Starting phenix.real_space_refine on Fri May 16 21:02:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuo_35728/05_2025/8iuo_35728.cif" } resolution = 3.96 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= 0.007 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 85 5.16 5 C 9225 2.51 5 N 2530 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14785 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "A" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "F" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'RNA': 35} Modifications used: {'rna2p_pyr': 5, 'rna3p_pyr': 30} Link IDs: {'rna2p': 5, 'rna3p': 29} Chain: "B" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "D" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2817 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 8, 'TRANS': 353} Time building chain proxies: 9.77, per 1000 atoms: 0.66 Number of scatterers: 14785 At special positions: 0 Unit cell: (171.7, 147.05, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 35 15.00 O 2910 8.00 N 2530 7.00 C 9225 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 71.5% alpha, 5.0% beta 0 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS C 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 87 Processing helix chain 'C' and resid 120 through 140 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.961A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 311 " --> pdb=" O LYS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN C 316 " --> pdb=" O SER C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN C 360 " --> pdb=" O GLN C 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 120 through 140 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.720A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.611A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.946A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS B 5 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 120 through 140 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.712A pdb=" N ILE B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 4.004A pdb=" N GLN B 316 " --> pdb=" O SER B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.776A pdb=" N ASN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS D 5 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 120 through 140 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.711A pdb=" N ILE D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.962A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.947A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 removed outlier: 4.003A pdb=" N GLN D 316 " --> pdb=" O SER D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.777A pdb=" N ASN D 360 " --> pdb=" O GLN D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 removed outlier: 3.628A pdb=" N LYS E 5 " --> pdb=" O ALA E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 87 Processing helix chain 'E' and resid 120 through 140 Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.719A pdb=" N ARG E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.712A pdb=" N ILE E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.961A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 250 removed outlier: 3.610A pdb=" N ALA E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.946A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.836A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 removed outlier: 4.004A pdb=" N GLN E 316 " --> pdb=" O SER E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.777A pdb=" N ASN E 360 " --> pdb=" O GLN E 356 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 104 removed outlier: 4.196A pdb=" N ASP C 96 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 104 removed outlier: 4.195A pdb=" N ASP A 96 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.195A pdb=" N ASP B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 104 removed outlier: 4.197A pdb=" N ASP D 96 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 104 removed outlier: 4.196A pdb=" N ASP E 96 " --> pdb=" O THR E 115 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 4.44 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: 4620 1.34 - 1.45: 2287 1.45 - 1.57: 7958 1.57 - 1.69: 69 1.69 - 1.81: 155 Bond restraints: 15089 Sorted by residual: bond pdb=" N GLY E 236 " pdb=" CA GLY E 236 " ideal model delta sigma weight residual 1.443 1.478 -0.035 1.17e-02 7.31e+03 8.81e+00 bond pdb=" N VAL E 239 " pdb=" CA VAL E 239 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N VAL C 239 " pdb=" CA VAL C 239 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.31e+00 bond pdb=" N SER D 237 " pdb=" CA SER D 237 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.17e-02 7.31e+03 8.23e+00 bond pdb=" N VAL B 239 " pdb=" CA VAL B 239 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.22e+00 ... (remaining 15084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 19055 1.31 - 2.63: 1174 2.63 - 3.94: 159 3.94 - 5.25: 56 5.25 - 6.56: 17 Bond angle restraints: 20461 Sorted by residual: angle pdb=" CA GLY A 236 " pdb=" C GLY A 236 " pdb=" O GLY A 236 " ideal model delta sigma weight residual 122.16 118.07 4.09 8.20e-01 1.49e+00 2.48e+01 angle pdb=" N ASN C 187 " pdb=" CA ASN C 187 " pdb=" C ASN C 187 " ideal model delta sigma weight residual 113.50 108.24 5.26 1.23e+00 6.61e-01 1.83e+01 angle pdb=" N ARG A 234 " pdb=" CA ARG A 234 " pdb=" C ARG A 234 " ideal model delta sigma weight residual 113.61 107.83 5.78 1.50e+00 4.44e-01 1.48e+01 angle pdb=" O3' U F1014 " pdb=" C3' U F1014 " pdb=" C2' U F1014 " ideal model delta sigma weight residual 113.70 118.87 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C ILE D 104 " pdb=" N ASN D 105 " pdb=" CA ASN D 105 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 ... (remaining 20456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 8937 34.98 - 69.96: 266 69.96 - 104.94: 15 104.94 - 139.92: 3 139.92 - 174.89: 1 Dihedral angle restraints: 9222 sinusoidal: 4032 harmonic: 5190 Sorted by residual: dihedral pdb=" C4' U F1028 " pdb=" C3' U F1028 " pdb=" O3' U F1028 " pdb=" P U F1029 " ideal model delta sinusoidal sigma weight residual 220.00 45.11 174.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA SER E 153 " pdb=" C SER E 153 " pdb=" N PRO E 154 " pdb=" CA PRO E 154 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER C 153 " pdb=" C SER C 153 " pdb=" N PRO C 154 " pdb=" CA PRO C 154 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 9219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1790 0.047 - 0.094: 457 0.094 - 0.141: 75 0.141 - 0.189: 9 0.189 - 0.236: 4 Chirality restraints: 2335 Sorted by residual: chirality pdb=" C3' U F1021 " pdb=" C4' U F1021 " pdb=" O3' U F1021 " pdb=" C2' U F1021 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3' U F1007 " pdb=" C4' U F1007 " pdb=" O3' U F1007 " pdb=" C2' U F1007 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' U F1014 " pdb=" C4' U F1014 " pdb=" O3' U F1014 " pdb=" C2' U F1014 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2332 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 215 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LYS C 215 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 215 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS C 216 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 215 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C LYS B 215 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS B 215 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 216 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 215 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C LYS A 215 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS A 215 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS A 216 " -0.014 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 387 2.69 - 3.24: 16470 3.24 - 3.80: 24264 3.80 - 4.35: 28856 4.35 - 4.90: 47479 Nonbonded interactions: 117456 Sorted by model distance: nonbonded pdb=" O2' U F1028 " pdb=" OP1 U F1029 " model vdw 2.141 3.040 nonbonded pdb=" OP2 U F1008 " pdb=" ND2 ASN E 188 " model vdw 2.203 3.120 nonbonded pdb=" OP2 U F1029 " pdb=" ND2 ASN D 188 " model vdw 2.216 3.120 nonbonded pdb=" OP2 U F1022 " pdb=" ND2 ASN B 188 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG A 184 " pdb=" OP1 U F1035 " model vdw 2.239 3.120 ... (remaining 117451 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.090 