Starting phenix.real_space_refine on Thu Jul 31 20:34:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crh_30452/07_2025/7crh_30452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crh_30452/07_2025/7crh_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_30452/07_2025/7crh_30452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crh_30452/07_2025/7crh_30452.map" model { file = "/net/cci-nas-00/data/ceres_data/7crh_30452/07_2025/7crh_30452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crh_30452/07_2025/7crh_30452_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.028 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 2, 'ARG: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: 5.31, per 1000 atoms: 0.66 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: 1.94 Conformation dependent library (CDL) restraints added in 894.3 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: 0.82 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: 2.09 Time building geometry restraints manager: 2.29 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- 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 : 10.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (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 TRP 0.008 0.001 TRP B 339 HIS 0.001 0.000 HIS B 311 PHE 0.007 0.001 PHE R 297 TYR 0.006 0.001 TYR B 59 ARG 0.002 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.16312 ( 405) hydrogen bonds : angle 6.25649 ( 1158) SS BOND : bond 0.18721 ( 4) SS BOND : angle 11.12532 ( 8) covalent geometry : bond 0.00406 ( 8236) covalent geometry : angle 0.58058 (11173) *********************** 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 : 0.931 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: 0.7886 (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: 0.7601 (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: 0.1945 time to fit residues: 79.4158 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 : 0.813 ------------------------------------------------------------------------------- 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 85 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 264 ASN A 271 ASN A 384 GLN B 175 GLN B 230 ASN G 44 HIS N 31 ASN N 39 GLN N 82 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097774 restraints weight = 20283.559| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.22 r_work: 0.3395 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8240 Z= 0.158 Angle : 0.642 10.021 11181 Z= 0.334 Chirality : 0.043 0.193 1271 Planarity : 0.004 0.054 1417 Dihedral : 6.769 111.758 1148 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.59 % Allowed : 22.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1015 helix: 0.24 (0.25), residues: 400 sheet: -0.96 (0.34), residues: 202 loop : -2.11 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.011 0.001 HIS B 225 PHE 0.022 0.001 PHE R 289 TYR 0.016 0.001 TYR B 145 ARG 0.005 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 405) hydrogen bonds : angle 4.76419 ( 1158) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.32074 ( 8) covalent geometry : bond 0.00352 ( 8236) covalent geometry : angle 0.64146 (11173) *********************** 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 263 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.892 Fit side-chains REVERT: A 309 GLU cc_start: 0.8299 (tp30) cc_final: 0.7294 (mt-10) REVERT: A 317 ARG cc_start: 0.7858 (mmp-170) cc_final: 0.7208 (mtm-85) REVERT: B 3 GLU cc_start: 0.7118 (mp0) cc_final: 0.6909 (mp0) REVERT: B 254 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7415 (p0) REVERT: B 293 ASN cc_start: 0.8482 (m110) cc_final: 0.8278 (p0) REVERT: R 25 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8028 (pp) REVERT: R 61 PHE cc_start: 0.8088 (m-80) cc_final: 0.7844 (m-10) REVERT: R 118 SER cc_start: 0.9173 (m) cc_final: 0.8918 (p) REVERT: R 157 ILE cc_start: 0.8465 (mt) cc_final: 0.8234 (mp) REVERT: R 290 ILE cc_start: 0.9476 (tp) cc_final: 0.9247 (tp) REVERT: R 333 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7828 (t80) REVERT: R 339 LYS cc_start: 0.8908 (tppt) cc_final: 0.8687 (tppt) outliers start: 48 outliers final: 25 residues processed: 248 average time/residue: 0.1799 time to fit residues: 62.6801 Evaluate side-chains 212 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 97 SER 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 29 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 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 ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096685 restraints weight = 20751.131| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.26 r_work: 0.3368 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8240 