Starting phenix.real_space_refine on Sat Mar 16 13:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_35728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_35728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_35728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_35728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuo_35728/03_2024/8iuo_35728.pdb" } 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 Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E ASP 96": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.73, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.96 Conformation dependent library (CDL) restraints added in 2.7 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: 5.20 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: 4.70 Time building geometry restraints manager: 6.42 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: 99.47 - 106.35: 424 106.35 - 113.23: 8236 113.23 - 120.12: 5381 120.12 - 127.00: 6305 127.00 - 133.88: 115 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 2.440 nonbonded pdb=" OP2 U F1008 " pdb=" ND2 ASN E 188 " model vdw 2.203 2.520 nonbonded pdb=" OP2 U F1029 " pdb=" ND2 ASN D 188 " model vdw 2.216 2.520 nonbonded pdb=" OP2 U F1022 " pdb=" ND2 ASN B 188 " model vdw 2.218 2.520 nonbonded pdb=" NH1 ARG A 184 " pdb=" OP1 U F1035 " model vdw 2.239 2.520 ... (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 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: 4.610 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: 0.030 Extract box with map and model: 17.920 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.020 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.670 ------------------------------------------------------------------------------- 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= 0.492 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 *********************** 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 fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 2.147 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: 0.3307 time to fit residues: 106.2867 Evaluate side-chains 125 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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: 8.9990 chunk 138 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 HIS A 13 ASN ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS D 16 GLN E 13 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN E 249 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15089 Z= 0.195 Angle : 0.571 9.438 20461 Z= 0.300 Chirality : 0.040 0.204 2335 Planarity : 0.004 0.036 2510 Dihedral : 11.752 177.253 2533 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.46 % Allowed : 9.83 % Favored : 88.70 % 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: -0.56 (0.20), residues: 1800 helix: 0.86 (0.15), residues: 1200 sheet: -3.25 (0.37), residues: 125 loop : -2.72 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 260 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE E 213 TYR 0.013 0.001 TYR A 301 ARG 0.008 0.000 ARG D 101 *********************** 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 153 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.582 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: 0.8891 (mtp) cc_final: 0.8582 (mtp) REVERT: C 105 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.5689 (p0) REVERT: C 271 MET cc_start: 0.9293 (mmm) cc_final: 0.8471 (mtp) REVERT: A 109 MET cc_start: 0.6261 (mmt) cc_final: 0.5869 (mmp) REVERT: B 50 MET cc_start: 0.8981 (mtp) cc_final: 0.8519 (ttm) REVERT: B 271 MET cc_start: 0.8439 (mtp) cc_final: 0.8073 (mtp) REVERT: B 297 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 305 ASN cc_start: 0.8090 (m-40) cc_final: 0.7493 (p0) REVERT: D 50 MET cc_start: 0.8764 (mtt) cc_final: 0.8457 (mtm) REVERT: D 67 MET cc_start: 0.9332 (mmm) cc_final: 0.8612 (mmm) REVERT: D 71 MET cc_start: 0.9065 (mtm) cc_final: 0.8514 (mtm) REVERT: D 158 MET cc_start: 0.8707 (mmt) cc_final: 0.7757 (mmt) REVERT: D 162 CYS cc_start: 0.9171 (m) cc_final: 0.8826 (m) REVERT: D 263 LEU cc_start: 0.8862 (tp) cc_final: 0.8653 (tt) REVERT: E 67 MET cc_start: 0.8512 (mmm) cc_final: 0.8228 (mmt) REVERT: E 282 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 297 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6822 (tm-30) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 0.2987 time to fit residues: 64.5096 Evaluate side-chains 116 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 113 optimal weight: 0.0000 chunk 45 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN C 230 GLN B 13 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN D 16 GLN D 58 ASN E 89 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3173 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= 0.164 Angle : 0.518 8.843 20461 Z= 0.271 Chirality : 0.038 0.204 2335 Planarity : 0.003 0.032 2510 Dihedral : 11.545 172.978 2519 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.79 % Allowed : 10.90 % Favored : 87.31 % 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: 0.20 (0.21), residues: 1800 helix: 1.42 (0.15), residues: 1200 sheet: -1.60 (0.53), residues: 70 loop : -2.73 (0.27), residues: 530 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 0.019 0.001 PHE A 111 TYR 0.009 0.001 TYR E 347 ARG 0.004 0.000 ARG D 84 *********************** 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 147 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 ASN cc_start: 0.8537 (t0) cc_final: 0.8103 (t0) REVERT: C 50 MET cc_start: 0.8892 (mtp) cc_final: 0.8579 (mtp) REVERT: C 96 ASP cc_start: 0.7710 (t0) cc_final: 0.7476 (t0) REVERT: C 105 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.5845 (p0) REVERT: C 271 MET cc_start: 0.9372 (mmm) cc_final: 0.8982 (mmp) REVERT: C 278 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: A 74 LEU cc_start: 0.8663 (tp) cc_final: 0.8287 (tt) REVERT: A 281 MET cc_start: 0.7992 (mmm) cc_final: 0.7553 (tpt) REVERT: B 50 MET cc_start: 0.8981 (mtp) cc_final: 0.8767 (ttm) REVERT: B 71 MET cc_start: 0.9172 (mtm) cc_final: 0.8834 (mtm) REVERT: B 297 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 305 ASN cc_start: 0.8291 (m-40) cc_final: 0.7651 (p0) REVERT: D 50 MET cc_start: 0.8784 (mtt) cc_final: 0.8491 (mtm) REVERT: D 67 MET cc_start: 0.9333 (mmm) cc_final: 0.8571 (mmm) REVERT: D 71 MET cc_start: 0.9037 (mtm) cc_final: 0.8499 (mtm) REVERT: D 142 MET cc_start: 0.8268 (ptp) cc_final: 0.8054 (ptt) REVERT: D 162 CYS cc_start: 0.9187 (m) cc_final: 0.8836 (m) REVERT: E 9 ASN cc_start: 0.8555 (t0) cc_final: 0.8105 (t0) REVERT: E 67 MET cc_start: 0.8557 (mmm) cc_final: 0.8302 (mmt) REVERT: E 289 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8893 (mm-30) REVERT: E 297 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6837 (tm-30) outliers start: 27 outliers final: 13 residues processed: 142 average time/residue: 0.2643 time to fit residues: 57.3367 Evaluate side-chains 117 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B 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 221 ASP Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 221 ASP 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 164 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 176 optimal weight: 0.0470 chunk 87 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15089 Z= 0.173 Angle : 0.529 8.373 20461 Z= 0.274 Chirality : 0.038 0.206 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.402 171.178 2517 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.40 % Allowed : 12.49 % Favored : 86.11 % 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: 0.50 (0.21), residues: 1800 helix: 1.60 (0.15), residues: 1200 sheet: -1.36 (0.55), residues: 70 loop : -2.50 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 260 HIS 0.005 0.001 HIS D 100 PHE 0.012 0.001 PHE A 111 TYR 0.010 0.001 TYR E 347 ARG 0.006 0.000 ARG A 84 *********************** 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 