Starting phenix.real_space_refine on Fri Aug 22 16:49:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.map" model { file = "/net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gec_29965/08_2025/8gec_29965.cif" } resolution = 3.5 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= -0.001 sd= 0.029 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 26 5.16 5 C 3961 2.51 5 N 1081 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6125 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1622 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 12, 'ASN:plan1': 2, 'GLU:plan': 17, 'ASP:plan': 10, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2236 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 7, 'GLU:plan': 6, 'ASN:plan1': 7, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 305 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1947 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 8, 'ASP:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.29 Number of scatterers: 6125 At special positions: 0 Unit cell: (67.84, 97.52, 127.2, 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 26 16.00 O 1057 8.00 N 1081 7.00 C 3961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 0.53 Conformation dependent library (CDL) restraints added in 320.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 49.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.461A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.555A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.907A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.122A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.622A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.536A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.933A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.384A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 270 through 298 removed outlier: 4.127A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.206A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 322 removed outlier: 3.955A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.709A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 5.828A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.005A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.665A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.591A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.897A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.917A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.69 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: 2008 1.34 - 1.46: 1459 1.46 - 1.58: 2758 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 6259 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.481 -0.030 2.00e-02 2.50e+03 2.28e+00 ... (remaining 6254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 8531 1.99 - 3.98: 51 3.98 - 5.96: 6 5.96 - 7.95: 3 7.95 - 9.94: 1 Bond angle restraints: 8592 Sorted by residual: angle pdb=" C THR B 223 " pdb=" CA THR B 223 " pdb=" CB THR B 223 " ideal model delta sigma weight residual 116.63 110.50 6.13 1.16e+00 7.43e-01 2.79e+01 angle pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N GLY B 224 " ideal model delta sigma weight residual 119.63 117.22 2.41 8.10e-01 1.52e+00 8.89e+00 angle pdb=" CA LEU A 282 " pdb=" CB LEU A 282 " pdb=" CG LEU A 282 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.06e+00 angle pdb=" N PHE B 235 " pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 109.64 106.67 2.97 1.27e+00 6.20e-01 5.45e+00 angle pdb=" C THR B 243 " pdb=" N GLY B 244 " pdb=" CA GLY B 244 " ideal model delta sigma weight residual 122.36 120.26 2.10 9.70e-01 1.06e+00 4.71e+00 ... (remaining 8587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.57: 3093 12.57 - 25.13: 312 25.13 - 37.70: 108 37.70 - 50.26: 47 50.26 - 62.83: 13 Dihedral angle restraints: 3573 sinusoidal: 972 harmonic: 2601 Sorted by residual: dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N LEU B 69 " pdb=" CA LEU B 69 " ideal model delta harmonic sigma weight residual -180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sinusoidal sigma weight residual -180.00 -120.08 -59.92 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 293 " pdb=" CD LYS A 293 " pdb=" CE LYS A 293 " pdb=" NZ LYS A 293 " ideal model delta sinusoidal sigma weight residual 60.00 4.05 55.95 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 3570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 699 0.033 - 0.067: 242 0.067 - 0.100: 76 0.100 - 0.133: 21 0.133 - 0.167: 2 Chirality restraints: 1040 Sorted by residual: chirality pdb=" CA ARG B 52 " pdb=" N ARG B 52 " pdb=" C ARG B 52 " pdb=" CB ARG B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1037 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO G 49 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 194 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.016 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1341 2.78 - 3.31: 5831 3.31 - 3.84: 10167 3.84 - 4.37: 10628 4.37 - 4.90: 19785 Nonbonded interactions: 47752 Sorted by model distance: nonbonded pdb=" NE ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.356 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.376 3.120 ... (remaining 47747 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.003 0.051 6260 Z= 0.151 Angle : 0.474 9.938 8594 Z= 0.264 Chirality : 0.039 0.167 1040 Planarity : 0.003 0.040 1094 Dihedral : 13.971 62.827 1878 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.43 % Allowed : 21.38 % Favored : 78.19 % 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: 1.35 (0.29), residues: 871 helix: 2.62 (0.26), residues: 399 sheet: -0.36 (0.39), residues: 173 loop : -0.71 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.014 0.001 TYR A 311 PHE 0.009 0.001 PHE B 235 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6259) covalent geometry : angle 0.47419 ( 8592) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.43136 ( 2) hydrogen bonds : bond 0.14679 ( 380) hydrogen bonds : angle 5.77129 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.233 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.0602 time to fit residues: 6.3030 Evaluate side-chains 68 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113217 restraints weight = 10627.