Starting phenix.real_space_refine on Fri Aug 22 17:41:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge8_29960/08_2025/8ge8_29960.map" } resolution = 3.4 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= 0.032 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 43 5.16 5 C 4226 2.51 5 N 1129 2.21 5 O 1159 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: 6557 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1719 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 3, 'GLU:plan': 16, 'ASP:plan': 13, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2400 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 11, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "G" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 340 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2082 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.80, per 1000 atoms: 0.27 Number of scatterers: 6557 At special positions: 0 Unit cell: (69.96, 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 43 16.00 O 1159 8.00 N 1129 7.00 C 4226 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: 0.55 Conformation dependent library (CDL) restraints added in 355.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 47.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.618A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.936A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.888A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.771A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.739A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.374A 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: 4.016A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.513A 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 236 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.716A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.696A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.860A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.244A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.612A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.221A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.307A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.126A 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: 6.641A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.003A 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: 6.824A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.285A 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: 3.794A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.962A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1155 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: 0.67 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2107 1.34 - 1.46: 1547 1.46 - 1.58: 2983 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 6696 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.62e+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 5.39e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.566 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.485 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9005 1.62 - 3.24: 128 3.24 - 4.87: 15 4.87 - 6.49: 5 6.49 - 8.11: 2 Bond angle restraints: 9155 Sorted by residual: angle pdb=" C ASP A 260 " pdb=" N ASN A 261 " pdb=" CA ASN A 261 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" CB MET R 40 " pdb=" CG MET R 40 " pdb=" SD MET R 40 " ideal model delta sigma weight residual 112.70 120.81 -8.11 3.00e+00 1.11e-01 7.31e+00 angle pdb=" N MET R 40 " pdb=" CA MET R 40 " pdb=" CB MET R 40 " ideal model delta sigma weight residual 110.16 113.10 -2.94 1.48e+00 4.57e-01 3.94e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.91 127.19 -3.28 1.66e+00 3.63e-01 3.90e+00 angle pdb=" C CYS R 285 " pdb=" N TRP R 286 " pdb=" CA TRP R 286 " ideal model delta sigma weight residual 122.79 119.45 3.34 1.78e+00 3.16e-01 3.52e+00 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 3570 15.93 - 31.86: 258 31.86 - 47.79: 41 47.79 - 63.71: 6 63.71 - 79.64: 3 Dihedral angle restraints: 3878 sinusoidal: 1244 harmonic: 2634 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS B 183 " pdb=" C HIS B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 734 0.032 - 0.064: 260 0.064 - 0.096: 72 0.096 - 0.128: 35 0.128 - 0.160: 3 Chirality restraints: 1104 Sorted by residual: 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 2.56 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-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 4.19e-01 ... (remaining 1101 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 312 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 313 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 326 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C ILE R 205 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 641 2.75 - 3.28: 6640 3.28 - 3.82: 11262 3.82 - 4.36: 12344 4.36 - 4.90: 22582 Nonbonded interactions: 53469 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.208 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.244 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.318 3.120 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.337 3.120 ... (remaining 53464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.270 Find NCS groups from input model: 0.030 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.054 6697 Z= 0.138 Angle : 0.513 8.112 9157 Z= 0.280 Chirality : 0.039 0.160 1104 Planarity : 0.003 0.039 1148 Dihedral : 11.591 79.643 2163 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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 (0.28), residues: 885 helix: 2.10 (0.26), residues: 404 sheet: 0.94 (0.41), residues: 162 loop : -1.03 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.011 0.001 TYR R 199 PHE 0.020 0.001 PHE B 234 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6696) covalent geometry : angle 0.51277 ( 9155) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.50118 ( 2) hydrogen bonds : bond 0.14314 ( 393) hydrogen bonds : angle 6.12611 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0657 time to fit residues: 8.4597 Evaluate side-chains 83 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 62 HIS B 88 ASN R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122511 restraints weight = 10142.705| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.05 r_work: 0.3442 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6697 Z= 0.175 Angle : 0.507 5.532 9157 Z= 0.281 Chirality : 0.041 0.145 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.721 75.658 972 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.66 % Allowed : 9.09 % Favored : 90.25 % 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 (0.27), residues: 885 helix: 2.07 (0.25), residues: 408 sheet: 0.59 (0.39), residues: 161 loop : -1.03 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.015 0.001 TYR R 199 PHE 0.017 0.001 PHE B 241 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6696) covalent geometry : angle 0.50689 ( 9155) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.49322 ( 2) hydrogen bonds : bond 0.04378 ( 393) hydrogen bonds : angle 4.71715 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.190 Fit side-chains REVERT: B 99 TRP cc_start: 0.8362 (m100) cc_final: 0.7911 (m100) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.0609 time to fit residues: 7.7709 Evaluate side-chains 85 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.141356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123111 restraints weight = 9996.471| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.03 r_work: 0.3453 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6697 Z= 0.127 Angle : 0.456 5.534 9157 Z= 0.252 Chirality : 0.040 0.143 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.566 73.093 972 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.65 % Allowed : 12.07 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.28), residues: 885 helix: 2.21 (0.25), residues: 408 sheet: 0.68 (0.40), residues: 156 loop : -0.79 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 49 TYR 0.012 0.001 TYR R 199 PHE 0.013 0.001 PHE B 241 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6696) covalent geometry : angle 0.45585 ( 9155) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.42209 ( 2) hydrogen bonds : bond 0.03856 ( 393) hydrogen bonds : angle 4.34574 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.183 Fit side-chains REVERT: A 233 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8498 (mtmm) REVERT: A 302 LEU cc_start: 0.8535 (mm) cc_final: 0.8314 (mm) REVERT: B 51 LEU cc_start: 0.9139 (mt) cc_final: 0.8859 (mt) REVERT: B 137 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8109 (mtp180) REVERT: B 188 MET cc_start: 0.8038 (mmm) cc_final: 0.7609 (mmm) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.0600 time to fit residues: 8.3700 Evaluate side-chains 92 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122939 restraints weight = 10154.457| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.04 r_work: 0.3453 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6697 Z= 0.126 Angle : 0.450 5.627 9157 Z= 0.247 Chirality : 0.040 0.164 1104 Planarity : 0.003 0.034 1148 Dihedral : 4.477 71.262 972 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.49 % Allowed : 15.37 % Favored : 83.14 % 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: 1.39 (0.28), residues: 885 helix: 2.25 (0.25), residues: 408 sheet: 0.78 (0.41), residues: 154 loop : -0.76 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.013 0.001 TYR R 199 PHE 0.013 0.001 PHE B 292 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6696) covalent geometry : angle 0.44949 ( 9155) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.53599 ( 2) hydrogen bonds : bond 0.03725 ( 393) hydrogen bonds : angle 4.19559 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.230 Fit side-chains REVERT: A 302 LEU cc_start: 0.8551 (mm) cc_final: 0.8327 (mm) REVERT: B 51 LEU cc_start: 0.9137 (mt) cc_final: 0.8848 (mt) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.0608 time to fit residues: 8.3371 Evaluate side-chains 88 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 0.0570 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN R 65 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122237 restraints weight = 10230.119| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.07 r_work: 0.3441 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6697 Z= 0.130 Angle : 0.451 5.729 9157 Z= 0.247 Chirality : 0.040 0.148 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.391 68.291 972 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.31 % Allowed : 15.70 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.28), residues: 885 helix: 2.29 (0.25), residues: 408 sheet: 0.65 (0.41), residues: 167 loop : -0.65 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.013 0.001 TYR R 199 PHE 0.016 0.001 PHE B 292 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6696) covalent geometry : angle 0.45124 ( 9155) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.56059 ( 2) hydrogen bonds : bond 0.03688 ( 393) hydrogen bonds : angle 4.11116 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.244 Fit side-chains REVERT: B 51 LEU cc_start: 0.9190 (mt) cc_final: 0.8875 (mt) REVERT: B 59 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: B 205 ASP cc_start: 0.8400 (p0) cc_final: 0.8128 (p0) REVERT: R 40 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7221 (mpp) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.0571 time to fit residues: 8.7682 Evaluate side-chains 94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 84 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123282 restraints weight = 10291.899| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.08 r_work: 0.3449 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6697 Z= 0.121 Angle : 0.458 5.554 9157 Z= 0.248 Chirality : 0.041 0.207 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.316 65.746 972 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.48 % Allowed : 17.36 % Favored : 80.17 % 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: 1.49 (0.29), residues: 885 helix: 2.30 (0.25), residues: 408 sheet: 0.68 (0.41), residues: 167 loop : -0.63 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.013 0.001 TYR R 199 PHE 0.015 0.001 PHE B 292 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6696) covalent geometry : angle 0.45756 ( 9155) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.54783 ( 2) hydrogen bonds : bond 0.03630 ( 393) hydrogen bonds : angle 4.09128 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.172 Fit side-chains REVERT: A 233 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8161 (mtmt) REVERT: B 51 LEU cc_start: 0.9201 (mt) cc_final: 0.8917 (mt) REVERT: B 59 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 188 MET cc_start: 0.7695 (mmm) cc_final: 0.7442 (mmm) REVERT: R 40 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7217 (mpp) outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 0.0592 time to fit residues: 8.1125 Evaluate side-chains 94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 60 optimal weight: 0.0270 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123787 restraints weight = 10046.227| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.05 r_work: 0.3462 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6697 