Starting phenix.real_space_refine on Tue Mar 3 19:28:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.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 { model { file = "/net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wey_65918/03_2026/9wey_65918.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5132 2.51 5 N 1412 2.21 5 O 1485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8084 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 423 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 969 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1824 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2550 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2318 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 4 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8084 At special positions: 0 Unit cell: (74.0625, 99.7375, 133.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1485 8.00 N 1412 7.00 C 5132 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=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 21 " - pdb=" SG CYS R 278 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 188 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 319.8 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 40.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 7 through 25 removed outlier: 3.914A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.549A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.669A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.720A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.754A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.384A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.484A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.543A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.956A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.781A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 393 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 27 through 46 removed outlier: 3.696A pdb=" N THR R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE R 42 " --> pdb=" O ASN R 38 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 56 Processing helix chain 'R' and resid 66 through 94 Proline residue: R 87 - end of helix removed outlier: 3.939A pdb=" N LEU R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 129 removed outlier: 3.850A pdb=" N SER R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 143 through 159 Processing helix chain 'R' and resid 160 through 167 removed outlier: 4.259A pdb=" N ALA R 164 " --> pdb=" O PHE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 197 through 213 Processing helix chain 'R' and resid 213 through 230 removed outlier: 3.812A pdb=" N VAL R 217 " --> pdb=" O GLY R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 273 removed outlier: 3.689A pdb=" N LEU R 256 " --> pdb=" O SER R 252 " (cutoff:3.500A) Proline residue: R 259 - end of helix removed outlier: 3.887A pdb=" N THR R 272 " --> pdb=" O SER R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 309 removed outlier: 3.553A pdb=" N ARG R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) Proline residue: R 295 - end of helix Proline residue: R 303 - end of helix removed outlier: 3.976A pdb=" N TYR R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 307 " --> pdb=" O PRO R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 321 Processing sheet with id=AA1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.503A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.081A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.023A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.958A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.507A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.387A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.498A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.641A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 3 through 6 removed outlier: 4.138A pdb=" N PHE R 192 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS R 6 " --> pdb=" O PHE R 192 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2628 1.34 - 1.46: 1836 1.46 - 1.58: 3704 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8248 Sorted by residual: bond pdb=" CG LEU R 83 " pdb=" CD2 LEU R 83 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" N VAL R 294 " pdb=" CA VAL R 294 " ideal model delta sigma weight residual 1.461 1.474 -0.013 1.23e-02 6.61e+03 1.14e+00 bond pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.98e-01 bond pdb=" C VAL R 293 " pdb=" N VAL R 294 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.13e-02 7.83e+03 9.52e-01 bond pdb=" N SER R 142 " pdb=" CA SER R 142 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.90e-02 