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116198 restraints weight = 6072.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118330 restraints weight = 4167.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119611 restraints weight = 3182.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.120753 restraints weight = 2648.584| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6260 Z= 0.135 Angle : 0.454 8.071 8594 Z= 0.250 Chirality : 0.039 0.138 1040 Planarity : 0.003 0.035 1094 Dihedral : 4.638 40.270 957 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.75 % Allowed : 18.79 % Favored : 76.46 % 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: 1.46 (0.29), residues: 871 helix: 2.69 (0.26), residues: 402 sheet: 0.03 (0.40), residues: 163 loop : -0.89 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.013 0.001 TYR R 199 PHE 0.013 0.001 PHE B 222 TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6259) covalent geometry : angle 0.45363 ( 8592) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.42604 ( 2) hydrogen bonds : bond 0.03863 ( 380) hydrogen bonds : angle 4.38160 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.282 Fit side-chains REVERT: B 54 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8059 (m-70) outliers start: 22 outliers final: 14 residues processed: 80 average time/residue: 0.0536 time to fit residues: 6.6667 Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113917 restraints weight = 10286.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116974 restraints weight = 5888.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119104 restraints weight = 4027.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120394 restraints weight = 3074.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121516 restraints weight = 2558.760| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6260 Z= 0.111 Angle : 0.424 6.325 8594 Z= 0.233 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.033 1094 Dihedral : 4.092 24.522 955 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.40 % Allowed : 19.65 % Favored : 74.95 % 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: 1.51 (0.29), residues: 871 helix: 2.72 (0.25), residues: 402 sheet: 0.03 (0.40), residues: 165 loop : -0.83 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.012 0.001 TYR R 199 PHE 0.011 0.001 PHE B 222 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6259) covalent geometry : angle 0.42440 ( 8592) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.35649 ( 2) hydrogen bonds : bond 0.03518 ( 380) hydrogen bonds : angle 4.08979 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.243 Fit side-chains REVERT: B 54 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8135 (m-70) REVERT: B 82 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8252 (t80) REVERT: R 82 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6343 (ttm) REVERT: R 113 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7554 (t0) outliers start: 25 outliers final: 10 residues processed: 87 average time/residue: 0.0543 time to fit residues: 7.1952 Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113610 restraints weight = 10077.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116723 restraints weight = 5658.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118913 restraints weight = 3841.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120211 restraints weight = 2913.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121376 restraints weight = 2420.565| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6260 Z= 0.103 Angle : 0.415 6.068 8594 Z= 0.228 Chirality : 0.039 0.136 1040 Planarity : 0.003 0.031 1094 Dihedral : 3.927 24.884 955 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.97 % Allowed : 19.65 % Favored : 75.38 % 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: 1.55 (0.29), residues: 871 helix: 2.77 (0.25), residues: 403 sheet: 0.03 (0.40), residues: 165 loop : -0.82 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.012 0.001 TYR R 199 PHE 0.009 0.001 PHE B 222 TRP 0.007 0.001 TRP R 99 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6259) covalent geometry : angle 0.41508 ( 8592) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.27320 ( 2) hydrogen bonds : bond 0.03330 ( 380) hydrogen bonds : angle 3.94026 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.264 Fit side-chains REVERT: A 237 CYS cc_start: 0.7837 (m) cc_final: 0.7616 (m) REVERT: B 45 MET cc_start: 0.8084 (mmt) cc_final: 0.7487 (mtp) REVERT: B 54 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: B 82 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: B 234 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8288 (t80) REVERT: R 82 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6330 (ttm) REVERT: R 113 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7583 (t0) outliers start: 23 outliers final: 14 residues processed: 85 average time/residue: 0.0488 time to fit residues: 6.4636 Evaluate side-chains 84 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114330 restraints weight = 10505.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117400 restraints weight = 5951.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119527 restraints weight = 4063.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120784 restraints weight = 3105.