP cc_start: 0.5987 (m-30) cc_final: 0.5693 (m-30) REVERT: R 113 MET cc_start: 0.6778 (ttp) cc_final: 0.6481 (ttp) REVERT: R 124 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7572 (t) REVERT: R 154 TRP cc_start: 0.7029 (m100) cc_final: 0.5077 (m100) REVERT: R 253 LEU cc_start: 0.7705 (mt) cc_final: 0.7492 (mm) REVERT: S 63 THR cc_start: 0.7986 (p) cc_final: 0.7650 (t) REVERT: S 83 MET cc_start: 0.6387 (mpp) cc_final: 0.5991 (mtm) REVERT: S 99 SER cc_start: 0.7788 (m) cc_final: 0.7505 (p) outliers start: 52 outliers final: 38 residues processed: 286 average time/residue: 0.1052 time to fit residues: 39.8652 Evaluate side-chains 289 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 239 ASN B 259 GLN B 340 ASN C 90 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.179167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156643 restraints weight = 14441.623| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.39 r_work: 0.3876 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9437 Z= 0.167 Angle : 0.642 13.791 12789 Z= 0.325 Chirality : 0.043 0.180 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.914 33.571 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 5.67 % Allowed : 25.75 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.26), residues: 1161 helix: 1.24 (0.26), residues: 407 sheet: -1.01 (0.31), residues: 274 loop : -1.50 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 168 TYR 0.017 0.002 TYR R 88 PHE 0.016 0.002 PHE R 257 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9434) covalent geometry : angle 0.64179 (12783) SS BOND : bond 0.00742 ( 3) SS BOND : angle 1.07222 ( 6) hydrogen bonds : bond 0.04125 ( 433) hydrogen bonds : angle 5.04948 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7877 (mtpp) REVERT: A 25 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6248 (tm-30) REVERT: A 308 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6272 (mt-10) REVERT: B 36 ASN cc_start: 0.7765 (m-40) cc_final: 0.7526 (m-40) REVERT: B 68 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7406 (ttt180) REVERT: B 123 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8270 (mm) REVERT: B 156 GLN cc_start: 0.7948 (mt0) cc_final: 0.7740 (mt0) REVERT: B 186 ASP cc_start: 0.7139 (m-30) cc_final: 0.6920 (m-30) REVERT: C 44 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7502 (tpp-160) REVERT: R 35 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: R 65 ASP cc_start: 0.6076 (m-30) cc_final: 0.5772 (m-30) REVERT: R 113 MET cc_start: 0.6808 (ttp) cc_final: 0.6510 (ttp) REVERT: R 120 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7628 (mp) REVERT: R 124 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7592 (t) REVERT: R 154 TRP cc_start: 0.7046 (m100) cc_final: 0.5116 (m100) REVERT: R 165 MET cc_start: 0.4841 (tmm) cc_final: 0.3817 (mpp) REVERT: R 253 LEU cc_start: 0.7756 (mt) cc_final: 0.7497 (mm) REVERT: S 63 THR cc_start: 0.8013 (p) cc_final: 0.7681 (t) REVERT: S 83 MET cc_start: 0.6504 (mpp) cc_final: 0.6151 (mtm) REVERT: S 95 TYR cc_start: 0.8273 (m-10) cc_final: 0.8044 (m-10) REVERT: S 99 SER cc_start: 0.7774 (m) cc_final: 0.7505 (p) outliers start: 57 outliers final: 41 residues processed: 280 average time/residue: 0.0973 time to fit residues: 36.3074 Evaluate side-chains 290 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 31 optimal weight: 0.0970 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.181431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159302 restraints weight = 14526.590| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.40 r_work: 0.3905 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9437 Z= 0.117 Angle : 0.618 13.864 12789 Z= 0.307 Chirality : 0.041 0.165 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.724 34.898 1280 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 4.47 % Allowed : 26.74 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.26), residues: 1161 helix: 1.37 (0.26), residues: 408 sheet: -0.98 (0.31), residues: 275 loop : -1.46 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.021 0.001 TYR R 88 PHE 0.019 0.002 PHE A 250 TRP 0.017 0.001 TRP B 211 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9434) covalent geometry : angle 0.61629 (12783) SS BOND : bond 0.00729 ( 3) SS BOND : angle 2.18968 ( 6) hydrogen bonds : bond 0.03694 ( 433) hydrogen bonds : angle 4.85094 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6298 (tm-30) REVERT: A 308 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6176 (mt-10) REVERT: B 36 ASN cc_start: 0.7728 (m-40) cc_final: 0.7494 (m-40) REVERT: B 123 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 129 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7107 (mmt180) REVERT: B 186 ASP cc_start: 0.7147 (m-30) cc_final: 0.6929 (m-30) REVERT: C 61 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7712 (t) REVERT: R 35 TYR cc_start: 0.6718 (m-10) cc_final: 0.6000 (m-80) REVERT: R 65 ASP cc_start: 0.6079 (m-30) cc_final: 0.5840 (m-30) REVERT: R 113 MET cc_start: 0.6810 (ttp) cc_final: 0.6505 (ttp) REVERT: R 120 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7576 (mp) REVERT: R 124 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7589 (t) REVERT: R 165 MET cc_start: 0.4196 (tmm) cc_final: 0.3603 (mmm) REVERT: S 63 THR cc_start: 0.8006 (p) cc_final: 0.7683 (t) REVERT: S 99 SER cc_start: 0.7747 (m) cc_final: 0.7508 (p) outliers start: 45 outliers final: 29 residues processed: 271 average time/residue: 0.0998 time to fit residues: 35.8184 Evaluate side-chains 277 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 156 GLN B 183 HIS B 220 GLN B 259 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157588 restraints weight = 14451.697| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.41 r_work: 0.3889 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9437 Z= 0.143 Angle : 0.648 16.863 12789 Z= 0.318 Chirality : 0.043 0.314 1440 Planarity : 0.004 0.055 1617 Dihedral : 4.757 34.373 1280 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 5.47 % Allowed : 27.83 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.26), residues: 1161 helix: 1.38 (0.26), residues: 404 sheet: -1.01 (0.31), residues: 282 loop : -1.43 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.025 0.002 TYR S 95 PHE 0.021 0.002 PHE A 250 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9434) covalent geometry : angle 0.64656 (12783) SS BOND : bond 0.00728 ( 3) SS BOND : angle 1.98118 ( 6) hydrogen bonds : bond 0.03799 ( 433) hydrogen bonds : angle 4.90200 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 308 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6244 (mt-10) REVERT: B 36 ASN cc_start: 0.7722 (m-40) cc_final: 0.7461 (m-40) REVERT: B 68 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7484 (ttt180) REVERT: B 129 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7128 (mmt180) REVERT: B 186 ASP cc_start: 0.7110 (m-30) cc_final: 0.6848 (m-30) REVERT: R 35 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5893 (m-80) REVERT: R 65 ASP cc_start: 0.6192 (m-30) cc_final: 0.5937 (m-30) REVERT: R 113 MET cc_start: 0.6735 (ttp) cc_final: 0.6500 (ttp) REVERT: R 120 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7535 (mp) REVERT: R 124 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7565 (t) REVERT: R 165 MET cc_start: 0.4506 (tmm) cc_final: 0.3699 (mmm) REVERT: S 63 THR cc_start: 0.8018 (p) cc_final: 0.7699 (t) REVERT: S 99 SER cc_start: 0.7815 (m) cc_final: 0.7564 (p) outliers start: 55 outliers final: 40 residues processed: 274 average time/residue: 0.0957 time to fit residues: 34.6971 Evaluate side-chains 287 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156847 restraints weight = 14506.802| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.41 r_work: 0.3882 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9437 Z= 0.155 Angle : 0.661 17.667 12789 Z= 0.323 Chirality : 0.043 0.307 1440 Planarity : 0.004 0.058 1617 Dihedral : 4.839 35.304 1280 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 5.67 % Allowed : 27.63 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1161 helix: 1.27 (0.26), residues: 411 sheet: -0.97 (0.30), residues: 282 loop : -1.41 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.028 0.002 TYR S 95 PHE 0.024 0.002 PHE A 250 TRP 0.012 0.001 TRP R 85 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9434) covalent geometry : angle 0.66033 (12783) SS BOND : bond 0.00738 ( 3) SS BOND : angle 1.72324 ( 6) hydrogen bonds : bond 0.03864 ( 433) hydrogen bonds : angle 4.92657 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6296 (tm-30) REVERT: A 273 LEU cc_start: 0.7787 (mt) cc_final: 0.7567 (mt) REVERT: A 308 GLU cc_start: 0.6345 (mt-10) cc_final: 0.6081 (mt-10) REVERT: B 36 ASN cc_start: 0.7695 (m-40) cc_final: 0.7436 (m-40) REVERT: B 68 