Starting phenix.real_space_refine on Wed Sep 17 14:24:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfz_60072/09_2025/8zfz_60072.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5763 2.51 5 N 1564 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9065 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2576 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1932 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2377 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 287} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9065 At special positions: 0 Unit cell: (89.28, 115.32, 130.2, 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 59 16.00 O 1679 8.00 N 1564 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 134 " distance=2.04 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 0.71 Conformation dependent library (CDL) restraints added in 320.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 37.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.761A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 258 through 262 removed outlier: 4.096A pdb=" N VAL D 262 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.531A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 232 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.904A pdb=" N ARG A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.320A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 removed outlier: 3.854A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 23 through 56 removed outlier: 4.039A pdb=" N GLN R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 29 - end of helix removed outlier: 3.787A pdb=" N ILE R 33 " --> pdb=" O PRO R 29 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Proline residue: R 41 - end of helix Processing helix chain 'R' and resid 59 through 78 removed outlier: 3.991A pdb=" N LEU R 67 " --> pdb=" O TYR R 63 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 86 removed outlier: 4.117A pdb=" N ASP R 83 " --> pdb=" O PRO R 79 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 128 removed outlier: 4.521A pdb=" N PHE R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE R 109 " --> pdb=" O PHE R 105 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR R 110 " --> pdb=" O TYR R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 157 Processing helix chain 'R' and resid 159 through 164 removed outlier: 3.664A pdb=" N HIS R 163 " --> pdb=" O ALA R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 219 removed outlier: 5.731A pdb=" N ALA R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 223 through 259 Proline residue: R 247 - end of helix Processing helix chain 'R' and resid 269 through 295 removed outlier: 3.926A pdb=" N GLY R 274 " --> pdb=" O GLU R 270 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 298 through 314 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.374A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.130A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.058A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 160 removed outlier: 7.040A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.543A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.356A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.814A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 45 Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.709A pdb=" N VAL D 135 " --> pdb=" O HIS D 73 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N MET D 72 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR D 88 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP D 74 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 197 Processing sheet with id=AB2, first strand: chain 'D' and resid 213 through 217 Processing sheet with id=AB3, first strand: chain 'A' and resid 203 through 207 removed outlier: 5.997A pdb=" N LEU A 36 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 237 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 273 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 239 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN A 275 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1164 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: 1.27 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2959 1.34 - 1.46: 2277 1.46 - 1.58: 3946 1.58 - 1.70: 1 1.70 - 1.82: 84 Bond restraints: 9267 Sorted by residual: bond pdb=" CB PRO A 344 " pdb=" CG PRO A 344 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.93e+00 bond pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CG PRO A 344 " pdb=" CD PRO A 344 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 2.03e+00 bond pdb=" CB ASP A 26 " pdb=" CG ASP A 