Starting phenix.real_space_refine on Wed Feb 4 06:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.map" model { file = "/net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l8l_62885/02_2026/9l8l_62885.cif" } resolution = 3.22 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= -0.000 sd= 0.056 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 47 5.16 5 C 5744 2.51 5 N 1568 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8997 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1631 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 11, 'ASN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 8, 'PHE:plan': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2425 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 16, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 154 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2375 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'TYR:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 172 Chain: "G" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 357 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2131 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Classifications: {'peptide': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'P0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.25 Number of scatterers: 8997 At special positions: 0 Unit cell: (97.2, 103.68, 142.56, 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 47 16.00 O 1638 8.00 N 1568 7.00 C 5744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 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: 0.85 Conformation dependent library (CDL) restraints added in 346.2 milliseconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 35.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.550A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.719A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.918A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.751A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.130A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.839A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 removed outlier: 4.168A pdb=" N ARG C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'G' and resid 11 through 22 removed outlier: 3.587A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.540A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 66 through 86 removed outlier: 3.871A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.640A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.522A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 172 removed outlier: 4.308A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.405A pdb=" N VAL R 277 " --> pdb=" O ARG R 273 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR R 281 " --> pdb=" O VAL R 277 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR R 283 " --> pdb=" O MET R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.051A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.609A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.949A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 214 removed outlier: 3.518A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.680A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.392A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.866A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.027A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.056A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 6.348A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 10 Processing sheet with id=AB1, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.577A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 85 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.668A pdb=" N ASN C 217 " --> pdb=" O SER C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.994A pdb=" N VAL C 343 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 254 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1173 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: 1.50 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1576 1.32 - 1.45: 2393 1.45 - 1.57: 5150 1.57 - 1.70: 1 1.70 - 1.82: 61 Bond restraints: 9181 Sorted by residual: bond pdb=" N THR R 164 " pdb=" CA THR R 164 " ideal model delta sigma weight residual 1.455 1.552 -0.098 1.38e-02 5.25e+03 5.02e+01 bond pdb=" N ASP C 194 " pdb=" CA ASP C 194 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.06e-02 8.90e+03 1.66e+01 bond pdb=" CA SER R 165 " pdb=" CB SER R 165 " ideal model delta sigma weight residual 1.536 1.477 