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121932 restraints weight = 2587.092| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6260 Z= 0.112 Angle : 0.419 6.386 8594 Z= 0.229 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.031 1094 Dihedral : 3.887 25.816 955 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.40 % Allowed : 19.87 % Favored : 74.73 % 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: 1.51 (0.29), residues: 871 helix: 2.71 (0.25), residues: 404 sheet: 0.03 (0.40), residues: 165 loop : -0.83 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.011 0.001 TYR R 199 PHE 0.009 0.001 PHE B 222 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6259) covalent geometry : angle 0.41886 ( 8592) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.28809 ( 2) hydrogen bonds : bond 0.03353 ( 380) hydrogen bonds : angle 3.90658 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.256 Fit side-chains REVERT: B 45 MET cc_start: 0.8112 (mmt) cc_final: 0.7580 (mtp) REVERT: B 54 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.8063 (m-70) REVERT: B 82 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: B 234 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8254 (t80) REVERT: B 286 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8126 (mt) REVERT: R 82 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6365 (ttm) REVERT: R 113 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7595 (t0) outliers start: 25 outliers final: 15 residues processed: 85 average time/residue: 0.0520 time to fit residues: 6.8864 Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113615 restraints weight = 10602.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116588 restraints weight = 6126.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118707 restraints weight = 4233.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120079 restraints weight = 3255.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121064 restraints weight = 2700.286| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6260 Z= 0.134 Angle : 0.445 8.419 8594 Z= 0.240 Chirality : 0.039 0.136 1040 Planarity : 0.003 0.030 1094 Dihedral : 3.934 26.669 955 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.91 % Allowed : 18.79 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.29), residues: 871 helix: 2.62 (0.25), residues: 404 sheet: -0.05 (0.40), residues: 168 loop : -0.82 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 175 TYR 0.014 0.001 TYR R 185 PHE 0.009 0.001 PHE B 235 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6259) covalent geometry : angle 0.44538 ( 8592) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.41305 ( 2) hydrogen bonds : bond 0.03503 ( 380) hydrogen bonds : angle 3.93635 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.251 Fit side-chains REVERT: A 372 ILE cc_start: 0.9171 (mm) cc_final: 0.8821 (mt) REVERT: B 54 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8113 (m-70) REVERT: B 82 TRP cc_start: 0.7968 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: B 234 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8341 (t80) REVERT: B 286 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8122 (mt) REVERT: R 82 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6376 (ttm) REVERT: R 113 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7640 (t0) outliers start: 32 outliers final: 19 residues processed: 90 average time/residue: 0.0523 time to fit residues: 7.2508 Evaluate side-chains 87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114673 restraints weight = 10362.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117755 restraints weight = 5909.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119926 restraints weight = 4039.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.121210 restraints weight = 3067.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122315 restraints weight = 2571.615| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6260 Z= 0.101 Angle : 0.433 7.813 8594 Z= 0.228 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.821 25.679 955 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.83 % Allowed : 19.65 % Favored : 74.51 % 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: 1.51 (0.29), residues: 871 helix: 2.69 (0.25), residues: 404 sheet: -0.05 (0.39), residues: 169 loop : -0.76 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.011 0.001 TYR R 199 PHE 0.008 0.001 PHE B 222 TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6259) covalent geometry : angle 0.43314 ( 8592) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.30123 ( 2) hydrogen bonds : bond 0.03265 ( 380) hydrogen bonds : angle 3.82262 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.251 Fit side-chains REVERT: B 54 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.8053 (m-70) REVERT: B 82 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: B 234 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8287 (t80) REVERT: B 286 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (mt) REVERT: R 82 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6349 (ttm) REVERT: R 113 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7586 (t0) outliers start: 27 outliers final: 16 residues processed: 86 average time/residue: 0.0503 time to fit residues: 6.6866 Evaluate side-chains 87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 16 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114189 restraints weight = 10480.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117293 restraints weight = 5953.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119414 restraints weight = 4052.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120862 restraints weight = 3102.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121723 restraints weight = 2546.202| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6260 Z= 0.109 Angle : 0.436 6.969 8594 Z= 0.233 Chirality : 0.039 0.135 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.817 26.205 955 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.62 % Allowed : 21.17 % Favored : 73.22 % 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: 1.51 (0.29), residues: 871 helix: 2.67 (0.25), residues: 405 sheet: -0.07 (0.39), residues: 169 loop : -0.74 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.012 0.001 TYR R 199 PHE 0.008 0.001 PHE B 222 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6259) covalent geometry : angle 0.43601 ( 8592) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.27856 ( 2) hydrogen bonds : bond 0.03290 ( 380) hydrogen bonds : angle 3.81848 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.239 Fit side-chains REVERT: A 372 ILE cc_start: 0.9148 (mm) cc_final: 0.8792 (mt) REVERT: B 45 MET cc_start: 0.7535 (mtt) cc_final: 0.7035 (mtp) REVERT: B 54 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.8063 (m-70) REVERT: B 82 TRP cc_start: 0.7827 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: B 234 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 286 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8105 (mt) REVERT: R 82 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6368 (ttm) REVERT: R 113 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7600 (t0) outliers start: 26 outliers final: 19 residues processed: 84 average time/residue: 0.0517 time to fit residues: 6.7402 Evaluate side-chains 91 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112955 restraints weight = 10537.