Starting phenix.real_space_refine on Thu Nov 14 14:32:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_29960.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_29960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_29960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_29960.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge8_29960/11_2024/8ge8_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-5513/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: 5.05, per 1000 atoms: 0.77 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 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: 1.96 Time building geometry restraints manager: 1.98 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: 2.620 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: 0.100 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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 : 0.696 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1665 time to fit residues: 21.5337 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 : 0.742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 5.519 9155 Z= 0.262 Chirality : 0.040 0.150 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.605 74.493 972 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 : 0.693 Fit side-chains REVERT: B 205 ASP cc_start: 0.8579 (p0) cc_final: 0.8293 (p0) outliers start: 3 outliers final: 2 residues processed: 91 average time/residue: 0.1577 time to fit residues: 20.5042 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 : 0.797 ------------------------------------------------------------------------------- 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 44 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6696 Z= 0.239 Angle : 0.478 5.675 9155 Z= 0.263 Chirality : 0.041 0.146 1104 Planarity : 0.003 0.028 1148 Dihedral : 4.624 72.956 972 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.30 (0.28), residues: 885 helix: 2.19 (0.25), residues: 408 sheet: 0.66 (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 0.016 0.001 PHE B 241 TYR 0.015 0.001 TYR R 199 ARG 0.002 0.000 ARG A 347 *********************** 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 : 0.738 Fit side-chains REVERT: A 233 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8510 (mtmm) REVERT: B 188 MET cc_start: 0.7767 (mmm) cc_final: 0.7256 (mmm) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 0.1690 time to fit residues: 23.2813 Evaluate side-chains 84 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1439 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= 0.197 Angle : 0.455 5.605 9155 Z= 0.251 Chirality : 0.041 0.177 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.499 70.385 972 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.32 % Allowed : 15.04 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.28), residues: 885 helix: 2.20 (0.25), residues: 408 sheet: 0.57 (0.40), residues: 159 loop : -0.74 (0.33), residues: 318 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 0.013 0.001 TYR R 199 ARG 0.003 0.000 ARG B 219 *********************** 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 100 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.786 Fit side-chains REVERT: A 233 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8497 (mtmm) REVERT: B 51 LEU cc_start: 0.9139 (mt) cc_final: 0.8856 (mt) REVERT: B 188 MET cc_start: 0.7888 (mmm) cc_final: 0.7439 (mmm) REVERT: B 219 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7331 (mtt90) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.1674 time to fit residues: 23.1277 Evaluate side-chains 89 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 1 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6696 Z= 0.223 Angle : 0.472 7.563 9155 Z= 0.257 Chirality : 0.041 0.206 1104 Planarity : 0.003 0.028 1148 Dihedral : 4.462 67.825 972 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.98 % Allowed : 16.03 % 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 (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: 1.34 (0.29), residues: 885 helix: 2.19 (0.25), residues: 408 sheet: 0.36 (0.40), residues: 179 loop : -0.58 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE B 292 TYR 0.015 0.001 TYR R 199 ARG 0.003 0.000 ARG B 219 *********************** 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 99 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.743 Fit side-chains REVERT: B 51 LEU cc_start: 0.9185 (mt) cc_final: 0.8876 (mt) REVERT: B 59 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: B 219 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7313 (mtt90) REVERT: R 40 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7234 (mpp) outliers start: 12 outliers final: 7 residues processed: 94 average time/residue: 0.1613 time to fit residues: 21.4348 Evaluate side-chains 91 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 153 ILE 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 50 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.0570 chunk 7 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6696 Z= 0.156 Angle : 0.438 6.924 9155 Z= 0.239 Chirality : 0.040 0.166 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.258 63.209 972 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 17.36 % 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: 1.44 (0.29), residues: 885 helix: 2.29 (0.25), residues: 408 sheet: 0.43 (0.40), residues: 179 loop : -0.57 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE B 292 TYR 0.011 0.001 TYR R 199 ARG 0.004 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 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.634 Fit side-chains REVERT: B 51 LEU cc_start: 0.9231 (mt) cc_final: 0.8937 (mt) REVERT: B 59 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 205 ASP cc_start: 0.8401 (p0) cc_final: 0.8186 (p0) REVERT: R 40 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7191 (mpp) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 0.1598 time to fit residues: 23.1767 Evaluate side-chains 94 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6696 Z= 0.209 Angle : 