Z= 0.152 Angle : 0.615 8.789 11181 Z= 0.321 Chirality : 0.043 0.175 1271 Planarity : 0.004 0.056 1417 Dihedral : 6.402 106.119 1142 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.01 % Allowed : 25.41 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1015 helix: 0.34 (0.25), residues: 412 sheet: -0.75 (0.33), residues: 202 loop : -2.08 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.011 0.001 HIS B 225 PHE 0.018 0.001 PHE R 203 TYR 0.012 0.001 TYR A 358 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 405) hydrogen bonds : angle 4.65399 ( 1158) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.34101 ( 8) covalent geometry : bond 0.00345 ( 8236) covalent geometry : angle 0.61385 (11173) *********************** 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 240 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.911 Fit side-chains REVERT: A 317 ARG cc_start: 0.7891 (mmp-170) cc_final: 0.7242 (mtm-85) REVERT: A 327 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: B 3 GLU cc_start: 0.7128 (mp0) cc_final: 0.6910 (mp0) REVERT: B 254 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7436 (p0) REVERT: B 264 TYR cc_start: 0.8743 (m-80) cc_final: 0.8433 (m-80) REVERT: N 64 VAL cc_start: 0.8748 (t) cc_final: 0.8326 (p) REVERT: N 108 PHE cc_start: 0.3407 (OUTLIER) cc_final: 0.1794 (p90) REVERT: N 109 ASP cc_start: 0.7586 (m-30) cc_final: 0.7177 (m-30) REVERT: R 25 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7938 (pp) REVERT: R 61 PHE cc_start: 0.8092 (m-80) cc_final: 0.7884 (m-10) REVERT: R 104 ILE cc_start: 0.8888 (pt) cc_final: 0.8646 (tt) REVERT: R 118 SER cc_start: 0.9200 (m) cc_final: 0.8944 (p) REVERT: R 157 ILE cc_start: 0.8561 (mt) cc_final: 0.8339 (mp) REVERT: R 290 ILE cc_start: 0.9468 (tp) cc_final: 0.9243 (tp) REVERT: R 333 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7917 (t80) REVERT: R 339 LYS cc_start: 0.8941 (tppt) cc_final: 0.8672 (tppt) REVERT: R 341 PHE cc_start: 0.7328 (t80) cc_final: 0.7053 (t80) outliers start: 43 outliers final: 26 residues processed: 227 average time/residue: 0.1635 time to fit residues: 53.1393 Evaluate side-chains 202 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 327 GLU 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 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER 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 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 15 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 31 ASN N 39 GLN N 53 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096675 restraints weight = 20522.220| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.27 r_work: 0.3355 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3218 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= 0.145 Angle : 0.599 9.690 11181 Z= 0.314 Chirality : 0.042 0.154 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.349 103.288 1142 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.29 % Allowed : 26.11 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1015 helix: 0.44 (0.25), residues: 414 sheet: -0.60 (0.34), residues: 198 loop : -2.03 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 90 HIS 0.007 0.001 HIS B 225 PHE 0.013 0.001 PHE R 203 TYR 0.011 0.001 TYR A 358 ARG 0.006 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 405) hydrogen bonds : angle 4.60770 ( 1158) SS BOND : bond 0.00555 ( 4) SS BOND : angle 1.67759 ( 8) covalent geometry : bond 0.00327 ( 8236) covalent geometry : angle 0.59785 (11173) *********************** 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 249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.862 Fit side-chains REVERT: A 255 MET cc_start: 0.2124 (pmm) cc_final: 0.0930 (pmm) REVERT: A 309 GLU cc_start: 0.7405 (tp30) cc_final: 0.5985 (mt-10) REVERT: A 327 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5688 (mp0) REVERT: B 3 GLU cc_start: 0.7071 (mp0) cc_final: 0.6856 (mp0) REVERT: B 254 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7420 (p0) REVERT: B 264 TYR cc_start: 0.8713 (m-80) cc_final: 0.8461 (m-80) REVERT: N 108 PHE cc_start: 0.3549 (OUTLIER) cc_final: 0.1883 (p90) REVERT: N 109 ASP cc_start: 0.7711 (m-30) cc_final: 0.7314 (m-30) REVERT: R 61 PHE cc_start: 0.8070 (m-80) cc_final: 0.7824 (m-10) REVERT: R 78 MET cc_start: 0.8778 (tpp) cc_final: 0.8575 (tpp) REVERT: R 118 SER cc_start: 0.9176 (m) cc_final: 0.8940 (p) REVERT: R 157 ILE cc_start: 0.8621 (mt) cc_final: 0.8395 (mp) REVERT: R 290 ILE cc_start: 0.9436 (tp) cc_final: 0.9206 (tp) REVERT: R 333 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.8004 (t80) REVERT: R 339 LYS cc_start: 0.8960 (tppt) cc_final: 0.8713 (tppt) REVERT: R 341 PHE cc_start: 0.7322 (t80) cc_final: 0.6905 (t80) outliers start: 54 outliers final: 34 residues processed: 233 average time/residue: 0.1567 time to fit residues: 52.5819 Evaluate side-chains 220 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 74 SER Chi-restraints excluded: chain B residue 102 THR 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 B residue 315 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 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR 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 Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 R 53 HIS ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095978 restraints weight = 20255.351| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.23 r_work: 0.3360 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8240 Z= 0.139 Angle : 0.602 10.207 11181 Z= 0.314 Chirality : 0.043 0.166 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.340 101.544 1142 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.64 % Allowed : 26.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.26), residues: 1015 helix: 0.59 (0.25), residues: 412 sheet: -0.45 (0.34), residues: 201 loop : -1.98 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.006 0.001 HIS B 225 PHE 0.019 0.001 PHE B 292 TYR 0.010 0.001 TYR A 358 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 405) hydrogen bonds : angle 4.52088 ( 1158) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.39932 ( 8) covalent geometry : bond 0.00317 ( 8236) covalent geometry : angle 0.60115 (11173) *********************** 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 256 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 0.866 Fit side-chains REVERT: A 216 LYS cc_start: 0.9227 (mppt) cc_final: 0.8911 (mmtt) REVERT: A 230 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7826 (tm-30) REVERT: A 255 MET cc_start: 0.2273 (pmm) cc_final: 0.1192 (pmm) REVERT: A 309 GLU cc_start: 0.7481 (tp30) cc_final: 0.6082 (mt-10) REVERT: A 327 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5747 (mp0) REVERT: A 356 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8460 (mmm160) REVERT: B 3 GLU cc_start: 0.7130 (mp0) cc_final: 0.6917 (mp0) REVERT: B 254 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7504 (p0) REVERT: B 261 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7804 (mm) REVERT: B 264 TYR cc_start: 0.8655 (m-80) cc_final: 0.8403 (m-80) REVERT: N 39 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7786 (pp30) REVERT: N 108 PHE cc_start: 0.3490 (OUTLIER) cc_final: 0.1817 (p90) REVERT: N 109 ASP cc_start: 0.7728 (m-30) cc_final: 0.7525 (m-30) REVERT: R 61 PHE cc_start: 0.8034 (m-80) cc_final: 0.7796 (m-10) REVERT: R 118 SER cc_start: 0.9213 (m) cc_final: 0.9008 (p) REVERT: R 157 ILE cc_start: 0.8652 (mt) cc_final: 0.8428 (mp) REVERT: R 290 ILE cc_start: 0.9443 (tp) cc_final: 0.9202 (tp) REVERT: R 339 LYS cc_start: 0.8996 (tppt) cc_final: 0.8726 (tppt) REVERT: R 341 PHE cc_start: 0.7187 (t80) cc_final: 0.6678 (t80) outliers start: 57 outliers final: 35 residues processed: 238 average time/residue: 0.1543 time to fit residues: 52.6326 Evaluate side-chains 226 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 74 SER Chi-restraints excluded: chain B residue 102 THR 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 B residue 315 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 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR 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 187 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 87 optimal weight: 0.0670 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 R 53 HIS ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093418 restraints weight = 20714.118| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.24 r_work: 0.3329 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8240 Z= 0.192 Angle : 0.647 11.280 11181 Z= 0.339 Chirality : 0.044 0.208 1271 Planarity : 0.004 0.053 1417 Dihedral : 6.545 102.727 1142 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.53 % Allowed : 27.27 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.26), residues: 1015 helix: 0.60 (0.25), residues: 411 sheet: -0.60 (0.33), residues: 215 loop : -1.91 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS B 225 PHE 0.010 0.002 PHE R 62 TYR 0.012 0.002 TYR R 331 ARG 0.003 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 405) hydrogen bonds : angle 4.61511 ( 1158) SS BOND : bond 0.00309 ( 4) SS BOND : angle 1.36046 ( 8) covalent geometry : bond 0.00442 ( 8236) covalent geometry : angle 0.64632 (11173) *********************** 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 246 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.876 Fit side-chains