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.480 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.008 0.052 15089 Z= 0.370 Angle : 0.738 6.563 20461 Z= 0.443 Chirality : 0.043 0.236 2335 Planarity : 0.004 0.046 2510 Dihedral : 16.368 174.894 5912 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.19 % Allowed : 2.79 % Favored : 95.02 % 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: -2.44 (0.18), residues: 1800 helix: -0.79 (0.13), residues: 1165 sheet: -3.72 (0.41), residues: 125 loop : -2.70 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.004 0.001 HIS D 218 PHE 0.011 0.001 PHE A 247 TYR 0.010 0.001 TYR C 210 ARG 0.024 0.001 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.13710 ( 880) hydrogen bonds : angle 4.77197 ( 2520) covalent geometry : bond 0.00754 (15089) covalent geometry : angle 0.73764 (20461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 MET cc_start: 0.7972 (ptp) cc_final: 0.7409 (ptm) REVERT: C 271 MET cc_start: 0.9268 (mmm) cc_final: 0.8521 (mtp) REVERT: C 315 THR cc_start: 0.8675 (m) cc_final: 0.8434 (m) REVERT: A 194 MET cc_start: 0.7853 (mtm) cc_final: 0.7582 (mtt) REVERT: B 158 MET cc_start: 0.8021 (mmm) cc_final: 0.7776 (mmm) REVERT: B 286 GLU cc_start: 0.7953 (tp30) cc_final: 0.7261 (tp30) REVERT: B 297 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 305 ASN cc_start: 0.7947 (m-40) cc_final: 0.7445 (p0) REVERT: D 50 MET cc_start: 0.8635 (mtt) cc_final: 0.8327 (mtm) REVERT: D 71 MET cc_start: 0.8935 (mtm) cc_final: 0.8705 (mtt) REVERT: D 142 MET cc_start: 0.8464 (ptp) cc_final: 0.7780 (ptp) REVERT: D 263 LEU cc_start: 0.8843 (tp) cc_final: 0.8578 (tt) REVERT: E 134 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7402 (m) REVERT: E 216 HIS cc_start: 0.5384 (OUTLIER) cc_final: 0.5087 (m-70) outliers start: 33 outliers final: 9 residues processed: 234 average time/residue: 0.3396 time to fit residues: 109.5765 Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 216 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 249 ASN B 58 ASN B 216 HIS D 13 ASN D 16 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN E 230 GLN E 249 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046353 restraints weight = 79305.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047665 restraints weight = 43722.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048562 restraints weight = 29811.550| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15089 Z= 0.228 Angle : 0.685 9.991 20461 Z= 0.361 Chirality : 0.044 0.254 2335 Planarity : 0.004 0.035 2510 Dihedral : 11.726 155.720 2533 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.79 % Allowed : 11.10 % Favored : 87.11 % 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: -0.57 (0.20), residues: 1800 helix: 0.83 (0.15), residues: 1170 sheet: -3.15 (0.38), residues: 125 loop : -2.46 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 260 HIS 0.008 0.001 HIS B 225 PHE 0.014 0.002 PHE D 111 TYR 0.020 0.002 TYR C 88 ARG 0.007 0.001 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 880) hydrogen bonds : angle 4.14268 ( 2520) covalent geometry : bond 0.00491 (15089) covalent geometry : angle 0.68548 (20461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8696 (t0) cc_final: 0.8452 (t0) REVERT: C 50 MET cc_start: 0.8991 (mtp) cc_final: 0.8709 (mtp) REVERT: C 105 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6189 (p0) REVERT: C 271 MET cc_start: 0.9332 (mmm) cc_final: 0.8586 (mtp) REVERT: C 313 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 109 MET cc_start: 0.6812 (mmt) cc_final: 0.6470 (mmt) REVERT: A 194 MET cc_start: 0.8112 (mtm) cc_final: 0.7886 (mtt) REVERT: B 50 MET cc_start: 0.9042 (mtp) cc_final: 0.8426 (ttm) REVERT: B 71 MET cc_start: 0.9279 (mtm) cc_final: 0.8925 (mtm) REVERT: B 271 MET cc_start: 0.8608 (mtp) cc_final: 0.8283 (mtp) REVERT: B 297 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 305 ASN cc_start: 0.8347 (m-40) cc_final: 0.7686 (p0) REVERT: D 50 MET cc_start: 0.8810 (mtt) cc_final: 0.8474 (mtp) REVERT: D 67 MET cc_start: 0.9436 (mmm) cc_final: 0.8750 (mmm) REVERT: D 71 MET cc_start: 0.9110 (mtm) cc_final: 0.8533 (mtm) REVERT: D 158 MET cc_start: 0.8863 (mmt) cc_final: 0.8037 (mmt) REVERT: D 162 CYS cc_start: 0.9227 (m) cc_final: 0.8952 (m) REVERT: E 282 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8357 (tm-30) outliers start: 27 outliers final: 11 residues processed: 149 average time/residue: 0.3090 time to fit residues: 66.5472 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN A 9 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 GLN D 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.047151 restraints weight = 79031.