0.473 6.852 9155 Z= 0.256 Chirality : 0.041 0.221 1104 Planarity : 0.003 0.053 1148 Dihedral : 4.247 59.531 972 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.98 % Allowed : 17.52 % 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: 1.43 (0.29), residues: 885 helix: 2.26 (0.25), residues: 408 sheet: 0.53 (0.41), residues: 172 loop : -0.61 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE B 292 TYR 0.014 0.001 TYR R 199 ARG 0.007 0.000 ARG B 219 *********************** 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 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.682 Fit side-chains REVERT: A 233 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: B 51 LEU cc_start: 0.9240 (mt) cc_final: 0.8942 (mt) REVERT: B 59 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: B 188 MET cc_start: 0.7566 (mmm) cc_final: 0.7320 (mmm) REVERT: R 40 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7217 (mpp) REVERT: R 84 LEU cc_start: 0.8106 (mt) cc_final: 0.7850 (mt) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.1531 time to fit residues: 21.4355 Evaluate side-chains 92 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 312 ASN 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: 0.8980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6696 Z= 0.183 Angle : 0.466 6.501 9155 Z= 0.253 Chirality : 0.041 0.204 1104 Planarity : 0.003 0.029 1148 Dihedral : 4.157 55.803 972 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.29), residues: 885 helix: 2.37 (0.25), residues: 402 sheet: 0.52 (0.41), residues: 172 loop : -0.65 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 313 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE B 292 TYR 0.013 0.001 TYR R 199 ARG 0.002 0.000 ARG B 219 *********************** 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: 13 poor density : 88 time to evaluate : 0.737 Fit side-chains REVERT: A 233 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8238 (mtmm) REVERT: A 302 LEU cc_start: 0.8508 (mm) cc_final: 0.8211 (mm) REVERT: B 51 LEU cc_start: 0.9227 (mt) cc_final: 0.8941 (mt) REVERT: B 59 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: B 188 MET cc_start: 0.7625 (mmm) cc_final: 0.7358 (mmm) REVERT: R 40 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7205 (mpp) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.1548 time to fit residues: 20.6322 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 : 0.748 ------------------------------------------------------------------------------- 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 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 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 54 HIS R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1931 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= 0.219 Angle : 0.483 6.617 9155 Z= 0.261 Chirality : 0.041 0.183 1104 Planarity : 0.003 0.028 1148 Dihedral : 4.141 50.460 972 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 18.35 % Favored : 79.83 % 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: 1.40 (0.29), residues: 885 helix: 2.27 (0.25), residues: 408 sheet: 0.30 (0.40), residues: 174 loop : -0.52 (0.36), residues: 303 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 0.014 0.001 PHE B 292 TYR 0.015 0.001 TYR R 199 ARG 0.001 0.000 ARG A 336 *********************** 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 97 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.759 Fit side-chains REVERT: A 302 LEU cc_start: 0.8447 (mm) cc_final: 0.8162 (mm) REVERT: B 14 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8554 (mm) REVERT: B 51 LEU cc_start: 0.9208 (mt) cc_final: 0.8988 (mt) REVERT: B 59 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: B 188 MET cc_start: 0.7706 (mmm) cc_final: 0.7232 (mmm) REVERT: R 40 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7183 (mpp) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.1616 time to fit residues: 21.0345 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 : 0.719 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6696 Z= 0.158 Angle : 0.452 6.196 9155 Z= 0.246 Chirality : 0.040 0.189 1104 Planarity : 0.003 0.028 1148 Dihedral : 3.945 42.762 972 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.82 % Allowed : 18.51 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.29), residues: 885 helix: 2.39 (0.25), residues: 403 sheet: 0.41 (0.41), residues: 172 loop : -0.62 (0.35), residues: 310 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 0.012 0.001 PHE B 292 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG A 232 ********************** 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 102 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.719 Fit side-chains REVERT: A 302 LEU cc_start: 0.8458 (mm) cc_final: 0.8187 (mm) REVERT: B 14 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8543 (mm) REVERT: B 51 LEU cc_start: 0.9200 (mt) cc_final: 0.8985 (mt) REVERT: B 59 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: B 188 MET cc_start: 0.7407 (mmm) cc_final: 0.7117 (mmm) REVERT: R 40 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7005 (mpp) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.1411 time to fit residues: 19.9236 Evaluate side-chains 97 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.141153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123131 restraints weight = 10047.716| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.05 r_work: 0.3456 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6696 Z= 0.163 Angle : 0.464 6.767 9155 Z= 0.251 Chirality : 0.040 0.252 1104 Planarity : 0.003 0.028 1148 Dihedral : 3.841 35.916 972 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.15 % Allowed : 18.35 % Favored : 79.50 % 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: 1.47 (0.29), residues: 885 helix: 2.40 (0.25), residues: 403 sheet: 0.32 (0.41), residues: 174 loop : -0.55 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR R 199 ARG 0.002 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.64 seconds wall clock time: 32 minutes 21.62 seconds (1941.62 seconds total)