129 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8900 (mtp) cc_final: 0.8571 (mtp) REVERT: C 96 ASP cc_start: 0.7777 (t0) cc_final: 0.7558 (t0) REVERT: C 105 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.5805 (p0) REVERT: C 271 MET cc_start: 0.9414 (mmm) cc_final: 0.9202 (mmp) REVERT: C 278 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: A 194 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7126 (mtm) REVERT: A 281 MET cc_start: 0.7942 (mmm) cc_final: 0.7673 (tpt) REVERT: B 297 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 305 ASN cc_start: 0.8512 (m-40) cc_final: 0.7708 (p0) REVERT: D 50 MET cc_start: 0.8816 (mtt) cc_final: 0.8531 (mtm) REVERT: D 67 MET cc_start: 0.9336 (mmm) cc_final: 0.8621 (mmm) REVERT: D 71 MET cc_start: 0.9093 (mtm) cc_final: 0.8553 (mtm) REVERT: D 162 CYS cc_start: 0.9181 (m) cc_final: 0.8821 (m) REVERT: E 138 MET cc_start: 0.9222 (mmm) cc_final: 0.9010 (mmm) REVERT: E 297 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6966 (tm-30) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.2409 time to fit residues: 46.5173 Evaluate side-chains 117 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain B 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 221 ASP Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 221 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN C 327 ASN B 269 ASN B 327 ASN D 269 ASN D 327 ASN E 16 GLN E 58 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15089 Z= 0.351 Angle : 0.639 9.451 20461 Z= 0.339 Chirality : 0.042 0.227 2335 Planarity : 0.004 0.033 2510 Dihedral : 11.439 171.796 2517 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.19 % Allowed : 14.75 % Favored : 83.06 % 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: 0.26 (0.21), residues: 1800 helix: 1.41 (0.15), residues: 1160 sheet: -2.12 (0.41), residues: 125 loop : -2.13 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 260 HIS 0.007 0.001 HIS B 225 PHE 0.012 0.001 PHE C 219 TYR 0.019 0.002 TYR E 347 ARG 0.005 0.001 ARG A 84 *********************** 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 135 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 2.018 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: 0.8983 (mtp) cc_final: 0.8684 (mtp) REVERT: C 105 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.5888 (p0) REVERT: C 142 MET cc_start: 0.7877 (tmm) cc_final: 0.7491 (tmm) REVERT: C 162 CYS cc_start: 0.9077 (m) cc_final: 0.8555 (t) REVERT: C 278 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: A 48 CYS cc_start: 0.8095 (m) cc_final: 0.7612 (t) REVERT: A 74 LEU cc_start: 0.8715 (tp) cc_final: 0.8479 (tp) REVERT: B 162 CYS cc_start: 0.9162 (m) cc_final: 0.8753 (m) REVERT: B 271 MET cc_start: 0.8541 (mtp) cc_final: 0.8296 (mtp) REVERT: B 297 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 305 ASN cc_start: 0.8943 (m-40) cc_final: 0.7890 (p0) REVERT: D 67 MET cc_start: 0.9400 (mmm) cc_final: 0.8866 (mmm) REVERT: D 71 MET cc_start: 0.9101 (mtm) cc_final: 0.8617 (mtm) REVERT: D 158 MET cc_start: 0.8732 (mmt) cc_final: 0.8070 (mmp) REVERT: D 162 CYS cc_start: 0.9251 (m) cc_final: 0.8827 (m) REVERT: D 257 MET cc_start: 0.9058 (mmm) cc_final: 0.8785 (mmm) REVERT: E 271 MET cc_start: 0.8218 (mtt) cc_final: 0.7932 (mtt) REVERT: E 289 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8909 (mm-30) REVERT: E 297 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7006 (tm-30) outliers start: 33 outliers final: 22 residues processed: 128 average time/residue: 0.2639 time to fit residues: 50.5783 Evaluate side-chains 118 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 34 ASP 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 269 ASN Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS 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 59 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN E 16 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15089 Z= 0.142 Angle : 0.534 8.593 20461 Z= 0.275 Chirality : 0.038 0.199 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.289 172.119 2517 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.33 % Allowed : 15.61 % Favored : 83.06 % 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: 0.63 (0.21), residues: 1800 helix: 1.63 (0.15), residues: 1190 sheet: -1.97 (0.41), residues: 125 loop : -2.01 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 260 HIS 0.004 0.001 HIS D 100 PHE 0.008 0.001 PHE D 111 TYR 0.008 0.001 TYR C 347 ARG 0.006 0.000 ARG B 238 *********************** 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 132 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8961 (mtp) cc_final: 0.8633 (mtp) REVERT: C 105 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.5875 (p0) REVERT: C 142 MET cc_start: 0.7911 (tmm) cc_final: 0.7679 (tmm) REVERT: A 48 CYS cc_start: 0.8064 (m) cc_final: 0.7622 (t) REVERT: A 194 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7367 (mtm) REVERT: A 281 MET cc_start: 0.8065 (tpp) cc_final: 0.7795 (tpt) REVERT: B 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8936 (mtm) REVERT: B 162 CYS cc_start: 0.9204 (m) cc_final: 0.8804 (m) REVERT: B 271 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: B 297 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 305 ASN cc_start: 0.8860 (m-40) cc_final: 0.7854 (p0) REVERT: D 67 MET cc_start: 0.9342 (mmm) cc_final: 0.8698 (mmm) REVERT: D 71 MET cc_start: 0.9057 (mtm) cc_final: 0.8544 (mtm) REVERT: D 138 MET cc_start: 0.9044 (tpp) cc_final: 0.8837 (tmm) REVERT: D 162 CYS cc_start: 0.9237 (m) cc_final: 0.8840 (m) REVERT: E 297 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7044 (tm-30) outliers start: 20 outliers final: 14 residues processed: 127 average time/residue: 0.2522 time to fit residues: 49.2577 Evaluate side-chains 116 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 239 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 170 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN D 327 ASN E 16 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15089 Z= 0.216 Angle : 0.561 9.607 20461 Z= 0.290 Chirality : 0.039 0.212 2335 Planarity : 0.003 0.030 2510 Dihedral : 11.239 171.365 2517 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.66 % Allowed : 16.94 % Favored : 81.40 % 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: 0.48 (0.21), residues: 1800 helix: 1.57 (0.15), residues: 1190 sheet: -1.76 (0.43), residues: 125 loop : -2.35 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 260 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE C 219 TYR 0.011 0.001 TYR E 347 ARG 0.004 0.000 ARG B 238 *********************** 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 128 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.8995 (mtp) cc_final: 0.8671 (mtp) REVERT: C 105 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.5824 (p0) REVERT: C 142 MET cc_start: 0.7994 (tmm) cc_final: 0.7730 (tmm) REVERT: C 270 ILE cc_start: 0.9381 (pt) cc_final: 0.9122 (tp) REVERT: C 278 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: A 48 CYS cc_start: 0.8064 (m) cc_final: 0.7601 (t) REVERT: A 74 LEU cc_start: 0.8727 (tp) cc_final: 0.8400 (tt) REVERT: A 194 MET cc_start: 0.7849 (mtt) cc_final: 0.7488 (mtm) REVERT: B 162 CYS cc_start: 0.9203 (m) cc_final: 0.8763 (m) REVERT: B 271 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: B 297 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 305 ASN cc_start: 0.8955 (m-40) cc_final: 0.7878 (p0) REVERT: D 67 MET cc_start: 0.9358 (mmm) cc_final: 0.8788 (mmm) REVERT: D 71 MET cc_start: 0.9071 (mtm) cc_final: 0.8555 (mtm) REVERT: D 142 MET cc_start: 0.8218 (ptt) cc_final: 0.7581 (ppp) REVERT: D 162 CYS cc_start: 0.9258 (m) cc_final: 0.8574 (t) REVERT: E 104 ILE cc_start: 0.6494 (OUTLIER) cc_final: 0.6144 (mp) REVERT: E 141 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: E 297 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6982 (tm-30) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.2452 