2.77e+03 8.76e-01 ... (remaining 8243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 10937 2.15 - 4.31: 245 4.31 - 6.46: 16 6.46 - 8.61: 4 8.61 - 10.77: 1 Bond angle restraints: 11203 Sorted by residual: angle pdb=" CA LEU R 83 " pdb=" CB LEU R 83 " pdb=" CG LEU R 83 " ideal model delta sigma weight residual 116.30 127.07 -10.77 3.50e+00 8.16e-02 9.46e+00 angle pdb=" C ASN N 74 " pdb=" N ALA N 75 " pdb=" CA ALA N 75 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.22e+00 angle pdb=" NE ARG R 292 " pdb=" CZ ARG R 292 " pdb=" NH2 ARG R 292 " ideal model delta sigma weight residual 119.20 121.57 -2.37 9.00e-01 1.23e+00 6.93e+00 angle pdb=" NE ARG R 316 " pdb=" CZ ARG R 316 " pdb=" NH2 ARG R 316 " ideal model delta sigma weight residual 119.20 121.56 -2.36 9.00e-01 1.23e+00 6.88e+00 angle pdb=" NE ARG A 232 " pdb=" CZ ARG A 232 " pdb=" NH2 ARG A 232 " ideal model delta sigma weight residual 119.20 121.55 -2.35 9.00e-01 1.23e+00 6.83e+00 ... (remaining 11198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 4435 16.43 - 32.86: 357 32.86 - 49.28: 70 49.28 - 65.71: 14 65.71 - 82.14: 9 Dihedral angle restraints: 4885 sinusoidal: 1841 harmonic: 3044 Sorted by residual: dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 188 " pdb=" CB CYS R 188 " ideal model delta sinusoidal sigma weight residual -86.00 -34.99 -51.01 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CB CYS R 21 " pdb=" SG CYS R 21 " pdb=" SG CYS R 278 " pdb=" CB CYS R 278 " ideal model delta sinusoidal sigma weight residual -86.00 -135.81 49.81 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 4882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 825 0.035 - 0.069: 320 0.069 - 0.104: 110 0.104 - 0.138: 41 0.138 - 0.173: 4 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CG LEU R 250 " pdb=" CB LEU R 250 " pdb=" CD1 LEU R 250 " pdb=" CD2 LEU R 250 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 1297 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 25 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO R 26 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 26 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 26 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO N 88 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.014 2.00e-02 2.50e+03 9.92e-03 2.46e+00 pdb=" CG TRP B 169 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.002 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1538 2.77 - 3.31: 8064 3.31 - 3.84: 13840 3.84 - 4.37: 16329 4.37 - 4.90: 27852 Nonbonded interactions: 67623 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.256 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.259 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.267 3.120 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.297 3.120 ... (remaining 67618 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.003 0.036 8252 Z= 0.151 Angle : 0.662 10.767 11211 Z= 0.407 Chirality : 0.044 0.173 1300 Planarity : 0.005 0.054 1416 Dihedral : 13.147 82.140 2899 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.26), residues: 1020 helix: 0.62 (0.26), residues: 366 sheet: -0.49 (0.34), residues: 223 loop : -0.78 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.017 0.002 TYR N 60 PHE 0.022 0.002 PHE R 223 TRP 0.027 0.002 TRP B 169 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8248) covalent geometry : angle 0.66212 (11203) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.74080 ( 8) hydrogen bonds : bond 0.15001 ( 401) hydrogen bonds : angle 6.93778 ( 1149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 93 VAL cc_start: 0.8017 (t) cc_final: 0.7803 (p) REVERT: A 27 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 387 HIS cc_start: 0.7795 (t-170) cc_final: 0.6924 (t-170) REVERT: B 14 LEU cc_start: 0.8028 (mt) cc_final: 0.7504 (mt) REVERT: B 16 ASN cc_start: 0.7858 (m-40) cc_final: 0.7657 (t0) REVERT: B 52 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8063 (mtp-110) REVERT: B 197 ARG cc_start: 0.7696 (mpt180) cc_final: 0.7163 (mtm-85) REVERT: B 325 MET cc_start: 0.8195 (tpp) cc_final: 0.7658 (tpp) REVERT: R 131 ARG cc_start: 0.6645 (tpp-160) cc_final: 0.6423 (mtt180) REVERT: R 134 HIS cc_start: 0.8269 (t70) cc_final: 0.8058 (t70) REVERT: R 148 MET cc_start: 0.5985 (tpp) cc_final: 0.5773 (tmm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0924 time to fit residues: 28.7886 Evaluate side-chains 154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN N 84 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 198 HIS R 280 HIS R 311 HIS ** R 319 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120840 restraints weight = 16787.675| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.96 r_work: 0.3745 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8252 