Z= 0.110 Angle : 0.445 5.576 9157 Z= 0.242 Chirality : 0.040 0.180 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.160 60.639 972 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.15 % Allowed : 16.36 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.29), residues: 885 helix: 2.36 (0.25), residues: 408 sheet: 0.68 (0.41), residues: 167 loop : -0.62 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.012 0.001 TYR R 199 PHE 0.015 0.001 PHE B 292 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6696) covalent geometry : angle 0.44545 ( 9155) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.44719 ( 2) hydrogen bonds : bond 0.03504 ( 393) hydrogen bonds : angle 4.00587 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.244 Fit side-chains REVERT: A 233 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8077 (mtmt) REVERT: B 51 LEU cc_start: 0.9188 (mt) cc_final: 0.8892 (mt) REVERT: B 59 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: B 219 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7849 (mtt90) REVERT: R 40 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7186 (mpp) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.0568 time to fit residues: 8.1955 Evaluate side-chains 93 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0270 chunk 12 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.0040 overall best weight: 0.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.142871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124843 restraints weight = 10285.171| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.05 r_work: 0.3476 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6697 Z= 0.100 Angle : 0.456 6.137 9157 Z= 0.243 Chirality : 0.040 0.165 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.016 55.218 972 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.49 % Allowed : 17.52 % Favored : 80.99 % 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: 1.59 (0.29), residues: 885 helix: 2.48 (0.25), residues: 402 sheet: 0.74 (0.41), residues: 167 loop : -0.68 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.010 0.001 TYR R 199 PHE 0.013 0.001 PHE B 292 TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6696) covalent geometry : angle 0.45646 ( 9155) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.32766 ( 2) hydrogen bonds : bond 0.03404 ( 393) hydrogen bonds : angle 3.94176 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.244 Fit side-chains REVERT: B 51 LEU cc_start: 0.9189 (mt) cc_final: 0.8894 (mt) REVERT: B 59 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: B 219 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7750 (mtt90) REVERT: G 41 CYS cc_start: 0.7991 (m) cc_final: 0.7549 (m) REVERT: R 40 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7165 (mpp) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.0500 time to fit residues: 7.3762 Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 292 ASN B 54 HIS R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121624 restraints weight = 10209.143| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.05 r_work: 0.3431 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6697 Z= 0.147 Angle : 0.495 5.749 9157 Z= 0.266 Chirality : 0.042 0.198 1104 Planarity : 0.003 0.028 1148 Dihedral : 4.099 50.622 972 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.98 % Allowed : 16.69 % Favored : 81.32 % 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: 1.49 (0.29), residues: 885 helix: 2.40 (0.25), residues: 402 sheet: 0.50 (0.41), residues: 169 loop : -0.60 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.015 0.001 TYR R 199 PHE 0.023 0.001 PHE R 49 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6696) covalent geometry : angle 0.49502 ( 9155) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.88207 ( 2) hydrogen bonds : bond 0.03714 ( 393) hydrogen bonds : angle 4.01424 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.158 Fit side-chains REVERT: B 14 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 51 LEU cc_start: 0.9178 (mt) cc_final: 0.8937 (mt) REVERT: B 59 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: R 40 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7185 (mpp) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 0.0494 time to fit residues: 6.6931 Evaluate side-chains 94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121956 restraints weight = 10134.400| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.05 r_work: 0.3442 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6697 Z= 0.134 Angle : 0.484 5.806 9157 Z= 0.260 Chirality : 0.041 0.181 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.010 44.310 972 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.65 % Allowed : 17.02 % Favored : 81.32 % 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: 885 helix: 2.37 (0.25), residues: 402 sheet: 0.47 (0.41), residues: 169 loop : -0.58 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.013 0.001 TYR R 199 PHE 0.013 0.001 PHE B 292 TRP 0.013 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6696) covalent geometry : angle 0.48409 ( 9155) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.63670 ( 2) hydrogen bonds : bond 0.03626 ( 393) hydrogen bonds : angle 4.00664 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.261 Fit side-chains REVERT: B 14 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 59 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: R 40 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7177 (mpp) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0533 time to fit residues: 7.4897 Evaluate side-chains 92 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121715 restraints weight = 10084.384| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.04 r_work: 0.3437 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6697 Z= 0.135 Angle : 0.491 5.627 9157 Z= 0.263 Chirality : 0.042 0.190 1104 Planarity : 0.003 0.029 1148 Dihedral : 3.966 37.737 972 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 17.52 % Favored : 80.83 % 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: 1.42 (0.29), residues: 885 helix: 2.21 (0.25), residues: 408 sheet: 0.46 (0.41), residues: 169 loop : -0.48 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.013 0.001 TYR R 199 PHE 0.011 0.001 PHE B 199 TRP 0.012 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6696) covalent geometry : angle 0.49062 ( 9155) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.71748 ( 2) hydrogen bonds : bond 0.03652 ( 393) hydrogen bonds : angle 4.05802 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.73 seconds wall clock time: 26 minutes 58.95 seconds (1618.95 seconds total)