26 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.43e+00 ... (remaining 9262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 12298 2.13 - 4.25: 222 4.25 - 6.38: 33 6.38 - 8.50: 9 8.50 - 10.63: 4 Bond angle restraints: 12566 Sorted by residual: angle pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" CD PRO A 344 " ideal model delta sigma weight residual 112.00 103.02 8.98 1.40e+00 5.10e-01 4.11e+01 angle pdb=" CA LYS G 46 " pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " ideal model delta sigma weight residual 114.10 122.03 -7.93 2.00e+00 2.50e-01 1.57e+01 angle pdb=" CB MET D 131 " pdb=" CG MET D 131 " pdb=" SD MET D 131 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " pdb=" CD LYS G 46 " ideal model delta sigma weight residual 111.30 119.40 -8.10 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA MET G 21 " pdb=" CB MET G 21 " pdb=" CG MET G 21 " ideal model delta sigma weight residual 114.10 120.86 -6.76 2.00e+00 2.50e-01 1.14e+01 ... (remaining 12561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4527 17.52 - 35.05: 702 35.05 - 52.57: 193 52.57 - 70.10: 37 70.10 - 87.62: 15 Dihedral angle restraints: 5474 sinusoidal: 2126 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS D 60 " pdb=" SG CYS D 60 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual 93.00 24.70 68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -139.56 53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CA TRP D 85 " pdb=" C TRP D 85 " pdb=" N VAL D 86 " pdb=" CA VAL D 86 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 5471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 991 0.042 - 0.084: 305 0.084 - 0.126: 95 0.126 - 0.168: 9 0.168 - 0.211: 3 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CG LEU R 131 " pdb=" CB LEU R 131 " pdb=" CD1 LEU R 131 " pdb=" CD2 LEU R 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU R 280 " pdb=" CB LEU R 280 " pdb=" CD1 LEU R 280 " pdb=" CD2 LEU R 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 1400 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 85 " -0.018 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP D 85 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP D 85 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP D 85 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 85 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 85 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 85 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 85 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 85 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 85 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 343 " 0.045 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 344 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 48 " -0.019 2.00e-02 2.50e+03 1.53e-02 5.85e+00 pdb=" CG TRP R 48 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP R 48 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 48 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 48 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 48 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 48 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 48 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 48 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 388 2.71 - 3.25: 9694 3.25 - 3.80: 15798 3.80 - 4.35: 19422 4.35 - 4.90: 31889 Nonbonded interactions: 77191 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.158 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 177 " model vdw 2.213 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.214 3.040 ... (remaining 77186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 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 0.141 9269 Z= 0.157 Angle : 0.721 10.628 12570 Z= 0.375 Chirality : 0.045 0.211 1403 Planarity : 0.005 0.064 1604 Dihedral : 18.502 87.623 3314 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 0.72 % Allowed : 40.62 % Favored : 58.67 % 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: -1.00 (0.25), residues: 1141 helix: 0.56 (0.27), residues: 386 sheet: -0.76 (0.35), residues: 237 loop : -1.54 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 217 TYR 0.014 0.002 TYR R 84 PHE 0.025 0.002 PHE R 177 TRP 0.057 0.003 TRP D 85 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9267) covalent geometry : angle 0.72044 (12566) SS BOND : bond 0.00592 ( 2) SS BOND : angle 1.45702 ( 4) hydrogen bonds : bond 0.12685 ( 410) hydrogen bonds : angle 6.62322 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7344 (tpt170) REVERT: B 207 SER cc_start: 0.7893 (m) cc_final: 0.7454 (p) REVERT: B 325 MET cc_start: 0.7810 (ttt) cc_final: 