Starting phenix.real_space_refine on Fri Sep 11 15:45:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.cif Found real_map, /net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10dn_75093/09_2026/10dn_75093.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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 36 5.16 5 C 6228 2.51 5 N 1683 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9825 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3275 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 396} Chain: "B" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3275 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 396} Chain: "C" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3275 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 396} Time building chain proxies: 2.18, per 1000 atoms: 0.22 Number of scatterers: 9825 At special positions: 0 Unit cell: (97.37, 96.3, 94.16, 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 36 16.00 O 1878 8.00 N 1683 7.00 C 6228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 298.1 milliseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 10.7% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 63 through 78 removed outlier: 3.525A pdb=" N ASP A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.936A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.710A pdb=" N SER B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.899A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.733A pdb=" N SER C 79 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.921A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 411 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.840A pdb=" N ARG A 166 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 132 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 164 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY A 213 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 214 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 238 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 261 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 280 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN A 323 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 282 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A 321 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE A 284 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A 319 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 286 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 317 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS A 288 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 315 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A 290 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASN A 313 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 292 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLN A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 458 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 86 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 113 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 111 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 90 " --> pdb=" O TRP A 109 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRP A 109 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER A 92 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.884A pdb=" N ARG B 166 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER B 132 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 164 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 182 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY B 213 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 214 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 238 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 261 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 280 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN B 323 " --> pdb=" O ASN B 280 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 282 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE B 321 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE B 284 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE B 319 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 286 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 317 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS B 288 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 315 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR B 290 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 313 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 292 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B 458 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU B 86 