REVERT: A 309 GLU cc_start: 0.7636 (tp30) cc_final: 0.6165 (mt-10) REVERT: B 261 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7942 (mm) REVERT: N 108 PHE cc_start: 0.3873 (OUTLIER) cc_final: 0.2136 (p90) REVERT: R 20 PHE cc_start: 0.5029 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: R 61 PHE cc_start: 0.8099 (m-80) cc_final: 0.7806 (m-10) REVERT: R 104 ILE cc_start: 0.8882 (pt) cc_final: 0.8649 (tt) REVERT: R 118 SER cc_start: 0.9230 (m) cc_final: 0.9000 (p) REVERT: R 157 ILE cc_start: 0.8648 (mt) cc_final: 0.8416 (mp) REVERT: R 290 ILE cc_start: 0.9406 (tp) cc_final: 0.9199 (tp) REVERT: R 339 LYS cc_start: 0.9026 (tppt) cc_final: 0.8726 (tppt) outliers start: 56 outliers final: 41 residues processed: 232 average time/residue: 0.1547 time to fit residues: 51.8912 Evaluate side-chains 221 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 375 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR 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 207 SER 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 B residue 315 VAL 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 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 20 PHE 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 143 LEU Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 187 ASP 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 63 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 384 GLN N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094120 restraints weight = 20508.351| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.24 r_work: 0.3327 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8240 Z= 0.164 Angle : 0.646 11.936 11181 Z= 0.334 Chirality : 0.043 0.221 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.461 100.113 1142 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.64 % Allowed : 27.16 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1015 helix: 0.67 (0.26), residues: 411 sheet: -0.57 (0.34), residues: 213 loop : -1.87 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.012 0.001 HIS B 225 PHE 0.029 0.001 PHE N 103 TYR 0.019 0.001 TYR A 358 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 405) hydrogen bonds : angle 4.54636 ( 1158) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.03375 ( 8) covalent geometry : bond 0.00375 ( 8236) covalent geometry : angle 0.64535 (11173) *********************** 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 249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 0.896 Fit side-chains REVERT: A 216 LYS cc_start: 0.9206 (mppt) cc_final: 0.8928 (mmtt) REVERT: A 255 MET cc_start: 0.2900 (pmm) cc_final: 0.2585 (pmm) REVERT: A 309 GLU cc_start: 0.7662 (tp30) cc_final: 0.6161 (mt-10) REVERT: B 3 GLU cc_start: 0.7210 (mp0) cc_final: 0.6968 (mp0) REVERT: B 254 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7526 (p0) REVERT: B 261 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7766 (mm) REVERT: N 39 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8007 (pp30) REVERT: N 108 PHE cc_start: 0.3679 (OUTLIER) cc_final: 0.1990 (p90) REVERT: R 20 PHE cc_start: 0.5002 (OUTLIER) cc_final: 0.3685 (m-80) REVERT: R 61 PHE cc_start: 0.8101 (m-80) cc_final: 0.7808 (m-10) REVERT: R 78 MET cc_start: 0.8761 (tpp) cc_final: 0.8255 (tpp) REVERT: R 104 ILE cc_start: 0.8916 (pt) cc_final: 0.8680 (tt) REVERT: R 118 SER cc_start: 0.9224 (m) cc_final: 0.9008 (p) REVERT: R 157 ILE cc_start: 0.8683 (mt) cc_final: 0.8450 (mp) REVERT: R 290 ILE cc_start: 0.9398 (tp) cc_final: 0.9194 (tp) REVERT: R 339 LYS cc_start: 0.9016 (tppt) cc_final: 0.8725 (tppt) outliers start: 57 outliers final: 43 residues processed: 233 average time/residue: 0.1688 time to fit residues: 56.3600 Evaluate side-chains 230 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR 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 207 SER 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 281 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER 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 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 20 PHE 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 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094568 restraints weight = 20760.146| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.24 r_work: 0.3327 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8240 Z= 0.153 Angle : 0.660 13.194 11181 Z= 0.338 Chirality : 0.044 0.206 1271 Planarity : 0.004 0.058 1417 Dihedral : 6.411 98.265 1142 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 7.23 % Allowed : 27.16 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 1015 helix: 0.71 (0.26), residues: 411 sheet: -0.53 (0.35), residues: 208 loop : -1.85 