0.7318 (ttp) REVERT: D 125 ARG cc_start: 0.7072 (mtm180) cc_final: 0.6571 (ptt-90) REVERT: D 217 GLN cc_start: 0.6163 (tt0) cc_final: 0.5870 (tt0) REVERT: A 261 ASN cc_start: 0.7855 (m-40) cc_final: 0.7644 (m-40) REVERT: A 323 PHE cc_start: 0.7234 (t80) cc_final: 0.6893 (t80) REVERT: R 248 TYR cc_start: 0.7406 (t80) cc_final: 0.6837 (t80) outliers start: 7 outliers final: 4 residues processed: 178 average time/residue: 0.1056 time to fit residues: 25.6939 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.214165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.172765 restraints weight = 11007.108| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 3.06 r_work: 0.3805 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9269 Z= 0.231 Angle : 0.693 6.547 12570 Z= 0.364 Chirality : 0.046 0.157 1403 Planarity : 0.005 0.044 1604 Dihedral : 5.536 37.593 1266 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.89 % Favored : 91.94 % Rotamer: Outliers : 8.82 % Allowed : 31.28 % Favored : 59.90 % 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: -1.24 (0.25), residues: 1141 helix: 0.36 (0.27), residues: 384 sheet: -0.89 (0.34), residues: 235 loop : -1.66 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 137 TYR 0.020 0.002 TYR B 145 PHE 0.017 0.002 PHE R 177 TRP 0.031 0.003 TRP D 85 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9267) covalent geometry : angle 0.69295 (12566) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.14362 ( 4) hydrogen bonds : bond 0.04819 ( 410) hydrogen bonds : angle 5.74891 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 155 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 SER cc_start: 0.8212 (m) cc_final: 0.7921 (p) REVERT: B 219 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7764 (mtp-110) REVERT: B 234 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: D 72 MET cc_start: 0.6900 (mmp) cc_final: 0.6696 (mmp) REVERT: D 84 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6126 (pt0) REVERT: D 85 TRP cc_start: 0.6299 (t60) cc_final: 0.6072 (t60) REVERT: D 230 MET cc_start: 0.7899 (mmm) cc_final: 0.7590 (mmm) REVERT: A 46 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7607 (pttt) REVERT: A 261 ASN cc_start: 0.7679 (m-40) cc_final: 0.7427 (m110) REVERT: R 248 TYR cc_start: 0.7510 (t80) cc_final: 0.7035 (t80) outliers start: 86 outliers final: 55 residues processed: 223 average time/residue: 0.0816 time to fit residues: 25.7900 Evaluate side-chains 200 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** 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 = 0.4555 r_free = 0.4555 target = 0.220228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179253 restraints weight = 10894.261| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.90 r_work: 0.3901 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9269 Z= 0.133 Angle : 0.612 8.299 12570 Z= 0.317 Chirality : 0.043 0.152 1403 Planarity : 0.004 0.044 1604 Dihedral : 5.224 36.614 1264 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer: Outliers : 7.59 % Allowed : 30.67 % Favored : 61.74 % 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: -1.03 (0.25), residues: 1141 helix: 0.59 (0.27), residues: 381 sheet: -0.78 (0.35), residues: 223 loop : -1.58 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.014 0.001 TYR G 40 PHE 0.017 0.001 PHE R 177 TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9267) covalent geometry : angle 0.61166 (12566) SS BOND : bond 0.00545 ( 2) SS BOND : angle 1.31654 ( 4) hydrogen bonds : bond 0.04083 ( 410) hydrogen bonds : angle 5.36835 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.333 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: B 44 GLN cc_start: 0.7513 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 207 SER cc_start: 0.8127 (m) cc_final: 0.7889 (p) REVERT: B 234 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: D 72 MET cc_start: 0.6759 (mmp) cc_final: 0.6459 (mmp) REVERT: D 140 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: D 147 ASP cc_start: 0.7458 (m-30) cc_final: 0.7162 (m-30) REVERT: D 217 GLN cc_start: 0.7279 (tt0) cc_final: 0.6843 (tt0) REVERT: A 250 GLN cc_start: 0.7562 (tp40) cc_final: 0.7310 (tp-100) REVERT: A 340 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6620 (p90) REVERT: R 84 TYR cc_start: 0.7080 (t80) cc_final: 0.6700 (t80) REVERT: R 151 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.5546 (mt) REVERT: R 176 CYS cc_start: 0.5002 (OUTLIER) cc_final: 0.4780 (m) REVERT: R 248 TYR cc_start: 0.7491 (t80) cc_final: 0.7036 (t80) outliers start: 74 outliers final: 49 residues processed: 218 average time/residue: 0.0890 time to fit residues: 27.5420 Evaluate