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 113 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 111 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 90 " --> pdb=" O TRP B 109 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP B 109 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 92 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.685A pdb=" N LYS C 126 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU C 169 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR C 128 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 167 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG C 130 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 165 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY C 213 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 214 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 238 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 261 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C 280 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 323 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 282 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE C 321 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE C 284 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 319 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 286 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 317 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS C 288 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 315 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR C 290 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN C 313 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 292 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 445 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP C 458 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR C 94 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN C 106 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR C 96 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER C 104 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 209 through 210 478 hydrogen bonds defined for protein. 1359 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: 1.64 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3243 1.34 - 1.46: 2212 1.46 - 1.57: 4550 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 10077 Sorted by residual: bond pdb=" CA ASN C 344 " pdb=" C ASN C 344 " ideal model delta sigma weight residual 1.532 1.522 0.011 9.60e-03 1.09e+04 1.21e+00 bond pdb=" CA ASN A 344 " pdb=" C ASN A 344 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.12e+00 bond pdb=" CA ASN B 344 " pdb=" C ASN B 344 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.06e+00 bond pdb=" CA GLU C 86 " pdb=" C GLU C 86 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.51e-01 bond pdb=" CA GLU A 86 " pdb=" C GLU A 86 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.43e-01 ... (remaining 10072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.65: 12227 0.65 - 1.30: 1186 1.30 - 1.95: 167 1.95 - 2.60: 52 2.60 - 3.24: 36 Bond angle restraints: 13668 Sorted by residual: angle pdb=" CA ASN A 344 " pdb=" C ASN A 344 " pdb=" N ASN A 345 " ideal model delta sigma weight residual 114.17 117.09 -2.92 1.45e+00 4.76e-01 4.06e+00 angle pdb=" CA ASN B 344 " pdb=" C ASN B 344 " pdb=" N ASN B 345 " ideal model delta sigma weight residual 114.17 117.09 -2.92 1.45e+00 4.76e-01 4.04e+00 angle pdb=" CA ASN C 344 " pdb=" C ASN C 344 " pdb=" N ASN C 345 " ideal model delta sigma weight residual 114.17 117.07 -2.90 1.45e+00 4.76e-01 3.99e+00 angle pdb=" CA ASN A 344 " pdb=" C ASN A 344 " pdb=" O ASN A 344 " ideal model delta sigma weight residual 122.44 120.20 2.24 1.32e+00 5.74e-01 2.89e+00 angle pdb=" CA ASN B 344 " pdb=" C ASN B 344 " pdb=" O ASN B 344 " ideal model delta sigma weight residual 122.44 120.21 2.23 1.32e+00 5.74e-01 2.85e+00 ... (remaining 13663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.81: 5476 11.81 - 23.62: 303 23.62 - 35.43: 67 35.43 - 47.24: 20 47.24 - 59.05: 5 Dihedral angle restraints: 5871 sinusoidal: 2310 harmonic: 3561 Sorted by residual: dihedral pdb=" CA LYS A 135 " pdb=" C LYS A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LYS B 135 " pdb=" C LYS B 135 " pdb=" N ASN B 136 " pdb=" CA ASN B 136 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LYS C 135 " pdb=" C LYS C 135 " pdb=" N ASN C 136 " pdb=" CA ASN C 136 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 ... (remaining 5868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 868 0.027 - 0.053: 322 0.053 - 0.080: 94 0.080 - 0.107: 65 0.107 - 0.133: 49 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA ILE C 465 " pdb=" N