Z= 0.181 Angle : 0.643 7.865 11211 Z= 0.337 Chirality : 0.045 0.343 1300 Planarity : 0.004 0.050 1416 Dihedral : 5.248 66.898 1130 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.27 % Allowed : 12.15 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1020 helix: 0.66 (0.26), residues: 370 sheet: -0.65 (0.34), residues: 224 loop : -0.68 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.018 0.002 TYR R 224 PHE 0.015 0.002 PHE A 212 TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8248) covalent geometry : angle 0.64327 (11203) SS BOND : bond 0.00444 ( 4) SS BOND : angle 0.73034 ( 8) hydrogen bonds : bond 0.04823 ( 401) hydrogen bonds : angle 5.62222 ( 1149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 13 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6982 (tp40) REVERT: A 27 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 13 GLN cc_start: 0.7251 (pp30) cc_final: 0.6706 (pp30) REVERT: B 14 LEU cc_start: 0.7858 (mt) cc_final: 0.7483 (mt) REVERT: B 52 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8107 (mtp-110) REVERT: B 197 ARG cc_start: 0.7594 (mpt180) cc_final: 0.7198 (mtm-85) REVERT: B 325 MET cc_start: 0.8454 (tpp) cc_final: 0.8072 (tpp) REVERT: R 271 THR cc_start: 0.7617 (m) cc_final: 0.7407 (p) REVERT: R 290 LEU cc_start: 0.7585 (mm) cc_final: 0.7089 (tt) REVERT: R 316 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6990 (mtp180) outliers start: 28 outliers final: 16 residues processed: 179 average time/residue: 0.0953 time to fit residues: 23.3364 Evaluate side-chains 164 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 276 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.146655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.122652 restraints weight = 16552.073| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.96 r_work: 0.3765 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8252 Z= 0.131 Angle : 0.600 9.070 11211 Z= 0.311 Chirality : 0.043 0.167 1300 Planarity : 0.004 0.049 1416 Dihedral : 4.998 61.007 1130 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.50 % Allowed : 15.42 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1020 helix: 0.78 (0.26), residues: 370 sheet: -0.65 (0.34), residues: 216 loop : -0.80 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.016 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.001 TRP R 95 HIS 0.013 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8248) covalent geometry : angle 0.60033 (11203) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.65453 ( 8) hydrogen bonds : bond 0.04284 ( 401) hydrogen bonds : angle 5.35319 ( 1149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 13 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7021 (tp40) REVERT: N 93 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7807 (p) REVERT: N 123 GLN cc_start: 0.7914 (mp10) cc_final: 0.7529 (tp-100) REVERT: A 25 LYS cc_start: 0.7354 (mmmt) cc_final: 0.7112 (pttp) REVERT: A 60 MET cc_start: 0.5728 (ptp) cc_final: 0.5257 (ptp) REVERT: A 341 ILE cc_start: 0.8515 (mm) cc_final: 0.8290 (tp) REVERT: A 392 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 13 GLN cc_start: 0.7350 (pp30) cc_final: 0.6914 (pp30) REVERT: B 14 LEU cc_start: 0.7894 (mt) cc_final: 0.7495 (mt) REVERT: B 52 ARG cc_start: 0.8451 (mtt90) cc_final: 0.8130 (mtp-110) REVERT: B 197 ARG cc_start: 0.7580 (mpt180) cc_final: 0.7201 (mtm-85) REVERT: B 205 ASP cc_start: 0.7751 (p0) cc_final: 0.7285 (p0) REVERT: B 325 MET cc_start: 0.8453 (tpp) cc_final: 0.8094 (tpp) outliers start: 30 outliers final: 19 residues processed: 170 average time/residue: 0.0928 time to fit residues: 21.5904 Evaluate side-chains 167 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 276 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.0570 chunk 72 optimal weight: 9.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.146131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121807 restraints weight = 17089.799| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.06 r_work: 0.3752 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8252 Z= 0.135 Angle : 0.584 9.841 11211 Z= 0.302 Chirality : 0.043 0.180 1300 Planarity : 0.004 0.052 1416 Dihedral : 4.857 58.102 1130 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.86 % Allowed : 16.47 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1020 helix: 0.90 (0.27), residues: 372 sheet: -0.61 (0.35), residues: 217 loop : -0.74 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.002 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.017 0.001 TRP B 169 HIS 0.015 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8248) covalent geometry : angle 0.58426 (11203) SS BOND : bond 0.00314 ( 4) SS BOND : angle 0.67534 ( 8) hydrogen bonds : bond 0.04134 ( 