side-chains 204 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 40.0000 chunk 60 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172281 restraints weight = 11080.228| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.19 r_work: 0.3812 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9269 Z= 0.201 Angle : 0.658 7.486 12570 Z= 0.342 Chirality : 0.044 0.176 1403 Planarity : 0.004 0.044 1604 Dihedral : 5.361 34.780 1264 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.20 % Rotamer: Outliers : 10.15 % Allowed : 28.41 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.24), residues: 1141 helix: 0.56 (0.27), residues: 377 sheet: -0.96 (0.34), residues: 226 loop : -1.61 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.016 0.002 TYR R 209 PHE 0.020 0.002 PHE R 177 TRP 0.036 0.002 TRP B 297 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 9267) covalent geometry : angle 0.65790 (12566) SS BOND : bond 0.00435 ( 2) SS BOND : angle 1.16730 ( 4) hydrogen bonds : bond 0.04435 ( 410) hydrogen bonds : angle 5.46823 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 159 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.7883 (ptpt) cc_final: 0.7541 (ptpt) REVERT: B 75 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: B 207 SER cc_start: 0.8201 (m) cc_final: 0.7900 (p) REVERT: B 219 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7498 (mtp-110) REVERT: B 234 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: D 84 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5894 (pt0) REVERT: D 147 ASP cc_start: 0.7581 (m-30) cc_final: 0.7308 (m-30) REVERT: A 46 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7550 (pttt) REVERT: A 54 ARG cc_start: 0.4956 (ttm110) cc_final: 0.4710 (tmm160) REVERT: A 248 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7191 (mtp180) REVERT: R 151 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.5694 (mt) REVERT: R 176 CYS cc_start: 0.4976 (OUTLIER) cc_final: 0.4760 (m) REVERT: R 248 TYR cc_start: 0.7553 (t80) cc_final: 0.6962 (t80) outliers start: 99 outliers final: 71 residues processed: 233 average time/residue: 0.0938 time to fit residues: 30.5056 Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 149 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 12 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.218410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.178207 restraints weight = 11031.228| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.02 r_work: 0.3873 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9269 Z= 0.145 Angle : 0.622 6.950 12570 Z= 0.323 Chirality : 0.043 0.176 1403 Planarity : 0.004 0.043 1604 Dihedral : 5.208 32.696 1264 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.66 % Favored : 93.16 % Rotamer: Outliers : 9.23 % Allowed : 29.03 % Favored : 61.74 % 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: -1.05 (0.25), residues: 1141 helix: 0.67 (0.27), residues: 378 sheet: -0.88 (0.34), residues: 226 loop : -1.61 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.015 0.001 TYR G 40 PHE 0.018 0.001 PHE R 177 TRP 0.026 0.002 TRP B 297 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9267) covalent geometry : angle 0.62149 (12566) SS BOND : bond 0.00531 ( 2) SS BOND : angle 1.33244 ( 4) hydrogen bonds : bond 0.04037 ( 410) hydrogen bonds : angle 5.27058 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 167 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 SER cc_start: 0.8233 (m) cc_final: 0.7829 (p) REVERT: B 234 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: B 256 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7601 (tmt-80) REVERT: D 217 GLN cc_start: 0.7334 (tt0) cc_final: 0.6842 (tt0) REVERT: A 26 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6568 (t0) REVERT: A 46 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7598 (pttt) REVERT: A 340 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6649 (p90) REVERT: R 151 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.5592 (mt) REVERT: R 176 CYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4489 (m) REVERT: R 194 THR cc_start: 0.6300 (OUTLIER) cc_final: 0.5937 (m) REVERT: R 248 TYR cc_start: 0.7591 (t80) cc_final: 0.6893 (t80) outliers start: 90 outliers final: 63 residues processed: 233 average time/residue: 0.0893 time to fit residues: 29.4931 Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 0.0010 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 183 HIS D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.214261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.172836 restraints weight = 11094.694| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 3.33 