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7456 (ttt180) REVERT: B 129 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7119 (mmt180) REVERT: B 186 ASP cc_start: 0.7068 (m-30) cc_final: 0.6756 (m-30) REVERT: R 35 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.5935 (m-80) REVERT: R 113 MET cc_start: 0.6792 (ttp) cc_final: 0.6506 (ttp) REVERT: R 120 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7599 (mp) REVERT: R 124 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7567 (t) REVERT: R 154 TRP cc_start: 0.7019 (m100) cc_final: 0.5094 (m100) REVERT: S 63 THR cc_start: 0.8062 (p) cc_final: 0.7750 (t) REVERT: S 99 SER cc_start: 0.7821 (m) cc_final: 0.7589 (p) outliers start: 57 outliers final: 44 residues processed: 277 average time/residue: 0.1144 time to fit residues: 41.7842 Evaluate side-chains 290 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 90 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157522 restraints weight = 14321.661| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.40 r_work: 0.3887 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9437 Z= 0.145 Angle : 0.657 17.948 12789 Z= 0.321 Chirality : 0.043 0.302 1440 Planarity : 0.004 0.071 1617 Dihedral : 4.808 35.838 1280 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 6.16 % Allowed : 27.04 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1161 helix: 1.25 (0.26), residues: 407 sheet: -0.94 (0.31), residues: 282 loop : -1.42 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.030 0.002 TYR R 309 PHE 0.022 0.002 PHE A 250 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9434) covalent geometry : angle 0.65655 (12783) SS BOND : bond 0.00603 ( 3) SS BOND : angle 1.61880 ( 6) hydrogen bonds : bond 0.03768 ( 433) hydrogen bonds : angle 4.92207 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6259 (tm-30) REVERT: A 270 LYS cc_start: 0.7622 (mttp) cc_final: 0.7352 (mttp) REVERT: A 273 LEU cc_start: 0.7791 (mt) cc_final: 0.7574 (mt) REVERT: A 308 GLU cc_start: 0.6334 (mt-10) cc_final: 0.6090 (mt-10) REVERT: B 36 ASN cc_start: 0.7683 (m-40) cc_final: 0.7427 (m-40) REVERT: B 68 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: B 129 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7113 (mmt180) REVERT: B 186 ASP cc_start: 0.7087 (m-30) cc_final: 0.6759 (m-30) REVERT: B 294 CYS cc_start: 0.7546 (t) cc_final: 0.7344 (t) REVERT: C 61 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7719 (t) REVERT: R 35 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: R 82 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6317 (mt) REVERT: R 113 MET cc_start: 0.6825 (ttp) cc_final: 0.6565 (ttp) REVERT: R 120 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7550 (mp) REVERT: R 124 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7590 (t) REVERT: S 63 THR cc_start: 0.8075 (p) cc_final: 0.7766 (t) outliers start: 62 outliers final: 45 residues processed: 278 average time/residue: 0.1171 time to fit residues: 43.3240 Evaluate side-chains 291 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 0.0070 chunk 42 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157551 restraints weight = 14338.782| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.40 r_work: 0.3887 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9437 Z= 0.141 Angle : 0.674 18.302 12789 Z= 0.328 Chirality : 0.043 0.305 1440 Planarity : 0.004 0.054 1617 Dihedral : 4.842 36.472 1280 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 5.86 % Allowed : 27.93 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.25), residues: 1161 helix: 1.22 (0.26), residues: 407 sheet: -0.89 (0.31), residues: 271 loop : -1.46 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.030 0.001 TYR S 95 PHE 0.023 0.002 PHE A 250 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9434) covalent geometry : angle 0.67393 (12783) SS BOND : bond 0.00600 ( 3) SS BOND : angle 1.44243 ( 6) hydrogen bonds : bond 0.03729 ( 433) hydrogen bonds : angle 4.86981 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6257 (tm-30) REVERT: A 270 LYS cc_start: 0.7613 (mttp) cc_final: 0.7352 (mttp) REVERT: A 273 LEU cc_start: 0.7821 (mt) cc_final: 0.7602 (mt) REVERT: A 308 GLU cc_start: 0.6335 (mt-10) cc_final: 0.6086 (mt-10) REVERT: B 36 ASN cc_start: 0.7684 (m-40) cc_final: 0.7359 (m-40) REVERT: B 68 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7479 (ttt180) REVERT: B 129 