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116031 restraints weight = 6056.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118189 restraints weight = 4147.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119607 restraints weight = 3167.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120472 restraints weight = 2619.001| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6260 Z= 0.130 Angle : 0.448 6.910 8594 Z= 0.239 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.029 1094 Dihedral : 3.885 26.816 955 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.05 % Allowed : 20.95 % Favored : 73.00 % 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: 1.47 (0.29), residues: 871 helix: 2.64 (0.25), residues: 405 sheet: 0.10 (0.40), residues: 162 loop : -0.85 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.012 0.001 TYR R 199 PHE 0.008 0.001 PHE B 235 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6259) covalent geometry : angle 0.44756 ( 8592) SS BOND : bond 0.00287 ( 1) SS BOND : angle 0.42130 ( 2) hydrogen bonds : bond 0.03438 ( 380) hydrogen bonds : angle 3.88873 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.183 Fit side-chains REVERT: A 372 ILE cc_start: 0.9166 (mm) cc_final: 0.8813 (mt) REVERT: B 45 MET cc_start: 0.7790 (mtt) cc_final: 0.7394 (mtt) REVERT: B 54 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8145 (m-70) REVERT: B 82 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: B 234 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8333 (t80) REVERT: B 286 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (mt) REVERT: R 82 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6324 (ttm) REVERT: R 113 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7642 (t0) outliers start: 28 outliers final: 20 residues processed: 87 average time/residue: 0.0514 time to fit residues: 6.8866 Evaluate side-chains 94 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.0040 chunk 20 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115084 restraints weight = 10344.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118158 restraints weight = 5886.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120267 restraints weight = 4040.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121753 restraints weight = 3088.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122617 restraints weight = 2531.521| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6260 Z= 0.093 Angle : 0.425 6.745 8594 Z= 0.228 Chirality : 0.039 0.132 1040 Planarity : 0.003 0.028 1094 Dihedral : 3.808 25.785 955 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.32 % Allowed : 22.46 % Favored : 73.22 % 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: 1.52 (0.29), residues: 871 helix: 2.71 (0.25), residues: 405 sheet: 0.00 (0.39), residues: 164 loop : -0.81 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.011 0.001 TYR R 199 PHE 0.008 0.001 PHE B 222 TRP 0.010 0.001 TRP B 339 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 6259) covalent geometry : angle 0.42488 ( 8592) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.26290 ( 2) hydrogen bonds : bond 0.03220 ( 380) hydrogen bonds : angle 3.82276 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.243 Fit side-chains REVERT: A 372 ILE cc_start: 0.9139 (mm) cc_final: 0.8779 (mt) REVERT: B 45 MET cc_start: 0.7681 (mtt) cc_final: 0.7289 (mtt) REVERT: B 82 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: B 234 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8236 (t80) REVERT: B 286 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8072 (mt) REVERT: R 82 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6343 (ttm) REVERT: R 113 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7572 (t0) outliers start: 20 outliers final: 12 residues processed: 85 average time/residue: 0.0528 time to fit residues: 6.9791 Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114206 restraints weight = 10378.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117264 restraints weight = 5947.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119362 restraints weight = 4088.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120722 restraints weight = 3135.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121804 restraints weight = 2601.174| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6260 Z= 0.114 Angle : 0.443 6.848 8594 Z= 0.238 Chirality : 0.039 0.134 1040 Planarity : 0.003 0.029 1094 Dihedral : 3.806 25.217 955 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.54 % Allowed : 22.03 % Favored : 73.43 % 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: 1.46 (0.29), residues: 871 helix: 2.68 (0.25), residues: 405 sheet: -0.01 (0.39), residues: 162 loop : -0.87 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.012 0.001 TYR R 199 PHE 0.007 0.001 PHE R 289 TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6259) covalent geometry : angle 0.44290 ( 8592) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.28245 ( 2) hydrogen bonds : bond 0.03290 ( 380) hydrogen bonds : angle 3.83693 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1121.33 seconds wall clock time: 20 minutes 7.34 seconds (1207.34 seconds total)