Starting phenix.real_space_refine on Tue Mar 11 19:09:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge8_29960/03_2025/8ge8_29960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge8_29960/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge8_29960/03_2025/8ge8_29960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge8_29960/03_2025/8ge8_29960.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge8_29960/03_2025/8ge8_29960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge8_29960/03_2025/8ge8_29960.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'ASN:plan1': 3, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} 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, 'ASP:plan': 11, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} 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, 'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 4} 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: 5.01, per 1000 atoms: 0.76 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.81 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: 2.09 Time building geometry restraints manager: 2.03 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- 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 6696 Z= 0.177 Angle : 0.513 8.112 9155 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 : 7.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE B 234 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG R 328 *********************** 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 : 0.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1615 time to fit residues: 21.1000 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 : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.143356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125423 restraints weight = 9990.706| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.04 r_work: 0.3479 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6696 Z= 0.187 Angle : 0.475 5.517 9155 Z= 0.262 Chirality : 0.040 0.150 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.605 74.489 972 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.50 % Allowed : 8.93 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 885 helix: 2.19 (0.25), residues: 408 sheet: 0.81 (0.40), residues: 152 loop : -1.05 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG B 49 *********************** 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: 3 poor density : 89 time to evaluate : 0.826 Fit side-chains REVERT: B 205 ASP cc_start: 0.8505 (p0) cc_final: 0.8211 (p0) outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1643 time to fit residues: 21.5001 Evaluate side-chains 87 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 76 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.140900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122707 restraints weight = 10059.234| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.05 r_work: 0.3446 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6696 Z= 0.219 Angle : 0.469 5.795 9155 Z= 0.257 Chirality : 0.040 0.146 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.574 72.460 972 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.99 % Allowed : 12.23 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 885 helix: 2.23 (0.25), residues: 408 sheet: 0.69 (0.40), residues: 156 loop : -0.78 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 241 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG A 265 *********************** 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 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.760 Fit side-chains REVERT: A 233 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8551 (mtmm) REVERT: A 302 LEU cc_start: 0.8538 (mm) cc_final: 0.8318 (mm) REVERT: B 137 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8126 (mtp180) REVERT: B 188 MET cc_start: 0.8049 (mmm) cc_final: 0.7665 (mmm) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 0.1719 time to fit residues: 24.0494 Evaluate side-chains 86 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 349 SER 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 84 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122066 restraints weight = 10226.311| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.07 r_work: 0.3436 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6696 Z= 0.209 Angle : 0.460 5.622 9155 Z= 0.254 Chirality : 0.041 0.177 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.490 69.988 972 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.49 % Allowed : 14.71 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.28), residues: 885 helix: 2.23 (0.25), residues: 408 sheet: 0.80 (0.41), residues: 152 loop : -0.80 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 292 TYR 0.014 0.001 TYR R 199 ARG 0.001 0.000 ARG A 336 *********************** 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 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.787 Fit side-chains REVERT: A 233 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8515 (mtmm) REVERT: A 302 LEU cc_start: 0.8553 (mm) cc_final: 0.8329 (mm) REVERT: B 51 LEU cc_start: 0.9163 (mt) cc_final: 0.8866 (mt) REVERT: B 188 MET cc_start: 0.8197 (mmm) cc_final: 0.7837 (mmm) REVERT: B 219 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7935 (mtt90) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.1650 time to fit residues: 23.6587 Evaluate side-chains 90 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 R residue 153 ILE 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 38 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.141405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123114 restraints weight = 10157.916| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.08 r_work: 0.3454 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6696 Z= 0.161 Angle : 0.448 7.034 9155 Z= 0.243 Chirality : 0.040 0.200 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.309 66.135 972 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.65 % Allowed : 16.20 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 885 helix: 2.35 (0.25), residues: 408 sheet: 0.73 (0.41), residues: 167 loop : -0.70 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.012 0.001 TYR R 199 ARG 0.004 0.000 ARG B 137 *********************** 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 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.771 Fit side-chains REVERT: B 51 LEU cc_start: 0.9191 (mt) cc_final: 0.8870 (mt) REVERT: B 59 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: B 219 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7871 (mtt90) REVERT: R 40 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7208 (mpp) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.1598 time to fit residues: 22.6314 Evaluate side-chains 91 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 R residue 40 MET 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 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122524 restraints weight = 10009.158| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.05 r_work: 0.3448 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6696 Z= 0.184 Angle : 0.460 6.994 9155 Z= 0.248 Chirality : 0.040 0.172 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.248 61.820 972 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.98 % Allowed : 17.