0.058 1.65e-02 3.67e+03 1.26e+01 bond pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.51e+00 bond pdb=" C THR R 164 " pdb=" O THR R 164 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.33e-02 5.65e+03 7.49e+00 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12240 1.90 - 3.81: 244 3.81 - 5.71: 48 5.71 - 7.62: 22 7.62 - 9.52: 11 Bond angle restraints: 12565 Sorted by residual: angle pdb=" CA PHE R 166 " pdb=" C PHE R 166 " pdb=" O PHE R 166 " ideal model delta sigma weight residual 119.41 111.51 7.90 1.13e+00 7.83e-01 4.89e+01 angle pdb=" CA PHE R 166 " pdb=" CB PHE R 166 " pdb=" CG PHE R 166 " ideal model delta sigma weight residual 113.80 120.55 -6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA ASP C 35 " pdb=" CB ASP C 35 " pdb=" CG ASP C 35 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.30e+01 angle pdb=" CA THR R 164 " pdb=" CB THR R 164 " pdb=" OG1 THR R 164 " ideal model delta sigma weight residual 109.60 101.12 8.48 1.50e+00 4.44e-01 3.20e+01 angle pdb=" C GLN R 142 " pdb=" N SER R 143 " pdb=" CA SER R 143 " ideal model delta sigma weight residual 122.54 113.50 9.04 1.65e+00 3.67e-01 3.00e+01 ... (remaining 12560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 4961 21.14 - 42.28: 393 42.28 - 63.42: 65 63.42 - 84.56: 11 84.56 - 105.70: 2 Dihedral angle restraints: 5432 sinusoidal: 1807 harmonic: 3625 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 149.85 -56.85 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" N ASP C 194 " pdb=" C ASP C 194 " pdb=" CA ASP C 194 " pdb=" CB ASP C 194 " ideal model delta harmonic sigma weight residual 122.80 135.28 -12.48 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" CA MET B 262 " pdb=" C MET B 262 " pdb=" N THR B 263 " pdb=" CA THR B 263 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1372 0.080 - 0.160: 127 0.160 - 0.241: 6 0.241 - 0.321: 1 0.321 - 0.401: 1 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ASP C 194 " pdb=" N ASP C 194 " pdb=" C ASP C 194 " pdb=" CB ASP C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ASN R 322 " pdb=" N ASN R 322 " pdb=" C ASN R 322 " pdb=" CB ASN R 322 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ASP C 35 " pdb=" N ASP C 35 " pdb=" C ASP C 35 " pdb=" CB ASP C 35 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1504 not shown) Planarity restraints: 1607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM P0G R 501 " 0.018 2.00e-02 2.50e+03 5.64e-02 3.97e+01 pdb=" CAS P0G R 501 " 0.017 2.00e-02 2.50e+03 pdb=" CAX P0G R 501 " -0.068 2.00e-02 2.50e+03 pdb=" NAQ P0G R 501 " 0.088 2.00e-02 2.50e+03 pdb=" OAD P0G R 501 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 163 " -0.024 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LEU R 163 " 0.078 2.00e-02 2.50e+03 pdb=" O LEU R 163 " -0.028 2.00e-02 2.50e+03 pdb=" N THR R 164 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 191 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C LEU C 191 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU C 191 " 0.028 2.00e-02 2.50e+03 pdb=" N MET C 192 " 0.025 2.00e-02 2.50e+03 ... (remaining 1604 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1535 2.76 - 3.30: 8878 3.30 - 3.83: 14634 3.83 - 4.37: 16219 4.37 - 4.90: 28537 Nonbonded interactions: 69803 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR C 56 " pdb=" O ALA C 82 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP A 368 " pdb=" ND2 ASN A 371 " model vdw 2.256 3.120 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.272 3.040 nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.276 3.040 ... (remaining 69798 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: 2.040 Set stop_for_unknowns flag: 0.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 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 : 0.004 0.098 9183 Z= 0.218 Angle : 0.757 9.524 12569 Z= 0.434 Chirality : 0.046 0.401 1507 Planarity : 0.005 0.056 1607 Dihedral : 15.549 105.698 3066 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.80 % Allowed : 20.07 % Favored : 78.12 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.25), residues: 1222 helix: 1.15 (0.27), residues: 389 sheet: -1.14 (0.35), residues: 239 loop : -1.96 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.012 0.001 TYR B 59 PHE 0.024 0.001 PHE R 166 TRP 0.018 0.001 TRP R 173 HIS 0.018 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9181) covalent geometry : angle 0.75719 (12565) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.83235 ( 4) hydrogen bonds : bond 0.17118 ( 408) hydrogen