401) hydrogen bonds : angle 5.18858 ( 1149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 13 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6918 (tp40) REVERT: N 93 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7880 (p) REVERT: N 123 GLN cc_start: 0.7994 (mp10) cc_final: 0.7538 (tp-100) REVERT: A 60 MET cc_start: 0.5620 (ptp) cc_final: 0.5343 (ptp) REVERT: B 52 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8159 (mtp-110) REVERT: B 197 ARG cc_start: 0.7600 (mpt180) cc_final: 0.7214 (mtm-85) REVERT: B 234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: B 325 MET cc_start: 0.8461 (tpp) cc_final: 0.8106 (tpp) REVERT: R 59 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7253 (p) REVERT: R 72 MET cc_start: 0.7517 (tmm) cc_final: 0.6739 (tmm) REVERT: R 76 TYR cc_start: 0.5637 (m-80) cc_final: 0.5077 (m-80) outliers start: 33 outliers final: 23 residues processed: 173 average time/residue: 0.0953 time to fit residues: 22.4926 Evaluate side-chains 170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.143930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.119783 restraints weight = 17004.860| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.01 r_work: 0.3735 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8252 Z= 0.171 Angle : 0.625 8.693 11211 Z= 0.321 Chirality : 0.043 0.173 1300 Planarity : 0.004 0.050 1416 Dihedral : 4.903 53.998 1130 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.44 % Allowed : 17.29 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.27), residues: 1020 helix: 0.86 (0.27), residues: 372 sheet: -0.75 (0.34), residues: 219 loop : -0.71 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 316 TYR 0.016 0.002 TYR N 60 PHE 0.018 0.002 PHE R 266 TRP 0.018 0.002 TRP B 169 HIS 0.015 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8248) covalent geometry : angle 0.62449 (11203) SS BOND : bond 0.00439 ( 4) SS BOND : angle 0.77589 ( 8) hydrogen bonds : bond 0.04204 ( 401) hydrogen bonds : angle 5.24716 ( 1149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 13 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6912 (tp40) REVERT: N 70 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6451 (mt) REVERT: N 93 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7891 (p) REVERT: N 123 GLN cc_start: 0.7939 (mp10) cc_final: 0.7583 (tp-100) REVERT: A 60 MET cc_start: 0.5657 (ptp) cc_final: 0.5330 (ptp) REVERT: A 341 ILE cc_start: 0.8697 (tp) cc_final: 0.8486 (mt) REVERT: B 13 GLN cc_start: 0.7465 (pp30) cc_final: 0.6964 (pp30) REVERT: B 52 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8146 (mtp-110) REVERT: B 197 ARG cc_start: 0.7573 (mpt180) cc_final: 0.7241 (mtm-85) REVERT: B 234 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 325 MET cc_start: 0.8491 (tpp) cc_final: 0.8129 (tpp) REVERT: R 72 MET cc_start: 0.7663 (tmm) cc_final: 0.6746 (tmm) REVERT: R 76 TYR cc_start: 0.5674 (m-80) cc_final: 0.5083 (m-80) outliers start: 38 outliers final: 26 residues processed: 172 average time/residue: 0.0906 time to fit residues: 21.4626 Evaluate side-chains 180 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.120366 restraints weight = 16785.421| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.00 r_work: 0.3738 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8252 Z= 0.155 Angle : 0.609 8.434 11211 Z= 0.313 Chirality : 0.043 0.162 1300 Planarity : 0.004 0.052 1416 Dihedral : 4.837 51.755 1130 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.97 % Allowed : 17.99 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 1020 helix: 0.94 (0.27), residues: 372 sheet: -0.73 (0.34), residues: 218 loop : -0.70 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.015 0.002 TYR N 60 PHE 0.014 0.002 PHE R 80 TRP 0.019 0.002 TRP R 274 HIS 0.015 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8248) covalent geometry : angle 0.60906 (11203) SS BOND : bond 0.00389 ( 4) SS BOND : angle 0.70444 ( 8) hydrogen bonds : bond 0.04079 ( 401) hydrogen bonds : angle 5.17497 ( 1149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 13 GLN cc_start: 0.7299 (mm-40) cc_final: 0.6897 (tp40) REVERT: N 70 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6430 (mt) REVERT: N 93 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7959 (p) REVERT: N 123 GLN cc_start: 0.7958 (mp10) cc_final: 0.7627 (tp-100) REVERT: A 60 MET cc_start: 0.5927 (ptp) cc_final: 0.4989 (ptp) REVERT: A 341 ILE cc_start: 0.8725 (tp) cc_final: 0.8524 (mt) REVERT: B 197 ARG cc_start: 0.7623 (mpt180) cc_final: 0.7268 (mtm-85) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: B 325 MET cc_start: 0.8495 (tpp) cc_final: 0.8158 (tpp) REVERT: R 76 TYR cc_start: 0.5573 (m-80) cc_final: 0.5038 (m-80) outliers start: 34 outliers final: 25 residues processed: 