Starting phenix.real_space_refine on Fri May 16 01:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crh_30452/05_2025/7crh_30452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crh_30452/05_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_30452/05_2025/7crh_30452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crh_30452/05_2025/7crh_30452.map" model { file = "/net/cci-nas-00/data/ceres_data/7crh_30452/05_2025/7crh_30452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crh_30452/05_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-5687/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: 5.16, per 1000 atoms: 0.64 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: 1.99 Conformation dependent library (CDL) restraints added in 892.9 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: 0.78 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: 2.23 Time building geometry restraints manager: 2.34 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: 0.960 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- 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 : 0.876 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: 0.1930 time to fit residues: 78.8824 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 : 0.905 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.113804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097645 restraints weight = 20414.392| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.22 r_work: 0.3393 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2418 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 10.008 11181 Z= 0.334 Chirality : 0.043 0.194 1271 Planarity : 0.004 0.054 1417 Dihedral : 6.768 111.737 1148 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.66 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 0.04665 ( 405) hydrogen bonds : angle 4.76365 ( 1158) SS BOND : bond 0.00368 ( 4) SS BOND : angle 1.31343 ( 8) covalent geometry : bond 0.00352 ( 8236) covalent geometry : angle 0.64151 (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 : 0.929 Fit side-chains REVERT: A 309 GLU cc_start: 0.8301 (tp30) cc_final: 0.7292 (mt-10) REVERT: A 317 ARG cc_start: 0.7859 (mmp-170) cc_final: 0.7208 (mtm-85) REVERT: B 3 GLU cc_start: 0.7122 (mp0) cc_final: 0.6915 (mp0) REVERT: B 254 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7410 (p0) REVERT: B 293 ASN cc_start: 0.8482 (m110) cc_final: 0.8281 (p0) REVERT: R 25 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8032 (pp) REVERT: R 61 PHE cc_start: 0.8085 (m-80) cc_final: 0.7842 (m-10) REVERT: R 118 SER cc_start: 0.9171 (m) cc_final: 0.8916 (p) REVERT: R 157 ILE cc_start: 0.8466 (mt) cc_final: 0.8235 (mp) REVERT: R 290 ILE cc_start: 0.9476 (tp) cc_final: 0.9247 (tp) REVERT: R 333 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7828 (t80) REVERT: R 339 LYS cc_start: 0.8905 (tppt) cc_final: 0.8686 (tppt) outliers start: 48 outliers final: 25 residues processed: 248 average time/residue: 0.1793 time to fit residues: 62.2612 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 : 0.935 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3734 r_free = 0.3734 target = 0.112783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096759 restraints weight = 20753.553| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.26 r_work: 0.3371 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8240 Z= 0.149 Angle : 0.615 8.925 11181 Z= 0.321 Chirality : 0.043 0.172 1271 Planarity : 0.004 0.057 1417 Dihedral : 6.395 105.862 1142 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.24 % Allowed : 25.06 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1015 helix: 0.34 (0.25), residues: 412 sheet: -0.85 (0.34), residues: 198 loop : -2.07 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 N 115 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 405) hydrogen bonds : angle 4.65243 ( 1158) SS BOND : bond 0.00603 ( 4) SS BOND : angle 1.32584 ( 8) covalent geometry : bond 0.00338 ( 8236) covalent geometry : angle 0.61423 (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 242 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.881 Fit side-chains REVERT: A 317 ARG cc_start: 0.7886 (mmp-170) cc_final: 0.7241 (mtm-85) REVERT: A 327 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: B 3 GLU cc_start: 0.7145 (mp0) cc_final: 0.6927 (mp0) REVERT: B 254 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 264 TYR cc_start: 0.8737 (m-80) cc_final: 0.8408 (m-80) REVERT: N 64 VAL cc_start: 0.8718 (t) cc_final: 0.8309 (p) REVERT: N 108 PHE cc_start: 0.3393 (OUTLIER) cc_final: 0.1782 (p90) REVERT: N 109 ASP cc_start: 0.7619 (m-30) cc_final: 0.7223 (m-30) REVERT: R 25 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7937 (pp) REVERT: R 61 PHE cc_start: 0.8090 (m-80) cc_final: 0.7880 (m-10) REVERT: R 104 ILE cc_start: 0.8887 (pt) cc_final: 0.8655 (tt) REVERT: R 118 SER cc_start: 0.9203 (m) cc_final: 0.8945 (p) REVERT: R 157 ILE cc_start: 0.8558 (mt) cc_final: 0.8335 (mp) REVERT: R 290 ILE cc_start: 0.9467 (tp) cc_final: 0.9241 (tp) REVERT: R 333 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7920 (t80) REVERT: R 339 LYS cc_start: 0.8940 (tppt) cc_final: 0.8674 (tppt) REVERT: R 341 PHE cc_start: 0.7350 (t80) cc_final: 0.7064 (t80) outliers start: 45 outliers final: 27 residues processed: 229 average time/residue: 0.1605 time to fit residues: 52.4722 Evaluate side-chains 203 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 overall best weight: 1.6102 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.113499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097627 restraints weight = 20589.810| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.27 r_work: 0.3385 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3156 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= 0.125 Angle : 0.588 9.670 11181 Z= 0.305 Chirality : 0.042 0.153 1271 Planarity : 0.003 0.057 1417 Dihedral : 6.275 102.876 1142 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.13 % Allowed : 26.57 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.26), residues: 1015 helix: 0.49 (0.25), residues: 414 sheet: -0.54 (0.34), residues: 198 loop : -2.02 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 90 HIS 0.006 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 0.04109 ( 405) hydrogen bonds : angle 4.57028 ( 1158) SS BOND : bond 0.00256 ( 4) SS BOND : angle 1.56532 ( 8) covalent geometry : bond 0.00280 ( 8236) covalent geometry : angle 0.58702 (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 236 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.931 Fit side-chains REVERT: A 255 MET cc_start: 0.2188 (pmm) cc_final: 0.0913 (pmm) REVERT: A 309 GLU cc_start: 0.7428 (tp30) cc_final: 0.5982 (mt-10) REVERT: A 327 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5724 (mp0) REVERT: A 356 ARG cc_start: 0.8645 (mmt180) cc_final: 0.8375 (mmm160) REVERT: B 3 GLU cc_start: 0.7107 (mp0) cc_final: 0.6868 (mp0) REVERT: B 254 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7446 (p0) REVERT: B 264 TYR cc_start: 0.8657 (m-80) cc_final: 0.8425 (m-80) REVERT: N 108 PHE cc_start: 0.3388 (OUTLIER) cc_final: 0.1792 (p90) REVERT: N 109 ASP cc_start: 0.7688 (m-30) cc_final: 0.7325 (m-30) REVERT: R 25 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7933 (pp) REVERT: R 61 PHE cc_start: 0.8034 (m-80) cc_final: 0.7800 (m-10) REVERT: R 118 SER cc_start: 0.9157 (m) cc_final: 0.8919 (p) REVERT: R 157 ILE cc_start: 0.8619 (mt) cc_final: 0.8396 (mp) REVERT: R 290 ILE cc_start: 0.9425 (tp) cc_final: 0.9183 (tp) REVERT: R 339 LYS cc_start: 0.8941 (tppt) cc_final: 0.8660 (tppt) REVERT: R 341 PHE cc_start: 0.7307 (t80) cc_final: 0.6907 (t80) outliers start: 44 outliers final: 27 residues processed: 224 average time/residue: 0.1563 time to fit residues: 49.7584 Evaluate side-chains 213 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 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 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 71 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN 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 = 0.3713 r_free = 0.3713 target = 0.111450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095481 restraints weight = 20337.543| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.23 r_work: 0.3355 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8240 Z= 0.157 Angle : 0.605 10.319 11181 Z= 0.315 Chirality : 0.043 0.168 1271 Planarity : 0.004 0.056 1417 Dihedral : 6.355 102.245 1142 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.06 % Allowed : 26.22 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.26), residues: 1015 helix: 0.54 (0.25), residues: 414 sheet: -0.45 (0.34), residues: 201 loop : -1.96 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 90 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.001 PHE R 264 TYR 0.012 0.001 TYR A 358 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 405) hydrogen bonds : angle 4.53229 ( 1158) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.38282 ( 8) covalent geometry : bond 0.00356 ( 8236) covalent geometry : angle 0.60454 (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 243 