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.048475 restraints weight = 43834.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049365 restraints weight = 29937.426| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15089 Z= 0.128 Angle : 0.547 8.515 20461 Z= 0.288 Chirality : 0.039 0.251 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.501 160.623 2518 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.59 % Allowed : 12.69 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.20), residues: 1800 helix: 1.21 (0.15), residues: 1205 sheet: -1.65 (0.53), residues: 70 loop : -2.69 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 260 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 111 TYR 0.010 0.001 TYR E 347 ARG 0.004 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 880) hydrogen bonds : angle 3.62361 ( 2520) covalent geometry : bond 0.00272 (15089) covalent geometry : angle 0.54670 (20461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8675 (t0) cc_final: 0.8211 (t0) REVERT: C 50 MET cc_start: 0.8975 (mtp) cc_final: 0.8649 (mtp) REVERT: C 105 ASN cc_start: 0.6746 (OUTLIER) cc_final: 0.6292 (p0) REVERT: A 109 MET cc_start: 0.6701 (mmt) cc_final: 0.6465 (mmp) REVERT: A 194 MET cc_start: 0.8094 (mtm) cc_final: 0.7839 (mtt) REVERT: A 281 MET cc_start: 0.8113 (mmm) cc_final: 0.7705 (tpt) REVERT: B 71 MET cc_start: 0.9268 (mtm) cc_final: 0.8975 (mtm) REVERT: B 128 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: B 162 CYS cc_start: 0.9282 (m) cc_final: 0.8977 (m) REVERT: B 297 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7463 (tm-30) REVERT: B 305 ASN cc_start: 0.8460 (m-40) cc_final: 0.7710 (p0) REVERT: D 50 MET cc_start: 0.8788 (mtt) cc_final: 0.8489 (mtp) REVERT: D 67 MET cc_start: 0.9445 (mmm) cc_final: 0.8719 (mmm) REVERT: D 71 MET cc_start: 0.9068 (mtm) cc_final: 0.8555 (mtm) REVERT: D 142 MET cc_start: 0.8628 (ptp) cc_final: 0.8424 (ptt) REVERT: D 158 MET cc_start: 0.8804 (mmt) cc_final: 0.7962 (mmt) REVERT: D 162 CYS cc_start: 0.9186 (m) cc_final: 0.8955 (m) REVERT: E 9 ASN cc_start: 0.8586 (t0) cc_final: 0.8093 (t0) REVERT: E 282 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8144 (tm-30) outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 0.2570 time to fit residues: 52.4322 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048239 restraints weight = 77751.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049609 restraints weight = 43106.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050540 restraints weight = 29246.934| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15089 Z= 0.096 Angle : 0.533 10.156 20461 Z= 0.273 Chirality : 0.038 0.242 2335 Planarity : 0.003 0.033 2510 Dihedral : 11.383 159.657 2517 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.13 % Allowed : 14.09 % Favored : 84.78 % 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: 0.45 (0.21), residues: 1800 helix: 1.52 (0.15), residues: 1175 sheet: -1.09 (0.54), residues: 70 loop : -2.26 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.002 0.000 HIS B 225 PHE 0.009 0.001 PHE D 226 TYR 0.007 0.001 TYR D 23 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 880) hydrogen bonds : angle 3.38730 ( 2520) covalent geometry : bond 0.00193 (15089) covalent geometry : angle 0.53345 (20461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8922 (mtp) cc_final: 0.8577 (mtp) REVERT: C 105 ASN cc_start: 0.6694 (OUTLIER) cc_final: 0.6288 (p0) REVERT: C 271 MET cc_start: 0.9244 (mmp) cc_final: 0.8807 (mmp) REVERT: A 48 CYS cc_start: 0.8046 (m) cc_final: 0.7608 (t) REVERT: A 109 MET cc_start: 0.6838 (mmt) cc_final: 0.6528 (mmp) REVERT: A 281 MET cc_start: 0.7995 (mmm) cc_final: 0.7779 (tpt) REVERT: B 71 MET cc_start: 0.9218 (mtm) cc_final: 0.8573 (mtm) REVERT: B 162 CYS cc_start: 0.9243 (m) cc_final: 0.8869 (m) REVERT: B 297 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 305 ASN cc_start: 0.8408 (m-40) cc_final: 0.7727 (p0) REVERT: D 50 MET cc_start: 0.8730 (mtt) cc_final: 0.8451 (mtm) REVERT: D 67 MET cc_start: 0.9363 (mmm) cc_final: 0.8590 (mmm) REVERT: D 71 MET cc_start: 0.9063 (mtm) cc_final: 0.8569 (mtm) REVERT: D 158 MET cc_start: 0.8761 (mmt) cc_final: 0.8012 (mmp) REVERT: D 162 CYS cc_start: 0.9120 (m) cc_final: 0.8919 (m) REVERT: E 9 ASN cc_start: 0.8642 (t0) cc_final: 0.8411 (t0) REVERT: E 138 MET cc_start: 0.9233 (mmm) cc_final: 0.9014 (mmm) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.2441 time to fit residues: 49.1179 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN E 58 ASN E 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.043430 restraints weight = 80500.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044696 restraints weight = 44100.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045536 restraints weight = 29971.025| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15089 Z= 0.308 Angle : 0.711 8.781 20461 Z= 0.376 Chirality : 0.044 0.280 2335 Planarity : 0.004 0.041 2510 Dihedral : 11.418 159.327 2517 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.79 % Allowed : 14.95 % Favored : 83.26 % 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: 0.08 (0.20), residues: 1800 helix: 1.21 (0.15), residues: 1165 sheet: -0.75 (0.58), residues: 70 loop : -2.35 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 260 HIS 0.007 0.001 HIS B 225 PHE 0.028 0.002 PHE B 223 TYR 0.022 0.002 TYR E 347 ARG 0.005 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.04865 ( 880) hydrogen bonds : angle 4.31570 ( 2520) covalent geometry : bond 0.00670 (15089) covalent geometry : angle 0.71078 (20461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8996 (mtp) cc_final: 0.8706 (mtp) REVERT: C 142 MET cc_start: 0.8086 (tmm) cc_final: 0.7880 (tmm) REVERT: C 162 CYS cc_start: 0.9073 (m) cc_final: 0.8737 (t) REVERT: C 194 MET cc_start: 0.9031 (mmp) cc_final: 0.8744 (mpp) REVERT: A 109 MET cc_start: 0.6635 (mmt) cc_final: 0.6307 (mmp) REVERT: B 71 MET cc_start: 0.9382 (mtm) cc_final: 0.9155 (mtm) REVERT: B 162 CYS cc_start: 0.9243 (m) cc_final: 0.8861 (m) REVERT: B 271 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: B 297 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 305 ASN cc_start: 0.8881 (m-40) cc_final: 0.7852 (p0) REVERT: D 67 MET cc_start: 0.9462 (mmm) cc_final: 0.8931 (mmm) REVERT: D 71 MET cc_start: 0.9083 (mtm) cc_final: 0.8632 (mtm) REVERT: D 162 CYS cc_start: 0.9248 (m) cc_final: 0.8923 (t) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 0.2676 time to fit residues: 48.4381 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 176 optimal weight: 0.0970 chunk 45 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 249 ASN B 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047144 restraints weight = 78605.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048500 restraints weight = 42174.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049400 restraints weight = 28194.091| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15089 Z= 0.100 Angle : 0.535 8.620 20461 Z= 0.277 Chirality : 0.038 0.239 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.265 160.122 2517 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.53 % Allowed : 15.55 % Favored : 82.92 % 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: 0.57 (0.21), residues: 1800 helix: 1.52 (0.15), residues: 1195 sheet: -0.48 (0.61), residues: 70 loop : -2.21 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 260 HIS 0.002 0.001 HIS C 225 PHE 0.021 0.001 PHE B 223 TYR 0.009 0.001 TYR A 69 ARG 0.003 0.000 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 880) hydrogen bonds : angle 3.48928 ( 2520) covalent geometry : bond 0.00199 (15089) covalent geometry : angle 0.53543 (20461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8996 (mtp) cc_final: 0.8660 (mtp) REVERT: C 142 MET cc_start: 0.8046 (tmm) cc_final: 0.7783 (tmm) REVERT: C 194 MET cc_start: 0.9018 (mmp) cc_final: 0.8751 (mpp) REVERT: C 271 MET cc_start: 0.9256 (mmp) cc_final: 0.8811 (tpp) REVERT: C 334 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8271 (ppp) REVERT: A 48 CYS cc_start: 0.8052 (m) cc_final: 0.7644 (t) REVERT: A 109 MET cc_start: 0.6748 (mmt) cc_final: 0.6444 (mmp) REVERT: A 257 MET cc_start: 0.8740 (mmt) cc_final: 0.8434 (mmt) REVERT: A 281 MET cc_start: 0.8169 (tpp) cc_final: 0.7951 (tpt) REVERT: B 71 MET cc_start: 0.9247 (mtm) cc_final: 0.8820 (mtm) REVERT: B 162 CYS cc_start: 0.9320 (m) cc_final: 0.8935 (m) REVERT: B 271 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: B 297 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 305 ASN cc_start: 0.8748 (m-40) cc_final: 0.7868 (p0) REVERT: D 50 MET cc_start: 0.8777 (mtt) cc_final: 0.8442 (mtp) REVERT: D 67 MET cc_start: 0.9392 (mmm) cc_final: 0.8717 (mmm) REVERT: D 71 MET cc_start: 0.9057 (mtm) cc_final: 0.8563 (mtm) REVERT: D 138 MET cc_start: 0.9226 (tpp) cc_final: 0.8995 (tmm) REVERT: D 158 MET cc_start: 0.8821 (mmp) cc_final: 0.8068 (mmm) REVERT: D 162 CYS cc_start: 0.9169 (m) cc_final: 0.8956 (m) REVERT: E 109 MET cc_start: 0.7661 (tpp) cc_final: 0.6737 (mtt) REVERT: E 282 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 297 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 23 outliers final: 14 residues processed: 127 average time/residue: 0.2626 time to fit residues: 50.9106 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 133 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN D 327 ASN E 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.044510 restraints weight = 80996.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045717 restraints weight = 45799.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046524 restraints weight = 31639.730| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15089 Z= 0.237 Angle : 0.654 11.473 20461 Z= 0.340 Chirality : 0.042 0.272 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.294 160.224 2517 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.53 % Allowed : 17.54 % Favored : 80.93 % 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: 0.48 (0.21), residues: 1800 helix: 1.47 (0.15), residues: 1165 sheet: -0.19 (0.62), residues: 70 loop : -2.14 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 260 HIS 0.007 0.001 HIS B 225 PHE 0.018 0.001 PHE B 223 TYR 0.017 0.002 TYR E 347 ARG 0.004 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 880) hydrogen bonds : angle 4.04257 ( 2520) covalent geometry : bond 0.00516 (15089) covalent geometry : angle 0.65413 (20461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8956 (mtp) cc_final: 0.8598 (mtp) REVERT: C 142 MET cc_start: 0.8145 (tmm) cc_final: 0.7863 (tmm) REVERT: C 162 CYS cc_start: 0.9218 (m) cc_final: 0.8727 (t) REVERT: C 194 MET cc_start: 0.8946 (mmp) cc_final: 0.8707 (mpp) REVERT: A 48 CYS cc_start: 0.8130 (m) cc_final: 0.7666 (t) REVERT: A 74 LEU cc_start: 0.8752 (tp) cc_final: 0.8476 (tt) REVERT: A 109 MET cc_start: 0.6709 (mmt) cc_final: 0.6387 (mmp) REVERT: B 71 MET cc_start: 0.9280 (mtm) cc_final: 0.9005 (mtm) REVERT: B 162 CYS cc_start: 0.9192 (m) cc_final: 0.8783 (m) REVERT: B 271 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: B 297 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 50 MET cc_start: 0.8693 (mtt) cc_final: 0.8395 (mtp) REVERT: D 67 MET cc_start: 0.9385 (mmm) cc_final: 0.8875 (mmm) REVERT: D 71 MET cc_start: 0.9006 (mtm) cc_final: 0.8582 (mtm) REVERT: D 142 MET cc_start: 0.8469 (ptt) cc_final: 0.7661 (ppp) REVERT: D 158 MET cc_start: 0.9000 (mmp) cc_final: 0.8154 (mmt) REVERT: D 162 CYS cc_start: 0.9194 (m) cc_final: 0.8929 (m) REVERT: D 257 MET cc_start: 0.8990 (mmm) cc_final: 0.8714 (mmm) REVERT: E 141 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8079 (pm20) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.2452 time to fit residues: 43.5522 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 139 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 156 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046657 restraints weight = 79734.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047919 restraints weight = 44341.