ILE C 465 " pdb=" C ILE C 465 " pdb=" CB ILE C 465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 465 " pdb=" N ILE B 465 " pdb=" C ILE B 465 " pdb=" CB ILE B 465 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1395 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 174 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 175 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 174 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 175 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 174 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO C 175 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 175 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 175 " -0.023 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3086 2.83 - 3.34: 7744 3.34 - 3.86: 15969 3.86 - 4.38: 19316 4.38 - 4.90: 35093 Nonbonded interactions: 81208 Sorted by model distance: nonbonded pdb=" NH2 ARG A 68 " pdb=" OD1 ASP B 70 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASP A 70 " pdb=" NH2 ARG C 68 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG B 68 " pdb=" OD1 ASP C 70 " model vdw 2.312 3.120 nonbonded pdb=" NE2 GLN C 432 " pdb=" OH TYR C 469 " model vdw 2.321 3.120 nonbonded pdb=" O ILE C 412 " pdb=" OG1 THR C 415 " model vdw 2.322 3.040 ... (remaining 81203 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.870 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.100 Find NCS groups from input model: 0.080 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.002 0.013 10077 Z= 0.107 Angle : 0.434 3.245 13668 Z= 0.257 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.042 1800 Dihedral : 8.434 59.051 3621 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.69 % Allowed : 3.64 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1227 helix: 3.91 (0.52), residues: 81 sheet: 1.61 (0.22), residues: 591 loop : -0.83 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 153 TYR 0.005 0.001 TYR A 172 PHE 0.008 0.001 PHE B 365 TRP 0.007 0.001 TRP C 242 HIS 0.001 0.000 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.11 (10077) covalent geometry : angle 0.43442 / 0.26 (13668) hydrogen bonds : bond 0.20598 / 13.59 ( 478) hydrogen bonds : angle 8.41220 / 5.85 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 SER cc_start: 0.8866 (p) cc_final: 0.8381 (m) REVERT: A 218 ILE cc_start: 0.8362 (mt) cc_final: 0.8159 (tp) REVERT: A 466 MET cc_start: 0.8361 (ttm) cc_final: 0.8123 (ttp) REVERT: B 80 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8349 (mmtm) REVERT: B 218 ILE cc_start: 0.8249 (mt) cc_final: 0.7921 (tp) REVERT: B 421 ASP cc_start: 0.8105 (t0) cc_final: 0.7729 (t0) REVERT: B 466 MET cc_start: 0.8430 (ttm) cc_final: 0.8215 (ttp) REVERT: C 137 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: C 218 ILE cc_start: 0.8292 (mt) cc_final: 0.8081 (tp) REVERT: C 421 ASP cc_start: 0.8131 (t0) cc_final: 0.7717 (t0) REVERT: C 466 MET cc_start: 0.8493 (ttm) cc_final: 0.8285 (ttp) outliers start: 7 outliers final: 2 residues processed: 153 average time/residue: 0.6077 time to fit residues: 99.2930 Evaluate side-chains 89 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain C residue 137 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 193 ASN A 197 ASN A 318 ASN A 332 ASN A 432 GLN B 193 ASN B 318 ASN B 332 ASN B 432 GLN C 193 ASN C 332 ASN C 432 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083810 restraints weight = 14588.239| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.25 r_work: 0.2900 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10077 Z= 0.229 Angle : 0.569 6.056 13668 Z= 0.318 Chirality : 0.046 0.142 1398 Planarity : 0.005 0.042 1800 Dihedral : 4.852 50.557 1378 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.75 % Allowed : 6.10 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1227 helix: 3.37 (0.50), residues: 81 sheet: 1.64 (0.21), residues: 591 loop : -0.97 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.011 0.002 TYR B 220 PHE 0.015 0.002 PHE B 365 TRP 0.009 0.001 TRP C 242 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (10077) covalent geometry : angle 0.56852 / 0.32 (13668) hydrogen bonds : bond 0.03589 / 2.37 ( 478) hydrogen bonds : angle 5.95993 / 4.14 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8883 (mt) cc_final: 0.8617 (tp) REVERT: A 243 ASP cc_start: 0.8860 (t0) cc_final: 0.8512 (t0) REVERT: A 468 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8511 (ttm) REVERT: B 289 MET cc_start: 0.8810 (mtm) cc_final: 0.8531 (mpp) REVERT: B 362 ASN cc_start: 0.8256 (p0) cc_final: 0.8043 (p0) REVERT: B 468 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8756 (ttm) REVERT: C 110 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: C 