r_work: 0.3798 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9269 Z= 0.200 Angle : 0.685 7.188 12570 Z= 0.354 Chirality : 0.045 0.210 1403 Planarity : 0.005 0.055 1604 Dihedral : 5.362 31.138 1264 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.33 % Favored : 91.50 % Rotamer: Outliers : 11.08 % Allowed : 27.59 % Favored : 61.33 % 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: -1.20 (0.25), residues: 1141 helix: 0.51 (0.27), residues: 379 sheet: -0.96 (0.34), residues: 224 loop : -1.67 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.017 0.002 TYR D 88 PHE 0.019 0.002 PHE R 177 TRP 0.037 0.002 TRP B 297 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9267) covalent geometry : angle 0.68441 (12566) SS BOND : bond 0.00425 ( 2) SS BOND : angle 1.22323 ( 4) hydrogen bonds : bond 0.04360 ( 410) hydrogen bonds : angle 5.44890 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 155 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7324 (ptpt) REVERT: B 75 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6700 (pt0) REVERT: B 207 SER cc_start: 0.8149 (m) cc_final: 0.7706 (p) REVERT: B 219 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7561 (mtp-110) REVERT: B 220 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: B 230 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (t0) REVERT: B 234 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: D 72 MET cc_start: 0.6855 (mmp) cc_final: 0.6561 (mmp) REVERT: D 84 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5913 (pt0) REVERT: D 217 GLN cc_start: 0.7329 (tt0) cc_final: 0.6935 (tt0) REVERT: A 46 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7636 (pttt) REVERT: A 291 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6354 (mm) REVERT: A 340 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6644 (p90) REVERT: R 48 TRP cc_start: 0.6217 (t-100) cc_final: 0.5803 (t-100) REVERT: R 151 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.5682 (mt) REVERT: R 176 CYS cc_start: 0.4798 (OUTLIER) cc_final: 0.4510 (m) REVERT: R 182 MET cc_start: 0.7323 (tpp) cc_final: 0.6962 (tpp) REVERT: R 194 THR cc_start: 0.6428 (OUTLIER) cc_final: 0.6034 (m) REVERT: R 248 TYR cc_start: 0.7622 (t80) cc_final: 0.6927 (t80) outliers start: 108 outliers final: 75 residues processed: 239 average time/residue: 0.0924 time to fit residues: 31.0252 Evaluate side-chains 236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.217624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177711 restraints weight = 11007.002| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.10 r_work: 0.3859 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9269 Z= 0.150 Angle : 0.658 10.949 12570 Z= 0.335 Chirality : 0.044 0.221 1403 Planarity : 0.004 0.042 1604 Dihedral : 5.241 29.997 1264 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 9.03 % Allowed : 29.33 % Favored : 61.64 % 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: -1.12 (0.25), residues: 1141 helix: 0.58 (0.27), residues: 380 sheet: -0.88 (0.34), residues: 224 loop : -1.64 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 54 TYR 0.015 0.001 TYR G 40 PHE 0.018 0.001 PHE R 177 TRP 0.026 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9267) covalent geometry : angle 0.65807 (12566) SS BOND : bond 0.00530 ( 2) SS BOND : angle 1.38233 ( 4) hydrogen bonds : bond 0.04040 ( 410) hydrogen bonds : angle 5.32959 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 153 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7003 (mp) REVERT: B 57 LYS cc_start: 0.7802 (ptpt) cc_final: 0.7386 (ptpt) REVERT: B 75 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6525 (pt0) REVERT: B 207 SER cc_start: 0.8173 (m) cc_final: 0.7714 (p) REVERT: B 219 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7431 (mtp-110) REVERT: B 234 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: D 84 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5875 (pt0) REVERT: D 147 ASP cc_start: 0.7546 (m-30) cc_final: 0.7235 (m-30) REVERT: D 217 GLN cc_start: 0.7321 (tt0) cc_final: 0.6961 (tt0) REVERT: D 269 GLN cc_start: 0.5264 (pm20) cc_final: 0.4817 (pm20) REVERT: A 46 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7648 (pttt) REVERT: A 261 ASN cc_start: 0.7267 (m110) cc_final: 0.7043 (m-40) REVERT: A 291 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6408 (mm) REVERT: A 340 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.6671 (p90) REVERT: R 48 TRP cc_start: 0.6285 (t-100) cc_final: 0.5909 (t-100) REVERT: R 151 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.5677 (mt) REVERT: R 176 CYS cc_start: 0.4879 (OUTLIER) cc_final: 0.4608 (m) REVERT: R 194 