time to fit residues: 46.7789 Evaluate side-chains 119 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 294 LEU 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 34 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 239 VAL 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 70 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15089 Z= 0.250 Angle : 0.591 9.846 20461 Z= 0.305 Chirality : 0.040 0.215 2335 Planarity : 0.003 0.031 2510 Dihedral : 11.263 171.784 2517 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.59 % Allowed : 17.87 % Favored : 80.53 % 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: 0.41 (0.21), residues: 1800 helix: 1.51 (0.15), residues: 1190 sheet: -1.77 (0.42), residues: 125 loop : -2.34 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 260 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE C 219 TYR 0.013 0.001 TYR E 347 ARG 0.004 0.000 ARG B 238 *********************** 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 127 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.9014 (mtp) cc_final: 0.8690 (mtp) REVERT: C 105 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.5862 (p0) REVERT: C 142 MET cc_start: 0.7919 (tmm) cc_final: 0.7655 (tmm) REVERT: C 270 ILE cc_start: 0.9417 (pt) cc_final: 0.9143 (tp) REVERT: C 278 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: A 48 CYS cc_start: 0.8048 (m) cc_final: 0.7604 (t) REVERT: A 74 LEU cc_start: 0.8712 (tp) cc_final: 0.8387 (tt) REVERT: B 162 CYS cc_start: 0.9191 (m) cc_final: 0.8725 (m) REVERT: B 271 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: B 297 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 50 MET cc_start: 0.8656 (mtt) cc_final: 0.8345 (mtp) REVERT: D 67 MET cc_start: 0.9366 (mmm) cc_final: 0.8835 (mmm) REVERT: D 71 MET cc_start: 0.9070 (mtm) cc_final: 0.8555 (mtm) REVERT: D 142 MET cc_start: 0.8259 (ptt) cc_final: 0.7105 (ppp) REVERT: D 162 CYS cc_start: 0.9255 (m) cc_final: 0.8819 (m) REVERT: E 104 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6163 (mp) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.2431 time to fit residues: 46.5437 Evaluate side-chains 120 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 35 THR 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 262 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 239 VAL 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 154 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN A 59 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15089 Z= 0.138 Angle : 0.567 12.829 20461 Z= 0.286 Chirality : 0.038 0.250 2335 Planarity : 0.003 0.057 2510 Dihedral : 11.182 171.368 2517 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 18.21 % Favored : 80.47 % 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: 0.58 (0.21), residues: 1800 helix: 1.62 (0.15), residues: 1200 sheet: -1.59 (0.44), residues: 125 loop : -2.33 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 260 HIS 0.003 0.001 HIS C 225 PHE 0.009 0.001 PHE C 219 TYR 0.006 0.001 TYR C 347 ARG 0.012 0.000 ARG B 101 *********************** 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 125 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.9001 (mtp) cc_final: 0.8650 (mtp) REVERT: C 105 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.5735 (p0) REVERT: C 142 MET cc_start: 0.7988 (tmm) cc_final: 0.7667 (tmm) REVERT: C 270 ILE cc_start: 0.9380 (pt) cc_final: 0.9096 (tp) REVERT: C 278 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: A 48 CYS cc_start: 0.8066 (m) cc_final: 0.7665 (t) REVERT: A 74 LEU cc_start: 0.8816 (tp) cc_final: 0.8481 (tt) REVERT: A 257 MET cc_start: 0.8784 (mmt) cc_final: 0.8411 (mmt) REVERT: A 271 MET cc_start: 0.8101 (tpp) cc_final: 0.7743 (tpp) REVERT: B 162 CYS cc_start: 0.9172 (m) cc_final: 0.8739 (m) REVERT: B 271 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: B 297 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 50 MET cc_start: 0.8689 (mtt) cc_final: 0.8378 (mtp) REVERT: D 