bonds : angle 7.61950 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.273 Fit side-chains REVERT: C 352 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7051 (mtp) REVERT: R 156 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6812 (tpt) outliers start: 15 outliers final: 6 residues processed: 165 average time/residue: 0.0803 time to fit residues: 18.9377 Evaluate side-chains 154 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 219 HIS Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 187 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 210 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.212748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.186375 restraints weight = 11847.645| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.25 r_work: 0.4088 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9183 Z= 0.145 Angle : 0.621 8.704 12569 Z= 0.319 Chirality : 0.044 0.291 1507 Planarity : 0.004 0.047 1607 Dihedral : 9.219 87.267 1401 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.61 % Allowed : 20.67 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1222 helix: 1.24 (0.27), residues: 388 sheet: -0.92 (0.34), residues: 247 loop : -2.07 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.010 0.001 TYR R 199 PHE 0.030 0.001 PHE A 246 TRP 0.012 0.001 TRP R 173 HIS 0.014 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9181) covalent geometry : angle 0.62123 (12565) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.58552 ( 4) hydrogen bonds : bond 0.04011 ( 408) hydrogen bonds : angle 5.68427 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.389 Fit side-chains REVERT: A 373 ARG cc_start: 0.7415 (tpm170) cc_final: 0.6592 (tpm170) REVERT: B 259 GLN cc_start: 0.7632 (pm20) cc_final: 0.6704 (pm20) REVERT: C 352 MET cc_start: 0.7407 (mtt) cc_final: 0.7070 (mtp) REVERT: R 156 MET cc_start: 0.7107 (mmm) cc_final: 0.6470 (tpp) outliers start: 30 outliers final: 17 residues processed: 173 average time/residue: 0.0883 time to fit residues: 21.9824 Evaluate side-chains 168 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 20.0000 chunk 89 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** 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 = 0.4453 r_free = 0.4453 target = 0.215060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.188115 restraints weight = 11610.301| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.27 r_work: 0.4115 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9183 Z= 0.134 Angle : 0.585 7.758 12569 Z= 0.299 Chirality : 0.043 0.251 1507 Planarity : 0.004 0.038 1607 Dihedral : 8.655 85.895 1388 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.69 % Allowed : 19.35 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1222 helix: 1.23 (0.27), residues: 391 sheet: -0.70 (0.35), residues: 250 loop : -2.08 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.012 0.001 TYR B 59 PHE 0.021 0.001 PHE A 246 TRP 0.011 0.001 TRP B 82 HIS 0.013 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9181) covalent geometry : angle 0.58468 (12565) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.63726 ( 4) hydrogen bonds : bond 0.03654 ( 408) hydrogen bonds : angle 5.22229 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.334 Fit side-chains REVERT: A 23 ASN cc_start: 0.7770 (t0) cc_final: 0.7549 (t0) REVERT: B 258 ASP cc_start: 0.7851 (t0) cc_final: 0.7650 (t70) REVERT: C 352 MET cc_start: 0.7532 (mtt) cc_final: 0.7197 (mtp) REVERT: C 353 HIS cc_start: 0.8508 (m170) cc_final: 0.8279 (m-70) REVERT: R 147 LYS cc_start: 0.8586 (mttp) cc_final: 0.8173 (mttt) REVERT: R 156 MET cc_start: 0.7010 (mmm) cc_final: 0.6388 (tpp) outliers start: 39 outliers final: 22 residues processed: 188 average time/residue: 0.0951 time to fit residues: 24.8832 Evaluate side-chains 179 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** C 222 ASN ** 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 = 0.4439 r_free = 0.4439 target = 0.213970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.186443 restraints weight = 11850.906| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.30 r_work: 0.4091 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9183 Z= 0.145 Angle : 0.591 7.796 12569 Z= 0.302 Chirality : 0.043 0.244 1507 Planarity : 0.004 0.039 1607 Dihedral : 8.400 85.748 1388 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.81 % Allowed : 19.71 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1222 helix: 1.25 (0.27), residues: 391 sheet: -0.66 (0.34), residues: 257 loop : -2.12 