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.009 0.001 HIS B 225 PHE 0.014 0.001 PHE N 68 TYR 0.022 0.001 TYR B 264 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 405) hydrogen bonds : angle 4.57172 ( 1158) SS BOND : bond 0.00283 ( 4) SS BOND : angle 1.06057 ( 8) covalent geometry : bond 0.00353 ( 8236) covalent geometry : angle 0.65999 (11173) *********************** 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 252 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.981 Fit side-chains REVERT: A 216 LYS cc_start: 0.9165 (mppt) cc_final: 0.8952 (mmmm) REVERT: A 255 MET cc_start: 0.2877 (pmm) cc_final: 0.2616 (pmm) REVERT: A 309 GLU cc_start: 0.7783 (tp30) cc_final: 0.6202 (mt-10) REVERT: A 327 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: B 3 GLU cc_start: 0.7230 (mp0) cc_final: 0.6967 (mp0) REVERT: B 254 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7499 (p0) REVERT: B 261 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7824 (mm) REVERT: N 83 MET cc_start: 0.8188 (mpp) cc_final: 0.7951 (mmt) REVERT: N 108 PHE cc_start: 0.3636 (OUTLIER) cc_final: 0.1989 (p90) REVERT: R 20 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.3452 (m-80) REVERT: R 61 PHE cc_start: 0.8068 (m-80) cc_final: 0.7796 (m-10) REVERT: R 104 ILE cc_start: 0.8932 (pt) cc_final: 0.8696 (tt) REVERT: R 118 SER cc_start: 0.9224 (m) cc_final: 0.9024 (p) REVERT: R 157 ILE cc_start: 0.8696 (mt) cc_final: 0.8463 (mp) REVERT: R 290 ILE cc_start: 0.9403 (tp) cc_final: 0.9190 (tp) REVERT: R 339 LYS cc_start: 0.9005 (tppt) cc_final: 0.8725 (tppt) outliers start: 62 outliers final: 46 residues processed: 236 average time/residue: 0.1607 time to fit residues: 54.3085 Evaluate side-chains 231 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 215 ASP 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 378 ASP 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 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 CYS 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 171 ILE 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 207 SER 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 281 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER 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 N residue 128 SER Chi-restraints excluded: chain R residue 20 PHE 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 187 ASP 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 79 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 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 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.094698 restraints weight = 20918.949| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.28 r_work: 0.3328 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8240 Z= 0.154 Angle : 0.670 13.615 11181 Z= 0.342 Chirality : 0.044 0.212 1271 Planarity : 0.004 0.058 1417 Dihedral : 6.432 97.864 1142 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.18 % Allowed : 28.32 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.26), residues: 1015 helix: 0.71 (0.26), residues: 412 sheet: -0.68 (0.34), residues: 210 loop : -1.87 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.008 0.001 HIS B 225 PHE 0.030 0.001 PHE N 103 TYR 0.018 0.001 TYR B 264 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 405) hydrogen bonds : angle 4.56646 ( 1158) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.95248 ( 8) covalent geometry : bond 0.00353 ( 8236) covalent geometry : angle 0.66940 (11173) *********************** 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 247 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.875 Fit side-chains REVERT: A 216 LYS cc_start: 0.9161 (mppt) cc_final: 0.8941 (mmmm) REVERT: A 309 GLU cc_start: 0.7744 (tp30) cc_final: 0.6208 (mt-10) REVERT: A 327 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: B 3 GLU cc_start: 0.7274 (mp0) cc_final: 0.7007 (mp0) REVERT: B 246 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: B 254 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7460 (p0) REVERT: B 261 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7714 (mm) REVERT: N 108 PHE cc_start: 0.3540 (OUTLIER) cc_final: 0.1998 (p90) REVERT: R 20 PHE cc_start: 0.4831 (OUTLIER) cc_final: 0.3502 (m-80) REVERT: R 61 PHE cc_start: 0.8061 (m-80) cc_final: 0.7792 (m-10) REVERT: R 78 MET cc_start: 0.8788 (tpp) cc_final: 0.8442 (tpp) REVERT: R 104 ILE cc_start: 0.8908 (pt) cc_final: 0.8679 (tt) REVERT: R 118 SER cc_start: 0.9229 (m) cc_final: 0.9027 (p) REVERT: R 157 ILE cc_start: 0.8730 (mt) cc_final: 0.8491 (mp) REVERT: R 290 ILE cc_start: 0.9406 (tp) cc_final: 0.9195 (tp) REVERT: R 339 LYS cc_start: 0.9011 (tppt) cc_final: 0.8721 (tppt) outliers start: 53 outliers final: 45 residues processed: 