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048772 restraints weight = 30345.911| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15089 Z= 0.114 Angle : 0.575 11.281 20461 Z= 0.292 Chirality : 0.039 0.243 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.296 160.262 2517 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.26 % Allowed : 18.34 % Favored : 80.40 % 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: 0.70 (0.21), residues: 1800 helix: 1.57 (0.15), residues: 1195 sheet: -0.10 (0.62), residues: 70 loop : -2.09 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 260 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE B 223 TYR 0.007 0.001 TYR B 135 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 880) hydrogen bonds : angle 3.58175 ( 2520) covalent geometry : bond 0.00241 (15089) covalent geometry : angle 0.57461 (20461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8965 (mtp) cc_final: 0.8635 (mtp) REVERT: C 194 MET cc_start: 0.8993 (mmp) cc_final: 0.8753 (mpp) REVERT: C 334 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8142 (ppp) REVERT: A 48 CYS cc_start: 0.8109 (m) cc_final: 0.7693 (t) REVERT: A 74 LEU cc_start: 0.8680 (tp) cc_final: 0.8388 (tt) REVERT: A 109 MET cc_start: 0.6704 (mmt) cc_final: 0.6407 (mmp) REVERT: A 194 MET cc_start: 0.7871 (mtt) cc_final: 0.7648 (mtm) REVERT: A 257 MET cc_start: 0.8784 (mmt) cc_final: 0.8459 (mmt) REVERT: B 67 MET cc_start: 0.8737 (mmm) cc_final: 0.8509 (mmm) REVERT: B 71 MET cc_start: 0.9212 (mtm) cc_final: 0.8647 (mtm) REVERT: B 162 CYS cc_start: 0.9250 (m) cc_final: 0.8846 (m) REVERT: B 271 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7682 (mtp) REVERT: B 305 ASN cc_start: 0.8731 (m-40) cc_final: 0.7828 (p0) REVERT: D 50 MET cc_start: 0.8700 (mtt) cc_final: 0.8359 (mtp) REVERT: D 67 MET cc_start: 0.9339 (mmm) cc_final: 0.8710 (mmm) REVERT: D 71 MET cc_start: 0.9004 (mtm) cc_final: 0.8530 (mtm) REVERT: D 138 MET cc_start: 0.9202 (tpp) cc_final: 0.8984 (tmm) REVERT: D 142 MET cc_start: 0.8433 (ptt) cc_final: 0.7368 (ppp) REVERT: D 162 CYS cc_start: 0.9166 (m) cc_final: 0.8937 (m) REVERT: E 297 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7277 (tm-30) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.2503 time to fit residues: 44.0835 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 149 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045212 restraints weight = 80015.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.046444 restraints weight = 45034.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.047266 restraints weight = 31061.927| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15089 Z= 0.185 Angle : 0.619 12.092 20461 Z= 0.317 Chirality : 0.041 0.263 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.319 160.731 2517 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.46 % Allowed : 18.60 % Favored : 79.93 % 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: 0.69 (0.21), residues: 1800 helix: 1.61 (0.15), residues: 1165 sheet: -0.11 (0.62), residues: 70 loop : -2.01 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 260 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.001 PHE B 223 TYR 0.011 0.001 TYR E 347 ARG 0.005 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 880) hydrogen bonds : angle 3.80959 ( 2520) covalent geometry : bond 0.00403 (15089) covalent geometry : angle 0.61912 (20461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8966 (mtp) cc_final: 0.8596 (mtp) REVERT: C 142 MET cc_start: 0.8053 (tmm) cc_final: 0.7778 (tmm) REVERT: C 162 CYS cc_start: 0.9225 (m) cc_final: 0.8724 (t) REVERT: C 194 MET cc_start: 0.8984 (mmp) cc_final: 0.8738 (mpp) REVERT: C 334 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8167 (ppp) REVERT: A 1 MET cc_start: 0.6755 (pmm) cc_final: 0.6156 (ptm) REVERT: A 48 CYS cc_start: 0.8117 (m) cc_final: 0.7672 (t) REVERT: A 74 LEU cc_start: 0.8784 (tp) cc_final: 0.8508 (tt) REVERT: A 109 MET cc_start: 0.6678 (mmt) cc_final: 0.6374 (mmp) REVERT: A 194 MET cc_start: 0.7876 (mtt) cc_final: 0.7630 (mtm) REVERT: B 71 MET cc_start: 0.9250 (mtm) cc_final: 0.8715 (mtm) REVERT: B 162 CYS cc_start: 0.9230 (m) cc_final: 0.8816 (m) REVERT: B 271 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7751 (mtp) REVERT: D 50 MET cc_start: 0.8723 (mtt) cc_final: 0.8396 (mtp) REVERT: D 67 MET cc_start: 0.9358 (mmm) cc_final: 0.8841 (mmm) REVERT: D 71 MET cc_start: 0.9006 (mtm) cc_final: 0.8587 (mtm) REVERT: D 142 MET cc_start: 0.8459 (ptt) cc_final: 0.7577 (ppp) REVERT: D 162 CYS cc_start: 0.9198 (m) cc_final: 0.8922 (m) REVERT: E 1 MET cc_start: 0.4877 (ptt) cc_final: 0.4492 (ptp) REVERT: E 138 MET cc_start: 0.9210 (mmm) cc_final: 0.8858 (mmm) REVERT: E 141 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: E 297 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7414 (tm-30) outliers start: 22 outliers final: 15 residues processed: 113 average time/residue: 0.2455 time to fit residues: 43.0016 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 50 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 157 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047977 restraints weight = 79946.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049256 restraints weight = 44565.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050075 restraints weight = 30352.736| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15089 Z= 0.104 Angle : 0.579 12.659 20461 Z= 0.289 Chirality : 0.038 0.239 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.378 160.142 2517 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.46 % Allowed : 18.67 % Favored : 79.87 % 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: 0.66 (0.20), residues: 1800 helix: 1.68 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.003 0.000 HIS C 225 PHE 0.015 0.001 PHE B 223 TYR 0.007 0.001 TYR B 135 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 880) hydrogen bonds : angle 3.48455 ( 2520) covalent geometry : bond 0.00216 (15089) covalent geometry : angle 0.57935 (20461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8940 (mtp) cc_final: 0.8621 (mtp) REVERT: C 142 MET cc_start: 0.7997 (tmm) cc_final: 0.7707 (tmm) REVERT: C 194 MET cc_start: 0.8948 (mmp) cc_final: 0.8703 (mpp) REVERT: C 334 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (ppp) REVERT: A 1 MET cc_start: 0.6896 (pmm) cc_final: 0.6277 (ptm) REVERT: A 48 CYS cc_start: 0.8141 (m) cc_final: 0.7749 (t) REVERT: A 74 LEU cc_start: 0.8791 (tp) cc_final: 0.8506 (tt) REVERT: A 109 MET cc_start: 0.6730 (mmt) cc_final: 0.6456 (mmp) REVERT: A 257 MET cc_start: 0.8748 (mmt) cc_final: 0.8486 (mmt) REVERT: B 162 CYS cc_start: 0.9208 (m) cc_final: 0.8804 (m) REVERT: B 271 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7594 (mtp) REVERT: D 50 MET cc_start: 0.8664 (mtt) cc_final: 0.8301 (mtm) REVERT: D 67 MET cc_start: 0.9280 (mmm) cc_final: 0.8671 (mmm) REVERT: D 71 MET cc_start: 0.8961 (mtm) cc_final: 0.8512 (mtm) REVERT: D 142 MET cc_start: 0.8322 (ptt) cc_final: 0.8069 (ppp) REVERT: D 162 CYS cc_start: 0.9136 (m) cc_final: 0.8927 (m) REVERT: E 1 MET cc_start: 0.4817 (OUTLIER) cc_final: 0.4500 (ptp) REVERT: E 138 MET cc_start: 0.9161 (mmm) cc_final: 0.8831 (mmm) REVERT: E 297 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7208 (tm-30) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.2546 time to fit residues: 47.1224 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 181 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046864 restraints weight = 80919.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048111 restraints weight = 45013.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048918 restraints weight = 30821.027| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15089 Z= 0.134 Angle : 0.603 12.729 20461 Z= 0.303 Chirality : 0.039 0.251 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.411 160.322 2517 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.59 % Allowed : 18.94 % Favored : 79.47 % 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: 0.69 (0.20), residues: 1800 helix: 1.63 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 260 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE B 223 TYR 0.012 0.001 TYR C 288 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 880) hydrogen bonds : angle 3.62750 ( 2520) covalent geometry : bond 0.00290 (15089) covalent geometry : angle 0.60327 (20461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4600.80 seconds wall clock time: 82 minutes 43.40 seconds (4963.40 seconds total)