67 MET cc_start: 0.9305 (mmm) cc_final: 0.8686 (mmm) REVERT: D 71 MET cc_start: 0.9042 (mtm) cc_final: 0.8516 (mtm) REVERT: D 142 MET cc_start: 0.8098 (ptt) cc_final: 0.7084 (ppp) REVERT: D 162 CYS cc_start: 0.9181 (m) cc_final: 0.8825 (m) REVERT: E 67 MET cc_start: 0.8838 (mmm) cc_final: 0.8436 (mmt) REVERT: E 104 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6320 (mp) REVERT: E 138 MET cc_start: 0.9077 (mmm) cc_final: 0.8769 (mmm) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 0.2565 time to fit residues: 47.4432 Evaluate side-chains 115 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 35 THR 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 35 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 9.9990 chunk 106 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS E 16 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15089 Z= 0.161 Angle : 0.565 11.704 20461 Z= 0.285 Chirality : 0.038 0.220 2335 Planarity : 0.003 0.049 2510 Dihedral : 11.132 170.670 2517 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.26 % Allowed : 18.47 % Favored : 80.27 % 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: 0.62 (0.21), residues: 1800 helix: 1.61 (0.15), residues: 1205 sheet: -1.60 (0.44), residues: 125 loop : -2.23 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 260 HIS 0.004 0.001 HIS B 100 PHE 0.010 0.001 PHE C 219 TYR 0.008 0.001 TYR E 347 ARG 0.005 0.000 ARG B 101 ********************** 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 120 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.9016 (mtp) cc_final: 0.8678 (mtp) REVERT: C 105 ASN cc_start: 0.6664 (OUTLIER) cc_final: 0.5706 (p0) REVERT: C 142 MET cc_start: 0.7912 (tmm) cc_final: 0.7581 (tmm) REVERT: C 270 ILE cc_start: 0.9380 (pt) cc_final: 0.9130 (tp) REVERT: A 48 CYS cc_start: 0.8095 (m) cc_final: 0.7674 (t) REVERT: A 74 LEU cc_start: 0.8915 (tp) cc_final: 0.8602 (tt) REVERT: A 257 MET cc_start: 0.8846 (mmt) cc_final: 0.8505 (mmt) REVERT: A 271 MET cc_start: 0.8109 (tpp) cc_final: 0.7783 (tpp) REVERT: B 162 CYS cc_start: 0.9198 (m) cc_final: 0.8760 (m) REVERT: B 271 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: B 297 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 50 MET cc_start: 0.8674 (mtt) cc_final: 0.8367 (mtp) REVERT: D 67 MET cc_start: 0.9313 (mmm) cc_final: 0.8699 (mmm) REVERT: D 71 MET cc_start: 0.9055 (mtm) cc_final: 0.8526 (mtm) REVERT: D 142 MET cc_start: 0.8069 (ptt) cc_final: 0.7076 (ppp) REVERT: D 162 CYS cc_start: 0.9196 (m) cc_final: 0.8799 (m) REVERT: E 67 MET cc_start: 0.8837 (mmm) cc_final: 0.8451 (mmt) REVERT: E 109 MET cc_start: 0.7504 (tpt) cc_final: 0.6839 (mtm) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2704 time to fit residues: 48.1771 Evaluate side-chains 113 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 105 ASN 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 35 THR Chi-restraints excluded: chain E residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS E 16 GLN E 105 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.047023 restraints weight = 79865.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.048256 restraints weight = 45089.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049090 restraints weight = 31061.417| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15089 Z= 0.216 Angle : 0.604 11.841 20461 Z= 0.305 Chirality : 0.039 0.212 2335 Planarity : 0.003 0.058 2510 Dihedral : 11.155 171.183 2517 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.13 % Allowed : 18.47 % 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: 0.59 (0.21), residues: 1800 helix: 1.53 (0.15), residues: 1225 sheet: -1.58 (0.43), residues: 125 loop : -2.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 260 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.001 PHE C 219 TYR 0.018 0.001 TYR C 288 ARG 0.004 0.000 ARG B 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.18 seconds wall clock time: 49 minutes 46.86 seconds (2986.86 seconds total)