137 TRP cc_start: 0.8911 (OUTLIER) cc_final: 0.8584 (m-10) REVERT: C 218 ILE cc_start: 0.8768 (mt) cc_final: 0.8446 (tp) REVERT: C 289 MET cc_start: 0.8906 (mtm) cc_final: 0.8648 (mpp) REVERT: C 421 ASP cc_start: 0.8935 (t0) cc_final: 0.8676 (t0) REVERT: C 468 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: C 472 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (mttp) outliers start: 28 outliers final: 6 residues processed: 105 average time/residue: 0.5562 time to fit residues: 62.9942 Evaluate side-chains 90 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 472 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 332 ASN C 136 ASN C 332 ASN C 427 GLN C 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083626 restraints weight = 14569.756| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.24 r_work: 0.2897 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10077 Z= 0.203 Angle : 0.536 5.420 13668 Z= 0.300 Chirality : 0.045 0.153 1398 Planarity : 0.004 0.041 1800 Dihedral : 4.725 51.168 1373 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.85 % Allowed : 7.08 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1227 helix: 2.80 (0.51), residues: 81 sheet: 1.60 (0.21), residues: 591 loop : -1.02 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.010 0.001 TYR B 220 PHE 0.013 0.002 PHE B 284 TRP 0.013 0.001 TRP C 242 HIS 0.002 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (10077) covalent geometry : angle 0.53555 / 0.30 (13668) hydrogen bonds : bond 0.03307 / 2.19 ( 478) hydrogen bonds : angle 5.53823 / 3.87 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.378 Fit side-chains REVERT: A 218 ILE cc_start: 0.8917 (mt) cc_final: 0.8597 (tp) REVERT: A 243 ASP cc_start: 0.8951 (t0) cc_final: 0.8607 (t0) REVERT: A 458 ASP cc_start: 0.8307 (t70) cc_final: 0.8084 (t0) REVERT: A 468 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8620 (ttm) REVERT: B 289 MET cc_start: 0.8793 (mtm) cc_final: 0.8566 (mpp) REVERT: B 322 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 362 ASN cc_start: 0.8394 (p0) cc_final: 0.8100 (p0) REVERT: B 430 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.7944 (ptm-80) REVERT: B 466 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8677 (ttp) REVERT: B 468 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8707 (ttm) REVERT: C 89 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9027 (t) REVERT: C 137 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.8504 (m-10) REVERT: C 218 ILE cc_start: 0.8773 (mt) cc_final: 0.8435 (tp) REVERT: C 300 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6386 (tmm) REVERT: C 408 ASP cc_start: 0.8452 (t70) cc_final: 0.8223 (t0) REVERT: C 421 ASP cc_start: 0.8918 (t0) cc_final: 0.8670 (t0) REVERT: C 468 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8728 (ttm) REVERT: C 472 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (mttp) outliers start: 29 outliers final: 9 residues processed: 98 average time/residue: 0.5773 time to fit residues: 61.0357 Evaluate side-chains 96 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 472 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083269 restraints weight = 14689.249| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2892 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10077 Z= 0.203 Angle : 0.527 4.588 13668 Z= 0.295 Chirality : 0.045 0.151 1398 Planarity : 0.004 0.042 1800 Dihedral : 4.763 51.676 1373 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.15 % Allowed : 8.26 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1227 helix: 2.65 (0.52), residues: 81 sheet: 1.57 (0.21), residues: 591 loop : -1.05 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 461 TYR 0.009 0.001 TYR C 265 PHE 0.013 0.002 PHE B 284 TRP 0.013 0.001 TRP C 242 HIS 0.002 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (10077) covalent geometry : angle 0.52712 / 0.30 (13668) hydrogen bonds : bond 0.03149 / 2.09 ( 478) hydrogen bonds : angle 5.35893 / 3.75 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.351 Fit side-chains REVERT: A 362 ASN cc_start: 0.8405 (p0) cc_final: 0.8156 (p0) REVERT: A 458 ASP cc_start: 0.8243 (t70) cc_final: 0.8015 (t0) REVERT: A 468 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8609 (ttm) REVERT: B 110 MET cc_start: 0.8869 (mpp) cc_final: 0.8517 (mmm) REVERT: B 289 MET cc_start: 0.8808 (mtm) cc_final: 0.8531 (mpt) REVERT: B 322 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: B 362 ASN cc_start: 0.8411 (p0) cc_final: 0.8132 (p0) REVERT: B 468 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8737 (ttm) REVERT: C 89 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9039 (t) REVERT: C 137 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: C 218 ILE cc_start: 0.8781 (mt) cc_final: 0.8431 (tp) REVERT: C 289 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7503 (mtm) REVERT: C 408 ASP cc_start: 0.8582 (t70) cc_final: 0.8253 (t0) REVERT: C 421 ASP cc_start: 0.8921 (t0) cc_final: 0.8677 (t0) REVERT: C 468 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8732 (ttm) REVERT: C 472 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8643 (mttp) outliers start: 32 outliers final: 10 residues processed: 98 average time/residue: 0.5776 time to fit residues: 60.9231 Evaluate side-chains 92 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 472 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.101532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083709 restraints weight = 14603.049| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.24 r_work: 0.2900 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10077 Z= 0.183 Angle : 0.508 4.455 13668 Z= 0.285 Chirality : 0.044 0.148 1398 Planarity : 0.004 0.041 1800 Dihedral : 4.699 51.643 1373 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 8.65 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1227 helix: 2.61 (0.52), residues: 81 sheet: 1.54 (0.21), residues: 591 loop : -1.03 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 461 TYR 0.008 0.001 TYR A 265 PHE 0.012 0.001 PHE B 284 TRP 0.014 0.001 TRP C 242 HIS 0.001 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (10077) covalent geometry : angle 0.50844 / 0.29 (13668) hydrogen bonds : bond 0.02999 / 1.99 ( 478) hydrogen bonds : angle 5.22876 / 3.66 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: A 218 ILE cc_start: 0.8872 (mm) cc_final: 0.8486 (tp) REVERT: A 362 ASN cc_start: 0.8334 (p0) cc_final: 0.8054 (p0) REVERT: A 458 ASP cc_start: 0.8177 (t70) cc_final: 0.7950 (t0) REVERT: A 468 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8605 (ttm) REVERT: B 110 MET cc_start: 0.8804 (mpp) cc_final: 0.8447 (mmm) REVERT: B 226 GLN cc_start: 0.8442 (tt0) cc_final: 0.7929 (tt0) REVERT: B 289 MET cc_start: 0.8775 (mtm) cc_final: 0.8490 (mpt) REVERT: B 322 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: B 362 ASN cc_start: 0.8417 (p0) cc_final: 0.8136 (p0) REVERT: B 458 ASP cc_start: 0.8262 (t70) cc_final: 0.7989 (t0) REVERT: B 466 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8722 (ttp) REVERT: B 468 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8756 (ttm) REVERT: C 89 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.9014 (t) REVERT: C 110 MET cc_start: 0.9112 (mmt) cc_final: 0.8721 (mmt) REVERT: C 137 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8504 (m-10) REVERT: C 218 ILE cc_start: 0.8772 (mt) cc_final: 0.8395 (tp) REVERT: C 408 ASP cc_start: 0.8452 (t70) cc_final: 0.8083 (t0) REVERT: C 421 ASP cc_start: 0.8939 (t0) cc_final: 0.8700 (t0) REVERT: C 468 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8729 (ttm) REVERT: C 472 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8609 (mttp) outliers start: 32 outliers final: 13 residues processed: 98 average time/residue: 0.5776 time to fit residues: 60.9661 Evaluate side-chains 93 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 472 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN A 332 ASN B 310 ASN B 374 HIS C 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.086397 restraints weight = 14553.342| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.16 r_work: 0.2944 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10077 Z= 0.100 Angle : 0.449 4.227 13668 Z= 0.253 Chirality : 0.043 0.148 1398 Planarity : 0.004 0.041 1800 Dihedral : 4.345 50.015 1373 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.75 % Allowed : 9.44 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1227 helix: 2.67 (0.52), residues: 81 sheet: 1.61 (0.21), residues: 588 loop : -0.94 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 461 TYR 0.008 0.001 TYR A 168 PHE 0.008 0.001 PHE A 284 TRP 0.013 0.001 TRP C 242 HIS 0.001 0.000 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (10077) covalent geometry : angle 0.44918 / 0.25 (13668) hydrogen bonds : bond 0.02544 / 1.70 ( 478) hydrogen bonds : angle 4.93607 / 3.46 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8890 (mm) cc_final: 0.8521 (tp) REVERT: A 289 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8260 (mpp) REVERT: A 362 ASN cc_start: 0.8294 (p0) cc_final: 0.8078 (p0) REVERT: A 468 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: B 110 MET cc_start: 0.8825 (mpp) cc_final: 0.8458 (mmm) REVERT: B 226 GLN cc_start: 0.8432 (tt0) cc_final: 0.7942 (tt0) REVERT: B 322 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: B 362 ASN cc_start: 0.8358 (p0) cc_final: 0.8099 (p0) REVERT: B 408 ASP cc_start: 0.8295 (t70) cc_final: 0.7921 (t0) REVERT: B 458 ASP cc_start: 0.8066 (t70) cc_final: 0.7822 (t0) REVERT: B 466 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8681 (ttp) REVERT: C 110 MET cc_start: 0.9124 (mmt) cc_final: 0.8748 (mmt) REVERT: C 137 TRP cc_start: 0.8835 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: C 362 ASN cc_start: 0.8291 (p0) cc_final: 0.7975 (p0) REVERT: C 408 ASP cc_start: 0.8405 (t70) cc_final: 0.8022 (t0) REVERT: C 421 ASP cc_start: 0.8923 (t0) cc_final: 0.8720 (t0) outliers start: 28 outliers final: 7 residues processed: 103 average time/residue: 0.5578 time to fit residues: 62.0958 Evaluate side-chains 89 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.084328 restraints weight = 14521.913| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.24 r_work: 0.2910 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10077 Z= 0.184 Angle : 0.511 5.103 13668 Z= 0.284 Chirality : 0.044 0.147 1398 Planarity : 0.004 0.041 1800 Dihedral : 4.622 51.150 1373 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.06 % Allowed : 10.23 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1227 helix: 2.60 (0.52), residues: 81 sheet: 1.60 (0.21), residues: 591 loop : -1.01 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 461 TYR 0.009 0.001 TYR B 168 PHE 0.012 0.001 PHE B 284 TRP 0.013 0.001 TRP C 242 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (10077) covalent geometry : angle 0.51052 / 0.28 (13668) hydrogen bonds : bond 0.02915 / 1.94 ( 478) hydrogen bonds : angle 5.06634 / 3.56 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.8325 (p0) cc_final: 0.8108 (p0) REVERT: A 468 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8605 (ttm) REVERT: B 322 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 362 ASN cc_start: 0.8421 (p0) cc_final: 0.8130 (p0) REVERT: B 408 ASP cc_start: 0.8376 (t70) cc_final: 0.7987 (t0) REVERT: B 458 ASP cc_start: 0.8139 (t70) cc_final: 0.7855 (t0) REVERT: B 466 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8671 (ttp) REVERT: C 137 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: C 362 ASN cc_start: 0.8315 (p0) cc_final: 0.8009 (p0) REVERT: C 408 ASP cc_start: 0.8400 (t70) cc_final: 0.7962 (t0) REVERT: C 421 ASP cc_start: 0.8953 (t0) cc_final: 0.8720 (t0) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.5662 time to fit residues: 55.6031 Evaluate side-chains 86 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085611 restraints weight = 14500.507| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.15 r_work: 0.2931 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10077 Z= 0.134 Angle : 0.479 5.854 13668 Z= 0.267 Chirality : 0.043 0.146 1398 Planarity : 0.004 0.042 1800 Dihedral : 4.483 51.096 1373 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.67 % Allowed : 10.82 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1227 helix: 2.64 (0.52), residues: 81 sheet: 1.59 (0.21), residues: 588 loop : -1.01 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 461 TYR 0.008 0.001 TYR A 265 PHE 0.010 0.001 PHE A 284 TRP 0.013 0.001 TRP C 242 HIS 0.003 0.001 HIS C 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10077) covalent geometry : angle 0.47913 / 0.27 (13668) hydrogen bonds : bond 0.02658 / 1.78 ( 478) hydrogen bonds : angle 4.97521 / 3.50 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8900 (mm) cc_final: 0.8529 (tp) REVERT: A 362 ASN cc_start: 0.8308 (p0) cc_final: 0.8104 (p0) REVERT: A 468 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8423 (ttm) REVERT: B 110 MET cc_start: 0.8843 (mpp) cc_final: 0.8506 (mmm) REVERT: B 289 MET cc_start: 0.8507 (mpp) cc_final: 0.8271 (mpt) REVERT: B 322 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 362 ASN cc_start: 0.8393 (p0) cc_final: 0.8122 (p0) REVERT: B 408 ASP cc_start: 0.8356 (t70) cc_final: 0.7958 (t0) REVERT: B 458 ASP cc_start: 0.8080 (t70) cc_final: 0.7821 (t0) REVERT: B 466 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8655 (ttp) REVERT: C 137 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: C 362 ASN cc_start: 0.8315 (p0) cc_final: 0.8011 (p0) REVERT: C 408 ASP cc_start: 0.8385 (t70) cc_final: 0.7942 (t0) REVERT: C 421 ASP cc_start: 0.8938 (t0) cc_final: 0.8704 (t0) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 0.5473 time to fit residues: 53.0820 Evaluate side-chains 82 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.0270 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN C 118 ASN C 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085589 restraints weight = 14515.813| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.22 r_work: 0.2931 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10077 Z= 0.135 