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 273 TYR 0.014 0.001 TYR B 59 PHE 0.019 0.001 PHE A 246 TRP 0.010 0.001 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9181) covalent geometry : angle 0.59058 (12565) SS BOND : bond 0.00386 ( 2) SS BOND : angle 0.74839 ( 4) hydrogen bonds : bond 0.03501 ( 408) hydrogen bonds : angle 5.09593 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.257 Fit side-chains REVERT: A 23 ASN cc_start: 0.7869 (t0) cc_final: 0.7635 (t0) REVERT: B 258 ASP cc_start: 0.8020 (t0) cc_final: 0.7778 (t70) REVERT: C 352 MET cc_start: 0.7526 (mtt) cc_final: 0.7167 (mtp) REVERT: C 353 HIS cc_start: 0.8515 (m170) cc_final: 0.8264 (m-70) REVERT: R 147 LYS cc_start: 0.8580 (mttp) cc_final: 0.8206 (mttt) REVERT: R 156 MET cc_start: 0.7061 (mmm) cc_final: 0.6410 (tpp) outliers start: 40 outliers final: 28 residues processed: 190 average time/residue: 0.0784 time to fit residues: 21.1361 Evaluate side-chains 186 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.211372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.183944 restraints weight = 11834.357| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.31 r_work: 0.4091 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9183 Z= 0.172 Angle : 0.611 7.880 12569 Z= 0.316 Chirality : 0.044 0.252 1507 Planarity : 0.004 0.041 1607 Dihedral : 7.841 84.724 1388 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.05 % Allowed : 20.43 % Favored : 74.52 % 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: -1.07 (0.25), residues: 1222 helix: 1.16 (0.27), residues: 390 sheet: -0.75 (0.34), residues: 252 loop : -2.06 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.015 0.001 TYR B 59 PHE 0.016 0.001 PHE A 246 TRP 0.011 0.001 TRP B 82 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9181) covalent geometry : angle 0.61047 (12565) SS BOND : bond 0.00429 ( 2) SS BOND : angle 0.85395 ( 4) hydrogen bonds : bond 0.03656 ( 408) hydrogen bonds : angle 5.12295 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.326 Fit side-chains REVERT: A 23 ASN cc_start: 0.7931 (t0) cc_final: 0.7705 (t0) REVERT: A 34 LYS cc_start: 0.8629 (tppt) cc_final: 0.8115 (tmmt) REVERT: A 279 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7490 (m-40) REVERT: A 373 ARG cc_start: 0.7522 (tpm170) cc_final: 0.6853 (tpm170) REVERT: B 259 GLN cc_start: 0.7746 (pm20) cc_final: 0.7521 (pm20) REVERT: C 352 MET cc_start: 0.7583 (mtt) cc_final: 0.7192 (mtp) REVERT: C 353 HIS cc_start: 0.8498 (m170) cc_final: 0.8229 (m-70) REVERT: R 147 LYS cc_start: 0.8557 (mttp) cc_final: 0.8185 (mttt) REVERT: R 156 MET cc_start: 0.7124 (mmm) cc_final: 0.6792 (tpt) REVERT: R 166 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: R 277 VAL cc_start: 0.6038 (OUTLIER) cc_final: 0.4895 (m) outliers start: 42 outliers final: 34 residues processed: 180 average time/residue: 0.0826 time to fit residues: 21.0414 Evaluate side-chains 186 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 293 ASN Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 4 optimal weight: 0.0470 chunk 120 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.0050 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.215171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.187688 restraints weight = 11795.122| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.39 r_work: 0.4103 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9183 Z= 0.116 Angle : 0.565 7.863 12569 Z= 0.290 Chirality : 0.043 0.212 1507 Planarity : 0.003 0.039 1607 Dihedral : 7.726 84.344 1388 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.53 % Allowed : 20.91 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1222 helix: 1.24 (0.27), residues: 392 sheet: -0.66 (0.34), residues: 252 loop : -2.01 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.011 0.001 TYR R 199 PHE 0.013 0.001 PHE A 246 TRP 0.009 0.001 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9181) covalent geometry : angle 0.56526 (12565) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.68553 ( 4) hydrogen bonds : bond 0.03290 ( 408) hydrogen bonds : angle 4.88852 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.223 Fit side-chains REVERT: A 23 ASN cc_start: 0.7908 (t0) cc_final: 0.7708 (t0) REVERT: A 34 LYS cc_start: 0.8585 (tppt) cc_final: 0.8054 (tmmt) REVERT: A 279 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7435 (m-40) REVERT: A 347 ARG cc_start: 0.6285 (mtt90) cc_final: 0.5960 (mtt90) REVERT: A 362 HIS cc_start: 0.8413 (m170) cc_final: 0.7982 (m170) REVERT: C 352 MET cc_start: 0.7596 (mtt) cc_final: 