171 average time/residue: 0.0911 time to fit residues: 21.6183 Evaluate side-chains 171 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 0.0570 chunk 70 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 HIS R 296 HIS ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.147276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123273 restraints weight = 16856.275| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.04 r_work: 0.3775 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8252 Z= 0.120 Angle : 0.619 9.119 11211 Z= 0.318 Chirality : 0.043 0.149 1300 Planarity : 0.004 0.054 1416 Dihedral : 4.697 50.341 1130 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.04 % Allowed : 20.44 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1020 helix: 1.01 (0.27), residues: 370 sheet: -0.87 (0.34), residues: 215 loop : -0.63 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.015 0.001 TYR R 71 PHE 0.013 0.001 PHE R 223 TRP 0.039 0.002 TRP R 95 HIS 0.014 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8248) covalent geometry : angle 0.61865 (11203) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.61354 ( 8) hydrogen bonds : bond 0.03969 ( 401) hydrogen bonds : angle 4.95716 ( 1149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8795 (ptp-170) cc_final: 0.8382 (ptp-170) REVERT: N 13 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6909 (tp40) REVERT: N 93 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7978 (p) REVERT: N 123 GLN cc_start: 0.7934 (mp10) cc_final: 0.7621 (tp-100) REVERT: A 60 MET cc_start: 0.5679 (ptp) cc_final: 0.5188 (ptp) REVERT: B 13 GLN cc_start: 0.7466 (pp30) cc_final: 0.7109 (pp30) REVERT: B 197 ARG cc_start: 0.7559 (mpt180) cc_final: 0.7190 (mtm-85) REVERT: B 234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: B 325 MET cc_start: 0.8412 (tpp) cc_final: 0.8065 (tpp) REVERT: R 76 TYR cc_start: 0.5414 (m-80) cc_final: 0.5160 (m-80) REVERT: R 172 MET cc_start: 0.6677 (pmm) cc_final: 0.6361 (pmm) REVERT: R 290 LEU cc_start: 0.7453 (mm) cc_final: 0.7101 (tt) REVERT: R 317 MET cc_start: 0.7200 (ppp) cc_final: 0.6535 (ppp) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 0.0878 time to fit residues: 20.1360 Evaluate side-chains 163 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 245 PHE Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.147176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.123008 restraints weight = 16778.631| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.05 r_work: 0.3770 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8252 Z= 0.136 Angle : 0.622 8.771 11211 Z= 0.321 Chirality : 0.043 0.147 1300 Planarity : 0.004 0.053 1416 Dihedral : 4.689 48.056 1130 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.69 % Allowed : 20.44 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1020 helix: 1.02 (0.27), residues: 370 sheet: -0.89 (0.34), residues: 215 loop : -0.63 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 314 TYR 0.017 0.001 TYR R 71 PHE 0.034 0.002 PHE R 245 TRP 0.025 0.002 TRP R 95 HIS 0.024 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8248) covalent geometry : angle 0.62230 (11203) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.61201 ( 8) hydrogen bonds : bond 0.03887 ( 401) hydrogen bonds : angle 5.02017 ( 1149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8776 (ptp-170) cc_final: 0.8344 (ptp-170) REVERT: N 13 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6911 (tp40) REVERT: N 93 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8023 (p) REVERT: N 123 GLN cc_start: 0.7984 (mp10) cc_final: 0.7653 (tp-100) REVERT: A 60 MET cc_start: 0.5799 (ptp) cc_final: 0.4922 (ptp) REVERT: B 197 ARG cc_start: 0.7586 (mpt180) cc_final: 0.7230 (mtm-85) REVERT: B 234 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: B 325 MET cc_start: 0.8390 (tpp) cc_final: 0.8051 (tpp) REVERT: R 72 MET cc_start: 0.7454 (tmm) cc_final: 0.6826 (tmm) REVERT: R 76 TYR cc_start: 0.5557 (m-80) cc_final: 0.5313 (m-80) REVERT: R 290 LEU cc_start: 0.7553 (mm) cc_final: 0.7165 (tt) outliers start: 23 outliers final: 18 residues processed: 166 average time/residue: 0.0957 time to fit residues: 21.8220 Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 245 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.147781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.123507 restraints weight = 16919.640| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.08 r_work: 0.3777 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 8252 Z= 0.137 Angle : 0.641 8.704 11211 Z= 0.327 Chirality : 0.043 0.154 1300 Planarity : 0.004 0.053 1416 Dihedral : 4.695 45.875 1130 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.80 % Allowed : 20.79 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 