Starting phenix.real_space_refine on Wed Mar 4 13:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452.map" model { file = "/net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crh_30452/03_2026/7crh_30452_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.028 sd= 0.458 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7235 atoms to isotropic. 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 S 53 5.16 5 Cl 1 4.86 5 C 5128 2.51 5 N 1402 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8068 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2145 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'GBU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8068 At special positions: 0 Unit cell: (82.45, 100.3, 130.05, 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) Cl 1 17.00 S 53 16.00 O 1484 8.00 N 1402 7.00 C 5128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.41 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 303.3 milliseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 11 sheets defined 41.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.545A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.669A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.265A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.794A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.675A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.055A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'R' and resid 21 through 51 removed outlier: 3.661A pdb=" N LEU R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA R 27 " --> pdb=" O ARG R 23 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS R 28 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.122A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.750A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 124 removed outlier: 3.652A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 162 removed outlier: 3.698A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.752A pdb=" N LEU R 161 " --> pdb=" O ILE R 157 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER R 162 " --> pdb=" O PRO R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 203 removed outlier: 4.337A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.569A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS R 237 " --> pdb=" O ARG R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 295 removed outlier: 4.392A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.196A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 332 removed outlier: 3.665A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.947A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 290 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 248 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.511A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 123 Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.908A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.772A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.933A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 8.269A pdb=" N VAL N 12 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR N 125 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2627 1.35 - 1.46: 2032 1.46 - 1.58: 3504 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8236 Sorted by residual: bond pdb=" C01 GBU R 501 " pdb=" N02 GBU R 501 " ideal model delta sigma weight residual 1.448 1.279 0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C10 GBU R 501 " pdb=" O11 GBU R 501 " ideal model delta sigma weight residual 1.347 1.481 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C08 GBU R 501 " pdb=" O09 GBU R 501 " ideal model delta sigma weight residual 1.349 1.469 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C20 GBU R 501 " pdb=" C21 GBU R 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C08 GBU R 501 " pdb=" C10 GBU R 501 " ideal model delta sigma weight residual 1.395 1.331 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 8231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 10962 1.75 - 3.49: 178 3.49 - 5.24: 28 5.24 - 6.99: 3 6.99 - 8.73: 2 Bond angle restraints: 11173 Sorted by residual: angle pdb=" N GLY A 355 " pdb=" CA GLY A 355 " pdb=" C GLY A 355 " ideal model delta sigma weight residual 115.30 110.39 4.91 1.39e+00 5.18e-01 1.25e+01 angle pdb=" N ASN R 292 " pdb=" CA ASN R 292 " pdb=" C ASN R 292 " ideal model delta sigma weight residual 113.01 109.12 3.89 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 110.27 3.20 1.01e+00 9.80e-01 1.00e+01 angle pdb=" C LEU R 76 " pdb=" N VAL R 77 " pdb=" CA VAL R 77 " ideal model delta sigma weight residual 122.77 119.55 3.22 1.05e+00 9.07e-01 9.41e+00 angle pdb=" C PHE R 156 " pdb=" N ILE R 157 " pdb=" CA ILE R 157 " ideal model delta sigma weight residual 120.33 122.71 -2.38 8.00e-01 1.56e+00 8.86e+00 ... (remaining 11168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 4625 24.52 - 49.04: 247 49.04 - 73.56: 19 73.56 - 98.08: 3 98.08 - 122.60: 2 Dihedral angle restraints: 4896 sinusoidal: 1880 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -124.42 38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA SER R 162 " pdb=" C SER R 162 " pdb=" N TRP R 163 " pdb=" CA TRP R 163 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA CYS R 307 " pdb=" C CYS R 307 " pdb=" N ILE R 308 " pdb=" CA ILE R 308 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1153 0.071 - 0.142: 116 0.142 - 0.214: 1 0.214 - 0.285: 0 0.285 - 0.356: 1 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C14 GBU R 501 " pdb=" C06 GBU R 501 " pdb=" C15 GBU R 501 " pdb=" C16 GBU R 501 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB THR R 42 " pdb=" CA THR R 42 " pdb=" OG1 THR R 42 " pdb=" CG2 THR R 42 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA VAL B 100 " pdb=" N VAL B 100 " pdb=" C VAL B 100 " pdb=" CB VAL B 100 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1268 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 136 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO R 137 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 137 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 137 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 327 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO R 328 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 328 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 328 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 117 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ILE R 117 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 117 " -0.010 2.00e-02 2.50e+03 pdb=" N SER R 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 20 2.42 - 3.04: 4853 3.04 - 3.66: 12227 3.66 - 4.28: 16992 4.28 - 4.90: 28543 Nonbonded interactions: 62635 Sorted by model distance: nonbonded pdb=" NH2 ARG A 232 " pdb=" SG CYS B 204 " model vdw 1.798 3.480 nonbonded pdb=" O TYR B 59 " pdb=" SG CYS B 317 " model vdw 1.925 3.400 nonbonded pdb=" O ASP B 290 " pdb=" OD1 ASP B 290 " model vdw 2.121 3.040 nonbonded pdb=" O ALA R 322 " pdb=" OG SER R 325 " model vdw 2.176 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.238 3.040 ... (remaining 62630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.006 0.374 8240 Z= 0.298 Angle : 0.652 25.196 11181 Z= 0.377 Chirality : 0.041 0.356 1271 Planarity : 0.003 0.041 1417 Dihedral : 14.074 122.598 2924 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.40 % Allowed : 23.31 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.23), residues: 1015 helix: -1.18 (0.23), residues: 406 sheet: -1.48 (0.32), residues: 210 loop : -2.62 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 105 TYR 0.006 0.001 TYR B 59 PHE 0.007 0.001 PHE R 297 TRP 0.008 0.001 TRP B 339 HIS 0.001 0.000 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8236) covalent geometry : angle 0.58058 (11173) SS BOND : bond 0.18721 ( 4) SS BOND : angle 11.12532 ( 8) hydrogen bonds : bond 0.16312 ( 405) hydrogen bonds : angle 6.25649 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 297 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 284 THR cc_start: 0.9315 (p) cc_final: 0.9071 (t) REVERT: A 309 GLU cc_start: 0.7794 (tp30) cc_final: 0.6890 (mt-10) REVERT: A 317 ARG cc_start: 0.7887 (mmp-170) cc_final: 0.7286 (mtm-85) REVERT: B 32 GLN cc_start: 0.7103 (pt0) cc_final: 0.6708 (tp-100) REVERT: G 20 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8258 (tppt) REVERT: N 69 THR cc_start: 0.7474 (p) cc_final: 0.7232 (p) REVERT: R 61 PHE cc_start: 0.7811 (m-80) cc_final: 0.7602 (m-10) REVERT: R 118 SER cc_start: 0.9172 (m) cc_final: 0.8906 (p) REVERT: R 157 ILE cc_start: 0.8373 (mt) cc_final: 0.8145 (mp) REVERT: R 268 THR cc_start: 0.8352 (p) cc_final: 0.8052 (t) REVERT: R 290 ILE cc_start: 0.9350 (tp) cc_final: 0.9144 (tp) outliers start: 12 outliers final: 6 residues processed: 305 average time/residue: 0.0888 time to fit residues: 36.9179 Evaluate side-chains 205 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain R residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 213 GLN A 264 ASN A 271 ASN B 175 GLN B 230 ASN N 31 ASN N 39 GLN N 82 GLN R 323 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098667 restraints weight = 20416.161| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.25 r_work: 0.3403 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8240 Z= 0.154 Angle : 0.637 10.289 11181 Z= 0.330 Chirality : 0.043 0.182 1271 Planarity : 0.004 0.053 1417 Dihedral : 6.745 111.930 1148 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.71 % Allowed : 22.73 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.25), residues: 1015 helix: 0.12 (0.25), residues: 410 sheet: -0.95 (0.34), residues: 202 loop : -2.21 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.016 0.001 TYR B 145 PHE 0.022 0.001 PHE R 289 TRP 0.012 0.001 TRP B 339 HIS 0.011 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8236) covalent geometry : angle 0.63573 (11173) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.52391 ( 8) hydrogen bonds : bond 0.04596 ( 405) hydrogen bonds : angle 4.75582 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.323 Fit side-chains REVERT: A 264 ASN cc_start: 0.8319 (m-40) cc_final: 0.7695 (m110) REVERT: A 309 GLU cc_start: 0.8259 (tp30) cc_final: 0.7271 (mt-10) REVERT: A 317 ARG cc_start: 0.7821 (mmp-170) cc_final: 0.7168 (mtm-85) REVERT: B 254 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7373 (p0) REVERT: B 275 SER cc_start: 0.8982 (t) cc_final: 0.8763 (p) REVERT: R 25 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8033 (pp) REVERT: R 61 PHE cc_start: 0.8066 (m-80) cc_final: 0.7809 (m-10) REVERT: R 118 SER cc_start: 0.9189 (m) cc_final: 0.8922 (p) REVERT: R 157 ILE cc_start: 0.8480 (mt) cc_final: 0.8245 (mp) REVERT: R 290 ILE cc_start: 0.9477 (tp) cc_final: 0.9242 (tp) REVERT: R 333 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (t80) REVERT: R 339 LYS cc_start: 0.8900 (tppt) cc_final: 0.8680 (tppt) outliers start: 49 outliers final: 23 residues processed: 252 average time/residue: 0.0782 time to fit residues: 27.9793 Evaluate side-chains 214 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 384 GLN B 340 ASN N 31 ASN N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096735 restraints weight = 20512.229| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.25 r_work: 0.3380 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8240 Z= 0.149 Angle : 0.616 9.133 11181 Z= 0.321 Chirality : 0.043 0.171 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.432 107.556 1142 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.71 % Allowed : 24.48 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.25), residues: 1015 helix: 0.38 (0.25), residues: 412 sheet: -0.82 (0.33), residues: 208 loop : -2.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.013 0.001 TYR A 358 PHE 0.018 0.001 PHE R 203 TRP 0.010 0.001 TRP B 339 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8236) covalent geometry : angle 0.61491 (11173) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.38551 ( 8) hydrogen bonds : bond 0.04406 ( 405) hydrogen bonds : angle 4.67985 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.326 Fit side-chains REVERT: A 317 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7247 (mtm-85) REVERT: A 327 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5734 (mp0) REVERT: B 3 GLU cc_start: 0.7132 (mp0) cc_final: 0.6919 (mp0) REVERT: B 254 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7440 (p0) REVERT: B 264 TYR cc_start: 0.8736 (m-80) cc_final: 0.8497 (m-80) REVERT: N 64 VAL cc_start: 0.8736 (t) cc_final: 0.8323 (p) REVERT: N 108 PHE cc_start: 0.3406 (OUTLIER) cc_final: 0.1723 (p90) REVERT: N 109 ASP cc_start: 0.7508 (m-30) cc_final: 0.7080 (m-30) REVERT: R 25 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7960 (pp) REVERT: R 118 SER cc_start: 0.9201 (m) cc_final: 0.8943 (p) REVERT: R 157 ILE cc_start: 0.8570 (mt) cc_final: 0.8344 (mp) REVERT: R 290 ILE cc_start: 0.9470 (tp) cc_final: 0.9241 (tp) REVERT: R 333 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7896 (t80) REVERT: R 339 LYS cc_start: 0.8934 (tppt) cc_final: 0.8671 (tppt) REVERT: R 341 PHE cc_start: 0.7315 (t80) cc_final: 0.7052 (t80) outliers start: 49 outliers final: 31 residues processed: 233 average time/residue: 0.0724 time to fit residues: 24.6168 Evaluate side-chains 208 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 0.0470 chunk 29 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096790 restraints weight = 20711.884| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.27 r_work: 0.3380 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8240 Z= 0.129 Angle : 0.595 9.750 11181 Z= 0.309 Chirality : 0.042 0.155 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.308 104.145 1142 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.24 % Allowed : 26.46 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 1015 helix: 0.52 (0.25), residues: 414 sheet: -0.75 (0.34), residues: 209 loop : -2.02 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.011 0.001 TYR A 358 PHE 0.014 0.001 PHE B 292 TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8236) covalent geometry : angle 0.59379 (11173) SS BOND : bond 0.00615 ( 4) SS BOND : angle 1.58106 ( 8) hydrogen bonds : bond 0.04182 ( 405) hydrogen bonds : angle 4.63498 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.323 Fit side-chains REVERT: A 309 GLU cc_start: 0.7347 (tp30) cc_final: 0.6086 (mt-10) REVERT: A 327 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5721 (mp0) REVERT: B 3 GLU cc_start: 0.7133 (mp0) cc_final: 0.6897 (mp0) REVERT: B 254 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 264 TYR cc_start: 0.8646 (m-80) cc_final: 0.8432 (m-80) REVERT: N 108 PHE cc_start: 0.3302 (OUTLIER) cc_final: 0.1640 (p90) REVERT: N 109 ASP cc_start: 0.7634 (m-30) cc_final: 0.7227 (m-30) REVERT: R 25 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7929 (pp) REVERT: R 104 ILE cc_start: 0.8882 (pt) cc_final: 0.8676 (tt) REVERT: R 118 SER cc_start: 0.9159 (m) cc_final: 0.8921 (p) REVERT: R 157 ILE cc_start: 0.8606 (mt) cc_final: 0.8378 (mp) REVERT: R 290 ILE cc_start: 0.9431 (tp) cc_final: 0.9186 (tp) REVERT: R 339 LYS cc_start: 0.8953 (tppt) cc_final: 0.8671 (tppt) REVERT: R 341 PHE cc_start: 0.7305 (t80) cc_final: 0.6908 (t80) outliers start: 45 outliers final: 25 residues processed: 229 average time/residue: 0.0695 time to fit residues: 23.2762 Evaluate side-chains 214 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 384 GLN B 340 ASN N 31 ASN N 39 GLN R 53 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097885 restraints weight = 20731.290| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.32 r_work: 0.3395 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8240 Z= 0.115 Angle : 0.587 10.028 11181 Z= 0.303 Chirality : 0.041 0.170 1271 Planarity : 0.003 0.056 1417 Dihedral : 6.174 101.430 1142 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.01 % Allowed : 27.27 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1015 helix: 0.68 (0.25), residues: 413 sheet: -0.52 (0.34), residues: 209 loop : -1.92 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.009 0.001 TYR A 358 PHE 0.012 0.001 PHE R 203 TRP 0.008 0.001 TRP R 318 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8236) covalent geometry : angle 0.58624 (11173) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.29700 ( 8) hydrogen bonds : bond 0.03954 ( 405) hydrogen bonds : angle 4.53273 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.311 Fit side-chains REVERT: A 216 LYS cc_start: 0.9222 (mppt) cc_final: 0.8928 (mmtt) REVERT: A 255 MET cc_start: 0.2205 (pmm) cc_final: 0.1123 (pmm) REVERT: A 264 ASN cc_start: 0.8322 (m-40) cc_final: 0.7657 (m110) REVERT: A 309 GLU cc_start: 0.7318 (tp30) cc_final: 0.6115 (mt-10) REVERT: A 327 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5710 (mp0) REVERT: B 3 GLU cc_start: 0.7056 (mp0) cc_final: 0.6827 (mp0) REVERT: B 12 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 254 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7556 (p0) REVERT: B 261 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7831 (mm) REVERT: N 108 PHE cc_start: 0.3100 (OUTLIER) cc_final: 0.1631 (p90) REVERT: N 109 ASP cc_start: 0.7658 (m-30) cc_final: 0.7416 (m-30) REVERT: R 25 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7898 (pp) REVERT: R 104 ILE cc_start: 0.8877 (pt) cc_final: 0.8675 (tt) REVERT: R 118 SER