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.956 Fit side-chains REVERT: A 216 LYS cc_start: 0.9197 (mppt) cc_final: 0.8915 (mmtt) REVERT: A 230 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7762 (tm-30) REVERT: A 309 GLU cc_start: 0.7528 (tp30) cc_final: 0.6128 (mt-10) REVERT: A 327 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5725 (mp0) REVERT: B 254 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7559 (p0) REVERT: B 261 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7763 (mm) REVERT: N 39 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: N 108 PHE cc_start: 0.3535 (OUTLIER) cc_final: 0.1844 (p90) REVERT: R 61 PHE cc_start: 0.8058 (m-80) cc_final: 0.7811 (m-10) REVERT: R 118 SER cc_start: 0.9183 (m) cc_final: 0.8951 (p) REVERT: R 157 ILE cc_start: 0.8646 (mt) cc_final: 0.8423 (mp) REVERT: R 290 ILE cc_start: 0.9444 (tp) cc_final: 0.9211 (tp) REVERT: R 339 LYS cc_start: 0.8992 (tppt) cc_final: 0.8722 (tppt) REVERT: R 341 PHE cc_start: 0.7180 (t80) cc_final: 0.6666 (t80) outliers start: 52 outliers final: 34 residues processed: 229 average time/residue: 0.1567 time to fit residues: 51.3902 Evaluate side-chains 216 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 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 4 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 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 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: 3.9990 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 384 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.112775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096651 restraints weight = 20441.957| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.27 r_work: 0.3365 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8240 Z= 0.121 Angle : 0.594 11.119 11181 Z= 0.305 Chirality : 0.042 0.206 1271 Planarity : 0.003 0.055 1417 Dihedral : 6.191 99.251 1142 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.36 % Allowed : 27.86 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.26), residues: 413 sheet: -0.35 (0.35), residues: 201 loop : -1.83 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 90 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE B 292 TYR 0.016 0.001 TYR A 358 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 405) hydrogen bonds : angle 4.42165 ( 1158) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.13746 ( 8) covalent geometry : bond 0.00272 ( 8236) covalent geometry : angle 0.59328 (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 249 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.839 Fit side-chains REVERT: A 216 LYS cc_start: 0.9187 (mppt) cc_final: 0.8921 (mttt) REVERT: A 309 GLU cc_start: 0.7563 (tp30) cc_final: 0.6197 (mt-10) REVERT: A 327 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: B 3 GLU cc_start: 0.7196 (mp0) cc_final: 0.6942 (mp0) REVERT: B 254 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 261 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7854 (mm) REVERT: B 264 TYR cc_start: 0.8640 (m-80) cc_final: 0.8374 (m-80) REVERT: G 19 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8333 (mp) REVERT: N 108 PHE cc_start: 0.3380 (OUTLIER) cc_final: 0.1747 (p90) REVERT: R 20 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.3211 (m-80) REVERT: R 61 PHE cc_start: 0.8034 (m-80) cc_final: 0.7812 (m-10) REVERT: R 78 MET cc_start: 0.8775 (tpp) cc_final: 0.8167 (tpp) REVERT: R 118 SER cc_start: 0.9172 (m) cc_final: 0.8899 (p) REVERT: R 157 ILE cc_start: 0.8669 (mt) cc_final: 0.8439 (mp) REVERT: R 290 ILE cc_start: 0.9432 (tp) cc_final: 0.9192 (tp) REVERT: R 339 LYS cc_start: 0.8981 (tppt) cc_final: 0.8675 (tppt) REVERT: R 341 PHE cc_start: 0.7274 (t80) cc_final: 0.6717 (t80) outliers start: 46 outliers final: 28 residues processed: 234 average time/residue: 0.1620 time to fit residues: 54.0617 Evaluate side-chains 220 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 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 G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.112399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096260 restraints weight = 20504.573| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.30 r_work: 0.3363 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3591 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= 0.129 Angle : 0.627 11.831 11181 Z= 0.320 Chirality : 0.043 0.225 1271 Planarity : 0.003 0.056 1417 Dihedral : 6.184 97.335 1142 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.83 % Allowed : 27.62 % 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: -0.69 (0.26), residues: 