232 average time/residue: 0.1601 time to fit residues: 53.1068 Evaluate side-chains 232 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 LEU 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 378 ASP 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 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 CYS 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 171 ILE 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 207 SER 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 269 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL 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 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 187 ASP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095422 restraints weight = 20449.329| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.23 r_work: 0.3349 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8240 Z= 0.141 Angle : 0.672 14.506 11181 Z= 0.342 Chirality : 0.043 0.203 1271 Planarity : 0.004 0.059 1417 Dihedral : 6.354 95.828 1142 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.29 % Allowed : 28.44 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1015 helix: 0.76 (0.26), residues: 412 sheet: -0.57 (0.35), residues: 205 loop : -1.82 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 318 HIS 0.006 0.001 HIS B 225 PHE 0.015 0.001 PHE N 68 TYR 0.014 0.001 TYR A 358 ARG 0.002 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 405) hydrogen bonds : angle 4.53024 ( 1158) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.94749 ( 8) covalent geometry : bond 0.00324 ( 8236) covalent geometry : angle 0.67204 (11173) ********************** 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 244 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.968 Fit side-chains REVERT: A 216 LYS cc_start: 0.9197 (mppt) cc_final: 0.8963 (mmmm) REVERT: A 309 GLU cc_start: 0.7683 (tp30) cc_final: 0.6379 (mt-10) REVERT: A 327 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5784 (mp0) REVERT: B 3 GLU cc_start: 0.7292 (mp0) cc_final: 0.7020 (mp0) REVERT: B 246 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: B 254 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7444 (p0) REVERT: B 261 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7732 (mm) REVERT: N 108 PHE cc_start: 0.3517 (OUTLIER) cc_final: 0.2008 (p90) REVERT: R 20 PHE cc_start: 0.4764 (OUTLIER) cc_final: 0.3424 (m-80) REVERT: R 61 PHE cc_start: 0.8048 (m-80) cc_final: 0.7772 (m-10) REVERT: R 78 MET cc_start: 0.8828 (tpp) cc_final: 0.8594 (tpp) REVERT: R 118 SER cc_start: 0.9236 (m) cc_final: 0.9035 (p) REVERT: R 157 ILE cc_start: 0.8719 (mt) cc_final: 0.8481 (mp) REVERT: R 290 ILE cc_start: 0.9413 (tp) cc_final: 0.9201 (tp) REVERT: R 339 LYS cc_start: 0.8993 (tppt) cc_final: 0.8703 (tppt) outliers start: 54 outliers final: 44 residues processed: 226 average time/residue: 0.1604 time to fit residues: 52.2174 Evaluate side-chains 234 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 LEU 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 378 ASP 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 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 CYS 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 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER 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 269 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU 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 N residue 128 SER Chi-restraints excluded: chain R residue 20 PHE 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 263 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 341 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.114022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097888 restraints weight = 20579.866| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.33 r_work: 0.3390 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8240 Z= 0.122 Angle : 0.655 12.486 11181 Z= 0.330 Chirality : 0.043 0.200 1271 Planarity : 0.003 0.060 1417 Dihedral : 5.957 87.574 1141 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.08 % Allowed : 31.35 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 1015 helix: 0.88 (0.26), residues: 413 sheet: -0.47 (0.36), residues: 200 loop : -1.72 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 PHE 0.022 0.001 PHE N 68 TYR 0.017 0.001 TYR R 194 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 405) hydrogen bonds : angle 4.45090 ( 1158) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.77433 ( 8) covalent geometry : bond 0.00261 ( 8236) covalent geometry : angle 0.65499 (11173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.30 seconds wall clock time: 69 minutes 44.75 seconds (4184.75 seconds total)