0.7195 (mtp) REVERT: C 353 HIS cc_start: 0.8450 (m170) cc_final: 0.8172 (m-70) REVERT: G 16 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7574 (p) REVERT: R 147 LYS cc_start: 0.8562 (mttp) cc_final: 0.8185 (mttt) REVERT: R 156 MET cc_start: 0.7016 (mmm) cc_final: 0.6635 (tpp) REVERT: R 282 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6218 (t80) outliers start: 46 outliers final: 31 residues processed: 184 average time/residue: 0.0696 time to fit residues: 18.5358 Evaluate side-chains 186 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.211388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186527 restraints weight = 11841.442| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.02 r_work: 0.4086 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9183 Z= 0.168 Angle : 0.603 7.988 12569 Z= 0.311 Chirality : 0.044 0.235 1507 Planarity : 0.004 0.040 1607 Dihedral : 7.732 83.633 1388 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 5.77 % Allowed : 20.91 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1222 helix: 1.19 (0.27), residues: 390 sheet: -0.68 (0.33), residues: 268 loop : -2.12 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.009 0.001 TYR A 360 PHE 0.013 0.001 PHE A 246 TRP 0.010 0.001 TRP B 82 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9181) covalent geometry : angle 0.60251 (12565) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.85620 ( 4) hydrogen bonds : bond 0.03565 ( 408) hydrogen bonds : angle 4.98695 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.206 Fit side-chains REVERT: A 34 LYS cc_start: 0.8622 (tppt) cc_final: 0.8101 (tmmt) REVERT: A 279 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7484 (m-40) REVERT: A 373 ARG cc_start: 0.7512 (tpm170) cc_final: 0.6812 (tpm170) REVERT: C 353 HIS cc_start: 0.8461 (m170) cc_final: 0.8169 (m-70) REVERT: G 16 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (p) REVERT: R 144 LEU cc_start: 0.6930 (tp) cc_final: 0.6696 (tt) REVERT: R 147 LYS cc_start: 0.8537 (mttp) cc_final: 0.8191 (mttt) REVERT: R 156 MET cc_start: 0.7015 (mmm) cc_final: 0.6702 (tpt) REVERT: R 277 VAL cc_start: 0.5941 (OUTLIER) cc_final: 0.4790 (m) outliers start: 48 outliers final: 38 residues processed: 188 average time/residue: 0.0745 time to fit residues: 20.0869 Evaluate side-chains 194 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 63 optimal weight: 0.0070 chunk 79 optimal weight: 20.0000 chunk 41 optimal weight: 0.2980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** 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 = 0.4446 r_free = 0.4446 target = 0.214344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187392 restraints weight = 11721.953| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.29 r_work: 0.4103 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9183 Z= 0.118 Angle : 0.573 8.329 12569 Z= 0.295 Chirality : 0.043 0.208 1507 Planarity : 0.004 0.078 1607 Dihedral : 7.680 83.555 1388 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.93 % Allowed : 22.36 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1222 helix: 1.27 (0.27), residues: 392 sheet: -0.53 (0.34), residues: 261 loop : -2.03 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.009 0.001 TYR R 199 PHE 0.024 0.001 PHE R 194 TRP 0.011 0.001 TRP R 105 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9181) covalent geometry : angle 0.57296 (12565) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.82879 ( 4) hydrogen bonds : bond 0.03244 ( 408) hydrogen bonds : angle 4.81045 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.343 Fit side-chains REVERT: A 34 LYS cc_start: 0.8611 (tppt) cc_final: 0.8098 (tmmt) REVERT: A 279 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7426 (m-40) REVERT: A 347 ARG cc_start: 0.6289 (mtt90) cc_final: 0.5953 (mtt90) REVERT: A 362 HIS cc_start: 0.8355 (m170) cc_final: 0.8020 (m170) REVERT: A 373 ARG cc_start: 0.7096 (tpm170) cc_final: 0.6390 (tpm170) REVERT: C 353 HIS cc_start: 0.8453 (m170) cc_final: 0.8164 (m-70) REVERT: R 147 LYS cc_start: 0.8540 (mttp) cc_final: 0.8189 (mttt) REVERT: R 156 MET cc_start: 0.6979 (mmm) cc_final: 0.6615 (tpp) outliers start: 41 outliers final: 36 residues processed: 181 average time/residue: 0.0803 time to fit residues: 20.6773 Evaluate side-chains 186 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** 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 = 0.4435 r_free = 0.4435 target = 0.212872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.185156 restraints weight = 