1015 helix: 0.77 (0.26), residues: 408 sheet: -0.29 (0.35), residues: 202 loop : -1.81 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 80 HIS 0.010 0.001 HIS B 225 PHE 0.015 0.001 PHE N 68 TYR 0.012 0.001 TYR A 358 ARG 0.003 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 405) hydrogen bonds : angle 4.38933 ( 1158) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.04136 ( 8) covalent geometry : bond 0.00290 ( 8236) covalent geometry : angle 0.62665 (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 254 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.966 Fit side-chains REVERT: A 216 LYS cc_start: 0.9195 (mppt) cc_final: 0.8955 (mmtt) REVERT: A 309 GLU cc_start: 0.7635 (tp30) cc_final: 0.6222 (mt-10) REVERT: A 327 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: B 3 GLU cc_start: 0.7220 (mp0) cc_final: 0.6973 (mp0) REVERT: B 254 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7413 (p0) REVERT: B 261 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7864 (mm) REVERT: B 264 TYR cc_start: 0.8629 (m-80) cc_final: 0.8325 (m-80) REVERT: G 19 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8343 (mp) REVERT: N 32 TYR cc_start: 0.7962 (m-80) cc_final: 0.7567 (m-80) REVERT: N 39 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: N 108 PHE cc_start: 0.3267 (OUTLIER) cc_final: 0.1745 (p90) REVERT: R 20 PHE cc_start: 0.4939 (OUTLIER) cc_final: 0.3397 (m-80) REVERT: R 61 PHE cc_start: 0.8022 (m-80) cc_final: 0.7784 (m-10) REVERT: R 118 SER cc_start: 0.9165 (m) cc_final: 0.8909 (p) REVERT: R 157 ILE cc_start: 0.8667 (mt) cc_final: 0.8431 (mp) REVERT: R 290 ILE cc_start: 0.9426 (tp) cc_final: 0.9175 (tp) REVERT: R 339 LYS cc_start: 0.9010 (tppt) cc_final: 0.8724 (tppt) REVERT: R 341 PHE cc_start: 0.7281 (t80) cc_final: 0.6692 (t80) outliers start: 50 outliers final: 32 residues processed: 235 average time/residue: 0.1638 time to fit residues: 55.2219 Evaluate side-chains 228 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 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 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 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 G residue 19 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 20 PHE Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 123 TRP Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2868 > 50: distance: 49 - 72: 8.180 distance: 69 - 72: 6.167 distance: 72 - 73: 20.678 distance: 73 - 74: 21.562 distance: 73 - 76: 12.951 distance: 74 - 75: 20.632 distance: 74 - 82: 30.582 distance: 76 - 77: 17.951 distance: 77 - 78: 12.589 distance: 77 - 79: 10.253 distance: 78 - 80: 11.839 distance: 79 - 81: 20.744 distance: 80 - 81: 15.775 distance: 82 - 83: 44.828 distance: 83 - 84: 5.329 distance: 83 - 86: 42.301 distance: 84 - 85: 26.658 distance: 84 - 87: 46.490 distance: 87 - 88: 18.368 distance: 88 - 89: 19.620 distance: 88 - 91: 40.238 distance: 89 - 90: 13.236 distance: 89 - 96: 28.262 distance: 91 - 92: 33.753 distance: 92 - 93: 25.743 distance: 93 - 94: 19.266 distance: 94 - 95: 8.192 distance: 96 - 97: 3.312 distance: 97 - 98: 13.821 distance: 97 - 100: 7.122 distance: 98 - 99: 23.115 distance: 98 - 105: 23.882 distance: 100 - 101: 13.014 distance: 101 - 102: 15.034 distance: 102 - 103: 19.705 distance: 102 - 104: 10.905 distance: 105 - 106: 24.782 distance: 106 - 107: 32.535 distance: 106 - 109: 30.013 distance: 107 - 108: 52.553 distance: 107 - 113: 46.088 distance: 109 - 110: 37.632 distance: 110 - 111: 26.984 distance: 110 - 112: 20.255 distance: 113 - 114: 8.578 distance: 113 - 119: 21.497 distance: 114 - 115: 19.770 distance: 114 - 117: 36.870 distance: 115 - 116: 16.482 distance: 115 - 120: 18.509 distance: 117 - 118: 51.810 distance: 118 - 119: 28.768 distance: 120 - 121: 40.320 distance: 121 - 122: 19.114 distance: 121 - 124: 14.810 distance: 122 - 123: 16.871 distance: 122 - 128: 22.985 distance: 124 - 125: 24.979 distance: 125 - 126: 16.678 distance: 125 - 127: 9.506 distance: 128 - 129: 23.589 distance: 129 - 130: 21.327 distance: 129 - 132: 12.488 distance: 130 - 131: 34.949 distance: 130 - 136: 26.694 distance: 132 - 133: 33.622 distance: 133 - 134: 38.392 distance: 133 - 135: 31.165 distance: 136 - 137: 39.186 distance: 137 - 138: 39.573 distance: 137 - 140: 14.456 distance: 138 - 139: 21.174 distance: 138 - 143: 37.693 distance: 140 - 141: 4.918 distance: 140 - 142: 6.783 distance: 143 - 144: 31.637 distance: 143 - 149: 26.435 distance: 144 - 145: 23.276 distance: 144 - 147: 18.418 distance: 145 - 146: 19.129 distance: 145 - 150: 8.207 distance: 147 - 148: 10.620 distance: 148 - 149: 10.384