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5945 (m) REVERT: R 248 TYR cc_start: 0.7578 (t80) cc_final: 0.6867 (t80) REVERT: G 40 TYR cc_start: 0.8149 (t80) cc_final: 0.7863 (t80) outliers start: 88 outliers final: 70 residues processed: 222 average time/residue: 0.0871 time to fit residues: 27.4144 Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 148 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** 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 = 0.4531 r_free = 0.4531 target = 0.217579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175855 restraints weight = 10945.169| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.63 r_work: 0.3897 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9269 Z= 0.152 Angle : 0.666 12.031 12570 Z= 0.339 Chirality : 0.044 0.196 1403 Planarity : 0.004 0.042 1604 Dihedral : 5.203 29.251 1264 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 9.74 % Allowed : 29.23 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.08 (0.25), residues: 1141 helix: 0.65 (0.27), residues: 380 sheet: -0.86 (0.35), residues: 224 loop : -1.65 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.015 0.002 TYR G 40 PHE 0.017 0.001 PHE R 177 TRP 0.026 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9267) covalent geometry : angle 0.66563 (12566) SS BOND : bond 0.00495 ( 2) SS BOND : angle 1.32466 ( 4) hydrogen bonds : bond 0.04018 ( 410) hydrogen bonds : angle 5.28728 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 153 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.7685 (ptpt) cc_final: 0.7270 (ptpt) REVERT: B 75 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6455 (pt0) REVERT: B 207 SER cc_start: 0.8348 (m) cc_final: 0.7876 (p) REVERT: B 219 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7401 (mtp-110) REVERT: B 234 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: D 84 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5858 (pt0) REVERT: D 147 ASP cc_start: 0.7591 (m-30) cc_final: 0.7316 (m-30) REVERT: A 204 LYS cc_start: 0.5596 (tppt) cc_final: 0.5089 (ttpt) REVERT: A 250 GLN cc_start: 0.7637 (tp40) cc_final: 0.7377 (tp-100) REVERT: A 257 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6086 (tptp) REVERT: A 261 ASN cc_start: 0.7217 (m110) cc_final: 0.6934 (m-40) REVERT: A 291 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6560 (mm) REVERT: A 340 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6668 (p90) REVERT: R 45 MET cc_start: 0.6030 (ptp) cc_final: 0.5752 (ttm) REVERT: R 151 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.5674 (mt) REVERT: R 176 CYS cc_start: 0.4828 (OUTLIER) cc_final: 0.4535 (m) REVERT: R 194 THR cc_start: 0.6251 (OUTLIER) cc_final: 0.5898 (m) REVERT: R 248 TYR cc_start: 0.7540 (t80) cc_final: 0.6848 (t80) REVERT: G 40 TYR cc_start: 0.8137 (t80) cc_final: 0.7894 (t80) outliers start: 95 outliers final: 73 residues processed: 225 average time/residue: 0.0965 time to fit residues: 30.2734 Evaluate side-chains 231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 149 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 176 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.218462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176121 restraints weight = 11012.411| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.72 r_work: 0.3905 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9269 Z= 0.147 Angle : 0.672 11.574 12570 Z= 0.340 Chirality : 0.044 0.233 1403 Planarity : 0.004 0.042 1604 Dihedral : 5.134 29.986 1264 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.10 % Favored : 92.73 % Rotamer: Outliers : 8.72 % Allowed : 29.85 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.25), residues: 1141 helix: 0.66 (0.27), residues: 380 sheet: -0.95 (0.34), residues: 240 loop : -1.64 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.014 0.001 TYR G 40 PHE 0.017 0.001 PHE R 177 TRP 0.025 0.002 TRP B 63 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9267) covalent geometry : angle 0.67201 (12566) SS BOND : bond 0.00531 ( 2) SS BOND : angle 1.38131 ( 4) hydrogen bonds : bond 0.03940 ( 410) hydrogen bonds : angle 5.25063 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 155 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7341 (ptpt) REVERT: B 207 SER cc_start: 0.8368 (m) cc_final: 0.7891 (p) REVERT: B 219 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.7440 (mtp-110) REVERT: B 226 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 234 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: D 84 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5980 (pt0) REVERT: D 147 ASP cc_start: 0.7555 (m-30) cc_final: 0.7289 (m-30) REVERT: D 269 