11647.468| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.38 r_work: 0.4104 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9183 Z= 0.136 Angle : 0.584 8.387 12569 Z= 0.301 Chirality : 0.043 0.213 1507 Planarity : 0.004 0.068 1607 Dihedral : 7.648 83.076 1388 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.41 % Allowed : 21.51 % Favored : 73.08 % 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: -0.90 (0.25), residues: 1222 helix: 1.26 (0.27), residues: 392 sheet: -0.51 (0.34), residues: 261 loop : -2.03 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.014 0.001 TYR B 59 PHE 0.023 0.001 PHE R 194 TRP 0.008 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9181) covalent geometry : angle 0.58414 (12565) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.70287 ( 4) hydrogen bonds : bond 0.03322 ( 408) hydrogen bonds : angle 4.81835 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.304 Fit side-chains REVERT: A 19 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: A 34 LYS cc_start: 0.8606 (tppt) cc_final: 0.8076 (tmmt) REVERT: A 279 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7410 (m-40) REVERT: A 347 ARG cc_start: 0.6293 (mtt90) cc_final: 0.6005 (mtt90) REVERT: C 255 MET cc_start: 0.6542 (ppp) cc_final: 0.6082 (ppp) REVERT: C 353 HIS cc_start: 0.8452 (m170) cc_final: 0.8152 (m-70) REVERT: R 147 LYS cc_start: 0.8527 (mttp) cc_final: 0.8173 (mttt) REVERT: R 156 MET cc_start: 0.7029 (mmm) cc_final: 0.6647 (tpp) outliers start: 45 outliers final: 39 residues processed: 180 average time/residue: 0.0826 time to fit residues: 21.2385 Evaluate side-chains 192 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.213546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.185951 restraints weight = 11758.869| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.40 r_work: 0.4092 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9183 Z= 0.126 Angle : 0.578 8.381 12569 Z= 0.296 Chirality : 0.043 0.206 1507 Planarity : 0.004 0.064 1607 Dihedral : 7.628 82.345 1388 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.41 % Allowed : 21.39 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.25), residues: 1222 helix: 1.29 (0.27), residues: 392 sheet: -0.49 (0.34), residues: 261 loop : -2.00 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.009 0.001 TYR R 199 PHE 0.021 0.001 PHE R 194 TRP 0.009 0.001 TRP B 169 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9181) covalent geometry : angle 0.57748 (12565) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.69082 ( 4) hydrogen bonds : bond 0.03223 ( 408) hydrogen bonds : angle 4.73976 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.316 Fit side-chains REVERT: A 19 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: A 34 LYS cc_start: 0.8568 (tppt) cc_final: 0.8028 (tmmt) REVERT: A 279 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7367 (m-40) REVERT: A 347 ARG cc_start: 0.6312 (mtt90) cc_final: 0.6013 (mtt90) REVERT: C 147 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7903 (mtpp) REVERT: C 353 HIS cc_start: 0.8455 (m170) cc_final: 0.8161 (m-70) REVERT: R 147 LYS cc_start: 0.8509 (mttp) cc_final: 0.8146 (mttt) REVERT: R 156 MET cc_start: 0.7030 (mmm) cc_final: 0.6658 (tpp) outliers start: 45 outliers final: 37 residues processed: 183 average time/residue: 0.0706 time to fit residues: 18.4265 Evaluate side-chains 192 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 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 = 0.4400 r_free = 0.4400 target = 0.209077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.184093 restraints weight = 11591.342| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.03 r_work: 0.4061 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9183 Z= 0.204 Angle : 0.641 8.379 12569 Z= 0.334 Chirality : 0.045 0.254 1507 Planarity : 0.004 0.065 1607 Dihedral : 7.775 81.643 1388 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.29 % Allowed : 21.63 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1222 helix: 1.12 (0.27), residues: 392 sheet: -0.67 (0.33), residues: 268 loop : -2.08 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.009 0.001 TYR A 360 PHE 0.027 0.002 PHE R 194 TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9181) covalent geometry : angle 0.64110 (12565) SS BOND : bond 0.00446 ( 2) SS BOND : angle 0.79195 ( 4) hydrogen bonds : bond 0.03769 ( 408) hydrogen bonds : angle 5.03332 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.29 seconds wall clock time: 44 minutes 2.21 seconds (2642.21 seconds total)