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 885 helix: 2.37 (0.25), residues: 402 sheet: 0.74 (0.42), residues: 167 loop : -0.75 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE B 292 TYR 0.013 0.001 TYR R 199 ARG 0.005 0.000 ARG B 219 *********************** 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 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.811 Fit side-chains REVERT: A 233 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8546 (mtmm) REVERT: B 51 LEU cc_start: 0.9191 (mt) cc_final: 0.8876 (mt) REVERT: B 59 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: R 40 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7239 (mpp) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.1610 time to fit residues: 22.9842 Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 R residue 40 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 312 ASN 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 28 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122378 restraints weight = 10094.921| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.12 r_work: 0.3442 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6696 Z= 0.177 Angle : 0.461 6.637 9155 Z= 0.248 Chirality : 0.040 0.226 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.165 58.130 972 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.15 % Allowed : 16.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 885 helix: 2.50 (0.25), residues: 396 sheet: 0.72 (0.42), residues: 167 loop : -0.76 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.013 0.001 TYR R 199 ARG 0.003 0.000 ARG B 137 *********************** 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 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.779 Fit side-chains REVERT: A 233 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8527 (mtmm) REVERT: B 51 LEU cc_start: 0.9219 (mt) cc_final: 0.8891 (mt) REVERT: B 59 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: B 219 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7765 (mtt90) REVERT: R 40 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7216 (mpp) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.1595 time to fit residues: 22.4697 Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 218 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS 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 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122672 restraints weight = 10095.313| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.07 r_work: 0.3448 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6696 Z= 0.178 Angle : 0.461 6.405 9155 Z= 0.249 Chirality : 0.040 0.206 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.058 52.629 972 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.82 % Allowed : 17.52 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 885 helix: 2.51 (0.25), residues: 396 sheet: 0.61 (0.42), residues: 169 loop : -0.70 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 PHE 0.016 0.001 PHE B 292 TYR 0.013 0.001 TYR R 199 ARG 0.003 0.000 ARG B 137 *********************** 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 101 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.744 Fit side-chains REVERT: A 233 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8539 (mtmm) REVERT: B 51 LEU cc_start: 0.9228 (mt) cc_final: 0.8921 (mt) REVERT: B 59 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: B 205 ASP cc_start: 0.8393 (p0) cc_final: 0.8123 (p0) REVERT: B 219 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7766 (mtt90) REVERT: R 40 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7235 (mpp) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.1591 time to fit residues: 22.0032 Evaluate side-chains 97 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 B residue 218 CYS 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 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122931 restraints weight = 10185.418| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.09 r_work: 0.3453 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6696 Z= 0.169 Angle : 0.460 7.175 9155 Z= 0.247 Chirality : 0.040 0.181 1104 Planarity : 0.003 0.029 1148 Dihedral : 3.905 43.984 972 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 18.02 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 885 helix: 2.44 (0.25), residues: 403 sheet: 0.55 (0.42), residues: 169 loop : -0.63 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE B 292 TYR 0.012 0.001 TYR R 199 ARG 0.004 0.000 ARG B 219 *********************** 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 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.760 Fit side-chains REVERT: A 233 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8533 (mtmm) REVERT: A 279 ASN cc_start: 0.9298 (t0) cc_final: 0.9080 (t0) REVERT: B 51 LEU cc_start: 0.9225 (mt) cc_final: 0.8991 (mt) REVERT: B 59 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: B 205 ASP cc_start: 0.8386 (p0) cc_final: 0.8126 (p0) REVERT: B 219 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7715 (mtt90) REVERT: R 40 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7057 (mpp) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.1614 time to fit residues: 23.1333 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 : 0.812 ------------------------------------------------------------------------------- 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 B residue 218 CYS 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 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 54 HIS R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120612 restraints weight = 10250.912| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.07 r_work: 0.3424 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6696 Z= 0.236 Angle : 0.490 6.562 9155 Z= 0.264 Chirality : 0.041 0.203 1104 Planarity : 0.003 0.029 1148 Dihedral : 3.964 37.423 972 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 17.52 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 885 helix: 2.32 (0.25), residues: 402 sheet: 0.45 (0.41), residues: 169 loop : -0.58 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE B 292 TYR 0.015 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 ********************** 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 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.729 Fit side-chains REVERT: A 233 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8567 (mtmm) REVERT: B 14 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8466 (mm) REVERT: B 51 LEU cc_start: 0.9221 (mt) cc_final: 0.9007 (mt) REVERT: B 59 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 219 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7692 (mtt90) REVERT: R 40 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7204 (mpp) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.1581 time to fit residues: 21.2181 Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 218 ASN 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 B residue 218 CYS 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 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.0040 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 292 ASN 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 = 0.3818 r_free = 0.3818 target = 0.142506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124125 restraints weight = 10282.123| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.12 r_work: 0.3466 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6696 Z= 0.132 Angle : 0.457 6.564 9155 Z= 0.243 Chirality : 0.040 0.250 1104 Planarity : 0.003 0.029 1148 Dihedral : 3.722 29.395 972 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.98 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 885 helix: 2.42 (0.25), residues: 403 sheet: 0.54 (0.42), residues: 164 loop : -0.60 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 292 TYR 0.010 0.001 TYR R 199 ARG 0.004 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.58 seconds wall clock time: 65 minutes 26.13 seconds (3926.13 seconds total)