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7135 (mmt180) REVERT: B 186 ASP cc_start: 0.7072 (m-30) cc_final: 0.6722 (m-30) REVERT: B 195 ASP cc_start: 0.7443 (p0) cc_final: 0.7186 (p0) REVERT: B 197 ARG cc_start: 0.6707 (ptt180) cc_final: 0.6181 (ptt-90) REVERT: B 294 CYS cc_start: 0.7577 (t) cc_final: 0.7359 (t) REVERT: R 35 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: R 82 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6671 (tp) REVERT: R 113 MET cc_start: 0.6822 (ttp) cc_final: 0.6555 (ttp) REVERT: R 120 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7594 (mp) REVERT: R 124 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7591 (t) REVERT: R 308 LEU cc_start: 0.7423 (mm) cc_final: 0.7132 (pp) REVERT: S 63 THR cc_start: 0.8106 (p) cc_final: 0.7830 (t) outliers start: 59 outliers final: 45 residues processed: 276 average time/residue: 0.1190 time to fit residues: 43.7091 Evaluate side-chains 293 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN B 259 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157352 restraints weight = 14431.838| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.42 r_work: 0.3882 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9437 Z= 0.148 Angle : 0.680 18.770 12789 Z= 0.332 Chirality : 0.043 0.295 1440 Planarity : 0.004 0.055 1617 Dihedral : 4.839 36.853 1280 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 5.17 % Allowed : 28.53 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1161 helix: 1.18 (0.26), residues: 407 sheet: -0.84 (0.31), residues: 276 loop : -1.40 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 244 TYR 0.041 0.002 TYR S 95 PHE 0.024 0.002 PHE A 250 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9434) covalent geometry : angle 0.67968 (12783) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.49752 ( 6) hydrogen bonds : bond 0.03803 ( 433) hydrogen bonds : angle 4.91431 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6245 (tm-30) REVERT: A 270 LYS cc_start: 0.7606 (mttp) cc_final: 0.7334 (mttp) REVERT: A 273 LEU cc_start: 0.7826 (mt) cc_final: 0.7615 (mt) REVERT: A 308 GLU cc_start: 0.6360 (mt-10) cc_final: 0.6105 (mt-10) REVERT: B 36 ASN cc_start: 0.7706 (m-40) cc_final: 0.7381 (m-40) REVERT: B 68 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7462 (ttt180) REVERT: B 129 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7145 (mmt180) REVERT: B 186 ASP cc_start: 0.7074 (m-30) cc_final: 0.6721 (m-30) REVERT: B 195 ASP cc_start: 0.7548 (p0) cc_final: 0.7301 (p0) REVERT: B 197 ARG cc_start: 0.6761 (ptt180) cc_final: 0.6299 (ptt-90) REVERT: B 294 CYS cc_start: 0.7534 (t) cc_final: 0.7314 (t) REVERT: R 35 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: R 82 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6616 (tp) REVERT: R 113 MET cc_start: 0.6882 (ttp) cc_final: 0.6593 (ttp) REVERT: R 120 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7528 (mp) REVERT: R 124 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (t) REVERT: R 165 MET cc_start: 0.2853 (tpp) cc_final: 0.1943 (mtm) REVERT: R 182 TYR cc_start: 0.7379 (p90) cc_final: 0.7012 (p90) REVERT: R 308 LEU cc_start: 0.7411 (mm) cc_final: 0.7130 (pp) REVERT: S 63 THR cc_start: 0.8125 (p) cc_final: 0.7853 (t) outliers start: 52 outliers final: 44 residues processed: 269 average time/residue: 0.1191 time to fit residues: 42.6300 Evaluate side-chains 289 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158111 restraints weight = 14299.853| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.40 r_work: 0.3894 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9437 Z= 0.135 Angle : 0.671 18.590 12789 Z= 0.326 Chirality : 0.043 0.290 1440 Planarity : 0.004 0.054 1617 Dihedral : 4.810 37.167 1280 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 5.37 % Allowed : 28.93 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.26), residues: 1161 helix: 1.21 (0.26), residues: 406 sheet: -0.81 (0.31), residues: 287 loop : -1.38 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.035 0.002 TYR S 95 PHE 0.023 0.002 PHE A 250 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9434) covalent geometry : angle 0.67041 (12783) SS BOND : bond 0.00552 ( 3) SS BOND : angle 1.35772 ( 6) hydrogen bonds : bond 0.03718 ( 433) hydrogen bonds : angle 4.86263 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.35 seconds wall clock time: 42 minutes 36.43 seconds (2556.43 seconds total)