GLN cc_start: 0.5220 (pm20) cc_final: 0.4602 (pm20) REVERT: A 257 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6073 (tptp) REVERT: A 261 ASN cc_start: 0.7193 (m110) cc_final: 0.6881 (m-40) REVERT: A 291 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6553 (mm) REVERT: A 340 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6690 (p90) REVERT: R 45 MET cc_start: 0.6153 (ptp) cc_final: 0.5463 (tpt) REVERT: R 151 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.5670 (mt) REVERT: R 194 THR cc_start: 0.6192 (OUTLIER) cc_final: 0.5846 (m) REVERT: R 248 TYR cc_start: 0.7548 (t80) cc_final: 0.6817 (t80) REVERT: R 285 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8518 (mm) REVERT: G 40 TYR cc_start: 0.8069 (t80) cc_final: 0.7836 (t80) outliers start: 85 outliers final: 69 residues processed: 220 average time/residue: 0.0942 time to fit residues: 28.9990 Evaluate side-chains 227 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.218223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.175606 restraints weight = 10928.009| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.70 r_work: 0.3899 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9269 Z= 0.156 Angle : 0.687 11.786 12570 Z= 0.350 Chirality : 0.044 0.233 1403 Planarity : 0.004 0.042 1604 Dihedral : 5.192 30.745 1264 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 8.41 % Allowed : 30.56 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.11 (0.25), residues: 1141 helix: 0.65 (0.27), residues: 380 sheet: -1.04 (0.34), residues: 243 loop : -1.61 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.020 0.002 TYR A 301 PHE 0.015 0.001 PHE B 222 TRP 0.028 0.002 TRP B 297 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9267) covalent geometry : angle 0.68422 (12566) SS BOND : bond 0.00665 ( 2) SS BOND : angle 3.32473 ( 4) hydrogen bonds : bond 0.03978 ( 410) hydrogen bonds : angle 5.26914 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 146 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7290 (tpt170) cc_final: 0.6787 (ptt90) REVERT: B 207 SER cc_start: 0.8347 (m) cc_final: 0.7861 (p) REVERT: B 219 ARG cc_start: 0.7820 (mtp-110) cc_final: 0.7419 (mtp-110) REVERT: B 226 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 234 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: D 84 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5938 (pt0) REVERT: D 147 ASP cc_start: 0.7490 (m-30) cc_final: 0.7236 (m-30) REVERT: D 269 GLN cc_start: 0.5298 (pm20) cc_final: 0.4704 (pm20) REVERT: A 257 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6137 (tptp) REVERT: A 291 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6536 (mm) REVERT: A 340 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6688 (p90) REVERT: R 45 MET cc_start: 0.6028 (ptp) cc_final: 0.5392 (tpt) REVERT: R 151 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.5673 (mt) REVERT: R 194 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5837 (m) REVERT: R 248 TYR cc_start: 0.7538 (t80) cc_final: 0.6814 (t80) REVERT: R 285 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8530 (mm) REVERT: G 40 TYR cc_start: 0.8072 (t80) cc_final: 0.7847 (t80) outliers start: 82 outliers final: 70 residues processed: 211 average time/residue: 0.0985 time to fit residues: 28.9776 Evaluate side-chains 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 143 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 163 HIS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 277 HIS Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.220433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.179961 restraints weight = 10860.968| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.06 r_work: 0.3878 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9269 Z= 0.140 Angle : 0.681 12.916 12570 Z= 0.345 Chirality : 0.043 0.218 1403 Planarity : 0.004 0.042 1604 Dihedral : 5.122 32.549 1264 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.08 % Rotamer: Outliers : 7.79 % Allowed : 31.08 % Favored : 61.13 % 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: -1.03 (0.25), residues: 1141 helix: 0.77 (0.27), residues: 377 sheet: -1.00 (0.34), residues: 234 loop : -1.60 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.021 0.001 TYR R 84 PHE 0.038 0.001 PHE R 177 TRP 0.026 0.002 TRP B 63 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9267) covalent geometry : angle 0.67791 (12566) SS BOND : bond 0.00597 ( 2) SS BOND : angle 3.62110 ( 4) hydrogen bonds : bond 0.03802 ( 410) hydrogen bonds : angle 5.13854 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.99 seconds wall clock time: 41 minutes 53.51 seconds (2513.51 seconds total)