cc_start: 0.9113 (m) cc_final: 0.8862 (p) REVERT: R 157 ILE cc_start: 0.8663 (mt) cc_final: 0.8436 (mp) REVERT: R 290 ILE cc_start: 0.9418 (tp) cc_final: 0.9159 (tp) REVERT: R 339 LYS cc_start: 0.8975 (tppt) cc_final: 0.8661 (tppt) REVERT: R 341 PHE cc_start: 0.7215 (t80) cc_final: 0.6745 (t80) outliers start: 43 outliers final: 22 residues processed: 248 average time/residue: 0.0751 time to fit residues: 26.8712 Evaluate side-chains 214 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN N 31 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097184 restraints weight = 20424.257| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.26 r_work: 0.3378 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8240 Z= 0.128 Angle : 0.619 11.538 11181 Z= 0.314 Chirality : 0.042 0.202 1271 Planarity : 0.003 0.053 1417 Dihedral : 6.171 100.312 1142 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.94 % Allowed : 26.69 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1015 helix: 0.76 (0.26), residues: 414 sheet: -0.27 (0.34), residues: 211 loop : -1.86 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.017 0.001 TYR B 264 PHE 0.016 0.001 PHE N 68 TRP 0.011 0.001 TRP R 318 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8236) covalent geometry : angle 0.61863 (11173) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.34394 ( 8) hydrogen bonds : bond 0.04025 ( 405) hydrogen bonds : angle 4.49725 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.310 Fit side-chains REVERT: A 216 LYS cc_start: 0.9184 (mppt) cc_final: 0.8956 (mmtt) REVERT: A 309 GLU cc_start: 0.7419 (tp30) cc_final: 0.6203 (mt-10) REVERT: A 327 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: B 3 GLU cc_start: 0.7086 (mp0) cc_final: 0.6865 (mp0) REVERT: B 254 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7600 (p0) REVERT: B 261 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7802 (mm) REVERT: G 19 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8359 (mp) REVERT: N 32 TYR cc_start: 0.7982 (m-80) cc_final: 0.7698 (m-80) REVERT: N 108 PHE cc_start: 0.3287 (OUTLIER) cc_final: 0.1756 (p90) REVERT: N 109 ASP cc_start: 0.7764 (m-30) cc_final: 0.7552 (m-30) REVERT: R 25 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7899 (pp) REVERT: R 78 MET cc_start: 0.8821 (tpp) cc_final: 0.8171 (tpp) REVERT: R 118 SER cc_start: 0.9160 (m) cc_final: 0.8918 (p) REVERT: R 157 ILE cc_start: 0.8646 (mt) cc_final: 0.8411 (mp) REVERT: R 290 ILE cc_start: 0.9417 (tp) cc_final: 0.9170 (tp) REVERT: R 339 LYS cc_start: 0.8999 (tppt) cc_final: 0.8692 (tppt) REVERT: R 341 PHE cc_start: 0.7222 (t80) cc_final: 0.6688 (t80) outliers start: 51 outliers final: 34 residues processed: 235 average time/residue: 0.0694 time to fit residues: 23.9172 Evaluate side-chains 230 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN N 31 ASN N 39 GLN R 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097541 restraints weight = 20660.653| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.31 r_work: 0.3383 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8240 Z= 0.124 Angle : 0.645 12.609 11181 Z= 0.323 Chirality : 0.042 0.223 1271 Planarity : 0.003 0.054 1417 Dihedral : 6.347 105.013 1142 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.94 % Allowed : 27.51 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.26), residues: 1015 helix: 0.87 (0.26), residues: 409 sheet: -0.36 (0.34), residues: 203 loop : -1.82 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.015 0.001 TYR B 264 PHE 0.017 0.001 PHE N 68 TRP 0.008 0.001 TRP R 80 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8236) covalent geometry : angle 0.64393 (11173) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.33811 ( 8) hydrogen bonds : bond 0.03955 ( 405) hydrogen bonds : angle 4.45966 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.267 Fit side-chains REVERT: A 216 LYS cc_start: 0.9147 (mppt) cc_final: 0.8905 (mmtt) REVERT: A 309 GLU cc_start: 0.7465 (tp30) cc_final: 0.6235 (mt-10) REVERT: A 327 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5728 (mp0) REVERT: B 3 GLU cc_start: 0.7074 (mp0) cc_final: 0.6839 (mp0) REVERT: B 254 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7543 (p0) REVERT: B 261 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7763 (mm) REVERT: G 19 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (mp) REVERT: N 32 TYR cc_start: 0.7950 (m-80) cc_final: 0.7594 (m-80) REVERT: N 39 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8255 (pp30) REVERT: N 108 PHE cc_start: 0.3190 (OUTLIER) cc_final: 0.1688 (p90) REVERT: N 109 ASP cc_start: 0.7699 (m-30) cc_final: 0.7440 (m-30) REVERT: R 20 PHE cc_start: 0.4561 (OUTLIER) cc_final: 0.3068 (m-80) REVERT: R 25 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7889 (pp) REVERT: R 118 SER cc_start: 0.9123 (m) cc_final: 0.8881 (p) REVERT: R 157 ILE cc_start: 0.8703 (mt) cc_final: 0.8480 (mp) REVERT: R 290 ILE cc_start: 0.9415 (tp) cc_final: 0.9181 (tp) REVERT: R 339 LYS cc_start: 0.8997 (tppt) cc_final: 0.8703 (tppt) outliers start: 51 outliers final: 36 residues processed: 235 average time/residue: 0.0708 time to fit residues: 23.8521 Evaluate side-chains 232 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN R 53 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095625 restraints weight = 20781.401| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.24 r_work: 0.3357 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8240 Z= 0.155 Angle : 0.671 12.868 11181 Z= 0.339 Chirality : 0.044 0.209 1271 Planarity : 0.004 0.054 1417 Dihedral : 6.460 106.557 1142 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.83 % Allowed : 27.39 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 1015 helix: 0.79 (0.26), residues: 415 sheet: -0.40 (0.35), residues: 203 loop : -1.85 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.015 0.001 TYR B 264 PHE 0.017 0.001 PHE N 68 TRP 0.011 0.001 TRP B 339 HIS 0.009 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8236) covalent geometry : angle 0.66993 (11173) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.51243 ( 8) hydrogen bonds : bond 0.04212 ( 405) hydrogen bonds : angle 4.48235 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.336 Fit side-chains REVERT: A 213 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7278 (tt0) REVERT: A 216 LYS cc_start: 0.9139 (mppt) cc_final: 0.8829 (mmmm) REVERT: A 255 MET cc_start: 0.2430 (pmm) cc_final: 0.2015 (pmm) REVERT: A 309 GLU cc_start: 0.7563 (tp30) cc_final: 0.6277 (mt-10) REVERT: A 327 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: B 3 GLU cc_start: 0.7149 (mp0) cc_final: 0.6926 (mp0) REVERT: B 45 MET cc_start: 0.8049 (tpp) cc_final: 0.7662 (mtt) REVERT: B 254 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7525 (p0) REVERT: B 261 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7699 (mm) REVERT: N 108 PHE cc_start: 0.3252 (OUTLIER) cc_final: 0.1651 (p90) REVERT: R 20 PHE cc_start: 0.4626 (OUTLIER) cc_final: 0.3174 (m-80) REVERT: R 78 MET cc_start: 0.8745 (tpp) cc_final: 0.8532 (tpp) REVERT: R 118 SER cc_start: 0.9165 (m) cc_final: 0.8920 (p) REVERT: R 157 ILE cc_start: 0.8703 (mt) cc_final: 0.8483 (mp) REVERT: R 290 ILE cc_start: 0.9426 (tp) cc_final: 0.9216 (tp) REVERT: R 339 LYS cc_start: 0.8990 (tppt) cc_final: 0.8699 (tppt) outliers start: 50 outliers final: 39 residues processed: 227 average time/residue: 0.0732 time to fit residues: 24.0175 Evaluate side-chains 230 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 50.0000 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 271 ASN N 31 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098610 restraints weight = 20339.103| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.24 r_work: 0.3404 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8240 Z= 0.121 Angle : 0.668 13.666 11181 Z= 0.332 Chirality : 0.043 0.210 1271 Planarity : 0.003 0.055 1417 Dihedral : 6.289 102.122 1142 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.66 % Allowed : 28.67 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.26), residues: 1015 helix: 0.96 (0.26), residues: 406 sheet: -0.43 (0.35), residues: 200 loop : -1.81 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.010 0.001 TYR B 264 PHE 0.018 0.001 PHE N 68 TRP 0.007 0.001 TRP A 234 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8236) covalent geometry : angle 0.66699 (11173) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.28647 ( 8) hydrogen bonds : bond 0.03824 ( 405) hydrogen bonds : angle 4.42167 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.327 Fit side-chains REVERT: A 213 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7382 (tt0) REVERT: A 216 LYS cc_start: 0.9109 (mppt) cc_final: 0.8778 (mmmm) REVERT: A 255 MET cc_start: 0.2490 (pmm) cc_final: 0.2060 (pmm) REVERT: A 309 GLU cc_start: 0.7452 (tp30) cc_final: 0.6195 (mt-10) REVERT: A 327 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5775 (mp0) REVERT: B 3 GLU cc_start: 0.7060 (mp0) cc_final: 0.6832 (mp0) REVERT: B 45 MET cc_start: 0.7984 (tpp) cc_final: 0.7604 (mtt) REVERT: B 219 ARG cc_start: 0.8653 (mmt180) cc_final: 0.8320 (mmm160) REVERT: B 254 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7448 (p0) REVERT: B 261 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7734 (mm) REVERT: N 108 PHE cc_start: 0.2949 (OUTLIER) cc_final: 0.1602 (p90) REVERT: R 118 SER cc_start: 0.9099 (m) cc_final: 0.8862 (p) REVERT: R 157 ILE cc_start: 0.8662 (mt) cc_final: 0.8405 (mp) REVERT: R 290 ILE cc_start: 0.9405 (tp) cc_final: 0.9166 (tp) REVERT: R 339 LYS cc_start: 0.8951 (tppt) cc_final: 0.8660 (tppt) outliers start: 40 outliers final: 31 residues processed: 223 average time/residue: 0.0781 time to fit residues: 24.9624 Evaluate side-chains 225 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096977 restraints weight = 20835.336| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.25 r_work: 0.3373 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8240 Z= 0.136 Angle : 0.677 14.375 11181 Z= 0.340 Chirality : 0.043 0.207 1271 Planarity : 0.003 0.054 1417 Dihedral : 6.343 104.381 1142 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.55 % Allowed : 29.02 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.26), residues: 1015 helix: 0.97 (0.26), residues: 406 sheet: -0.30 (0.35), residues: 201 loop : -1.81 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.016 0.001 TYR N 117 PHE 0.010 0.001 PHE N 103 TRP 0.009 0.001 TRP B 339 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8236) covalent geometry : angle 0.67616 (11173) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.33401 ( 8) hydrogen bonds : bond 0.04008 ( 405) hydrogen bonds : angle 4.43925 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.337 Fit side-chains REVERT: A 213 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7377 (tt0) REVERT: A 216 LYS cc_start: 0.9148 (mppt) cc_final: 0.8839 (mmmm) REVERT: A 255 MET cc_start: 0.2509 (pmm) cc_final: 0.2110 (pmm) REVERT: A 309 GLU cc_start: 0.7520 (tp30) cc_final: 0.6304 (mt-10) REVERT: A 327 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5769 (mp0) REVERT: B 3 GLU cc_start: 0.7105 (mp0) cc_final: 0.6875 (mp0) REVERT: B 45 MET cc_start: 0.8062 (tpp) cc_final: 0.7734 (mtt) REVERT: B 219 ARG cc_start: 0.8653 (mmt180) cc_final: 0.8315 (mmm160) REVERT: B 246 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 254 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7499 (p0) REVERT: B 261 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7682 (mm) REVERT: N 108 PHE cc_start: 0.3048 (OUTLIER) cc_final: 0.1702 (p90) REVERT: R 78 MET cc_start: 0.8820 (tpp) cc_final: 0.8494 (tpp) REVERT: R 118 SER cc_start: 0.9133 (m) cc_final: 0.8895 (p) REVERT: R 157 ILE cc_start: 0.8616 (mt) cc_final: 0.8348 (mp) REVERT: R 290 ILE cc_start: 0.9397 (tp) cc_final: 0.9181 (tp) REVERT: R 339 LYS cc_start: 0.8950 (tppt) cc_final: 0.8659 (tppt) outliers start: 39 outliers final: 32 residues processed: 212 average time/residue: 0.0742 time to fit residues: 22.6785 Evaluate side-chains 219 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095791 restraints weight = 20716.437| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.22 r_work: 0.3357 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8240 Z= 0.152 Angle : 0.686 14.663 11181 Z= 0.346 Chirality : 0.044 0.208 1271 Planarity : 0.004 0.054 1417 Dihedral : 6.448 105.803 1142 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.66 % Allowed : 29.60 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1015 helix: 0.92 (0.26), residues: 406 sheet: -0.26 (0.35), residues: 201 loop : -1.80 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.016 0.002 TYR N 117 PHE 0.023 0.001 PHE N 103 TRP 0.012 0.001 TRP B 339 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8236) covalent geometry : angle 0.68521 (11173) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.39114 ( 8) hydrogen bonds : bond 0.04192 ( 405) hydrogen bonds : angle 4.44300 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.37 seconds wall clock time: 31 minutes 29.53 seconds (1889.53 seconds total)