Angle : 0.485 7.221 13668 Z= 0.269 Chirality : 0.043 0.151 1398 Planarity : 0.004 0.041 1800 Dihedral : 4.491 50.763 1373 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.67 % Allowed : 11.11 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1227 helix: 2.66 (0.52), residues: 81 sheet: 1.60 (0.21), residues: 588 loop : -1.03 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 461 TYR 0.008 0.001 TYR A 265 PHE 0.010 0.001 PHE A 284 TRP 0.013 0.001 TRP C 242 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (10077) covalent geometry : angle 0.48525 / 0.27 (13668) hydrogen bonds : bond 0.02662 / 1.78 ( 478) hydrogen bonds : angle 4.95232 / 3.48 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8903 (mm) cc_final: 0.8530 (tp) REVERT: A 468 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8417 (ttm) REVERT: B 110 MET cc_start: 0.8835 (mpp) cc_final: 0.8486 (mmm) REVERT: B 226 GLN cc_start: 0.8413 (tt0) cc_final: 0.7922 (tt0) REVERT: B 322 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 362 ASN cc_start: 0.8393 (p0) cc_final: 0.8126 (p0) REVERT: B 408 ASP cc_start: 0.8360 (t70) cc_final: 0.7952 (t0) REVERT: B 458 ASP cc_start: 0.8080 (t70) cc_final: 0.7815 (t0) REVERT: B 466 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8647 (ttp) REVERT: C 137 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8479 (m-10) REVERT: C 362 ASN cc_start: 0.8341 (p0) cc_final: 0.8053 (p0) REVERT: C 408 ASP cc_start: 0.8260 (t70) cc_final: 0.7808 (t0) REVERT: C 421 ASP cc_start: 0.8943 (t0) cc_final: 0.8711 (t0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.5474 time to fit residues: 50.9675 Evaluate side-chains 85 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 0.0060 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.0070 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.088469 restraints weight = 14232.774| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.17 r_work: 0.2981 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10077 Z= 0.078 Angle : 0.436 6.026 13668 Z= 0.244 Chirality : 0.042 0.148 1398 Planarity : 0.003 0.040 1800 Dihedral : 4.133 48.274 1373 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.47 % Allowed : 11.41 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1227 helix: 2.80 (0.52), residues: 81 sheet: 1.63 (0.21), residues: 594 loop : -0.87 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 461 TYR 0.008 0.001 TYR B 265 PHE 0.006 0.001 PHE C 422 TRP 0.014 0.001 TRP C 242 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00164 / 0.08 (10077) covalent geometry : angle 0.43563 / 0.24 (13668) hydrogen bonds : bond 0.02280 / 1.54 ( 478) hydrogen bonds : angle 4.74747 / 3.33 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 468 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8509 (ttm) REVERT: B 80 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8626 (mmtm) REVERT: B 362 ASN cc_start: 0.8335 (p0) cc_final: 0.8068 (p0) REVERT: B 408 ASP cc_start: 0.8279 (t70) cc_final: 0.7856 (t0) REVERT: B 458 ASP cc_start: 0.7907 (t70) cc_final: 0.7667 (t70) REVERT: C 137 TRP cc_start: 0.8721 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: C 362 ASN cc_start: 0.8258 (p0) cc_final: 0.7984 (p0) REVERT: C 408 ASP cc_start: 0.8295 (t70) cc_final: 0.7839 (t0) REVERT: C 418 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8852 (m) REVERT: C 421 ASP cc_start: 0.8938 (t0) cc_final: 0.8722 (t0) outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 0.4938 time to fit residues: 54.3210 Evaluate side-chains 91 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 121 optimal weight: 0.0970 chunk 119 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 332 ASN C 118 ASN C 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087723 restraints weight = 14376.627| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.19 r_work: 0.2968 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10077 Z= 0.092 Angle : 0.451 6.663 13668 Z= 0.252 Chirality : 0.042 0.146 1398 Planarity : 0.004 0.043 1800 Dihedral : 4.124 44.294 1373 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.98 % Allowed : 12.19 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1227 helix: 2.81 (0.52), residues: 81 sheet: 1.78 (0.21), residues: 588 loop : -0.91 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 461 TYR 0.008 0.001 TYR A 399 PHE 0.007 0.001 PHE A 284 TRP 0.013 0.001 TRP C 242 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (10077) covalent geometry : angle 0.45086 / 0.25 (13668) hydrogen bonds : bond 0.02383 / 1.60 ( 478) hydrogen bonds : angle 4.74517 / 3.33 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2781.67 seconds wall clock time: 48 minutes 22.16 seconds (2902.16 seconds total)