1020 helix: 1.05 (0.27), residues: 370 sheet: -0.89 (0.34), residues: 215 loop : -0.69 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.001 TYR N 60 PHE 0.013 0.001 PHE R 80 TRP 0.023 0.001 TRP R 95 HIS 0.017 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8248) covalent geometry : angle 0.64060 (11203) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.58640 ( 8) hydrogen bonds : bond 0.03809 ( 401) hydrogen bonds : angle 4.95967 ( 1149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8799 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: N 13 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6930 (tp40) REVERT: N 93 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8024 (p) REVERT: N 123 GLN cc_start: 0.7970 (mp10) cc_final: 0.7665 (tp-100) REVERT: A 60 MET cc_start: 0.5507 (ptp) cc_final: 0.4661 (ptp) REVERT: B 197 ARG cc_start: 0.7644 (mpt180) cc_final: 0.7246 (mtp-110) REVERT: B 234 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: B 325 MET cc_start: 0.8495 (tpp) cc_final: 0.8155 (tpp) REVERT: R 72 MET cc_start: 0.7429 (tmm) cc_final: 0.6689 (tmm) REVERT: R 76 TYR cc_start: 0.5603 (m-80) cc_final: 0.4872 (m-80) REVERT: R 172 MET cc_start: 0.6773 (pmm) cc_final: 0.6502 (pmm) REVERT: R 224 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.3189 (t80) REVERT: R 290 LEU cc_start: 0.7499 (mm) cc_final: 0.7095 (tt) outliers start: 24 outliers final: 18 residues processed: 168 average time/residue: 0.0908 time to fit residues: 21.0848 Evaluate side-chains 166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 224 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.147802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123633 restraints weight = 16812.356| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.06 r_work: 0.3778 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8252 Z= 0.138 Angle : 0.633 8.666 11211 Z= 0.324 Chirality : 0.043 0.151 1300 Planarity : 0.004 0.054 1416 Dihedral : 4.627 41.868 1130 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.57 % Allowed : 21.73 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 1020 helix: 1.07 (0.27), residues: 370 sheet: -0.89 (0.34), residues: 217 loop : -0.66 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.016 0.001 TYR N 60 PHE 0.016 0.001 PHE B 292 TRP 0.047 0.002 TRP R 95 HIS 0.018 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8248) covalent geometry : angle 0.63342 (11203) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.57204 ( 8) hydrogen bonds : bond 0.03801 ( 401) hydrogen bonds : angle 4.94368 ( 1149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8786 (ptp-170) cc_final: 0.8259 (ptp-170) REVERT: N 13 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6931 (tp40) REVERT: N 93 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8030 (p) REVERT: N 123 GLN cc_start: 0.7988 (mp10) cc_final: 0.7683 (tp-100) REVERT: A 60 MET cc_start: 0.5774 (ptp) cc_final: 0.4944 (ptp) REVERT: B 197 ARG cc_start: 0.7550 (mpt180) cc_final: 0.7173 (mtp-110) REVERT: B 234 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: B 325 MET cc_start: 0.8465 (tpp) cc_final: 0.8156 (tpp) REVERT: R 72 MET cc_start: 0.7487 (tmm) cc_final: 0.6820 (tmm) REVERT: R 76 TYR cc_start: 0.5363 (m-80) cc_final: 0.4910 (m-80) REVERT: R 172 MET cc_start: 0.6941 (pmm) cc_final: 0.6684 (pmm) REVERT: R 224 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.3199 (t80) outliers start: 22 outliers final: 18 residues processed: 167 average time/residue: 0.0906 time to fit residues: 21.0360 Evaluate side-chains 165 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 224 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.147353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.123227 restraints weight = 16718.796| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.05 r_work: 0.3773 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8252 Z= 0.143 Angle : 0.643 8.810 11211 Z= 0.329 Chirality : 0.044 0.162 1300 Planarity : 0.004 0.053 1416 Dihedral : 4.632 41.090 1130 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.80 % Allowed : 22.20 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.27), residues: 1020 helix: 1.09 (0.27), residues: 370 sheet: -0.90 (0.34), residues: 217 loop : -0.64 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.016 0.001 TYR N 60 PHE 0.012 0.001 PHE R 80 TRP 0.052 0.002 TRP R 95 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8248) covalent geometry : angle 0.64261 (11203) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.56473 ( 8) hydrogen bonds : bond 0.03803 ( 401) hydrogen bonds : angle 4.96575 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.72 seconds wall clock time: 34 minutes 20.20 seconds (2060.20 seconds total)