Starting phenix.real_space_refine on Tue Mar 3 15:55:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg2_29992/03_2026/8gg2_29992.cif" } resolution = 3.0 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= 0.031 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 46 5.16 5 C 4347 2.51 5 N 1167 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1769 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 3 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 13, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2449 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2180 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 21 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 6} Time building chain proxies: 1.33, per 1000 atoms: 0.20 Number of scatterers: 6800 At special positions: 0 Unit cell: (83.2992, 136.229, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 3 15.00 O 1237 8.00 N 1167 7.00 C 4347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 0.80 Conformation dependent library (CDL) restraints added in 380.7 milliseconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 48.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.548A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.617A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.730A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.579A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.029A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.798A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.634A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.605A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.645A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.565A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.525A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 86 removed outlier: 3.715A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 101 through 137 removed outlier: 4.363A pdb=" N TRP R 105 " --> pdb=" O PHE R 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.029A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.635A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 5.287A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.798A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.795A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.043A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 318 removed outlier: 3.880A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.554A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.673A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.988A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.143A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.821A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.861A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.657A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.824A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1023 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: 1.07 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2189 1.35 - 1.47: 1752 1.47 - 1.58: 2928 1.58 - 1.70: 5 1.70 - 1.82: 64 Bond restraints: 6938 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 4.99e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.542 -0.036 2.00e-02 2.50e+03 3.16e+00 ... (remaining 6933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9274 1.37 - 2.74: 140 2.74 - 4.11: 30 4.11 - 5.48: 12 5.48 - 6.84: 2 Bond angle restraints: 9458 Sorted by residual: angle pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C4' GTP A 401 " ideal model delta sigma weight residual 111.00 104.16 6.84 3.00e+00 1.11e-01 5.20e+00 angle pdb=" N LEU R 287 " pdb=" CA LEU R 287 " pdb=" C LEU R 287 " ideal model delta sigma weight residual 109.81 114.06 -4.25 2.21e+00 2.05e-01 3.69e+00 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 105.30 5.70 3.00e+00 1.11e-01 3.61e+00 angle pdb=" N TRP R 286 " pdb=" CA TRP R 286 " pdb=" C TRP R 286 " ideal model delta sigma weight residual 113.30 115.81 -2.51 1.34e+00 5.57e-01 3.50e+00 angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.58 118.87 3.71 2.07e+00 2.33e-01 3.21e+00 ... (remaining 9453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.89: 3787 20.89 - 41.78: 237 41.78 - 62.68: 20 62.68 - 83.57: 7 83.57 - 104.46: 3 Dihedral angle restraints: 4054 sinusoidal: 1441 harmonic: 2613 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 0.13 104.46 1 2.00e+01 2.50e-03 3.00e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 171.79 -102.52 1 2.00e+01 2.50e-03 2.92e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -152.75 96.54 1 2.00e+01 2.50e-03 2.67e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 702 0.032 - 0.063: 285 0.063 - 0.095: 82 0.095 - 0.127: 41 0.127 - 0.158: 1 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1108 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ILE R 205 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO B 236 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO B 194 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 848 2.75 - 3.29: 6128 3.29 - 3.83: 10682 3.83 - 4.36: 12208 4.36 - 4.90: 22869 Nonbonded interactions: 52735 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.246 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.258 3.120 nonbonded pdb=" O ILE R 47 " pdb=" ND2 ASN R 51 " model vdw 2.271 3.120 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.283 3.040 ... (remaining 52730 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: 2.530 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 0.053 6939 Z= 0.126 Angle : 0.478 6.844 9460 Z= 0.248 Chirality : 0.040 0.158 1111 Planarity : 0.003 0.031 1185 Dihedral : 13.478 104.461 2353 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.64 (0.28), residues: 878 helix: 1.41 (0.26), residues: 402 sheet: 0.27 (0.40), residues: 170 loop : -0.74 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.011 0.001 TYR A 339 PHE 0.009 0.001 PHE B 234 TRP 0.008 0.001 TRP R 105 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6938) covalent geometry : angle 0.47728 ( 9458) SS BOND : bond 0.00068 ( 1) SS BOND : angle 1.77891 ( 2) hydrogen bonds : bond 0.20913 ( 351) hydrogen bonds : angle 6.05399 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.5972 time to fit residues: 60.1737 Evaluate side-chains 76 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106224 restraints weight = 8712.969| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.25 r_work: 0.3095 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6939 Z= 0.127 Angle : 0.503 6.902 9460 Z= 0.268 Chirality : 0.041 0.136 1111 Planarity : 0.003 0.030 1185 Dihedral : 7.319 103.036 986 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.78 % Allowed : 7.43 % Favored : 90.79 % 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: 1.06 (0.29), residues: 878 helix: 1.82 (0.26), residues: 405 sheet: 0.54 (0.40), residues: 164 loop : -0.69 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.011 0.001 TYR R 185 PHE 0.010 0.001 PHE A 212 TRP 0.007 0.001 TRP R 105 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6938) covalent geometry : angle 0.50323 ( 9458) SS BOND : bond 0.00341 ( 1) SS BOND : angle 1.20551 ( 2) hydrogen bonds : bond 0.05559 ( 351) hydrogen bonds : angle 4.29897 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.260 Fit side-chains REVERT: A 17 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6750 (mtpp) REVERT: A 32 LYS cc_start: 0.7733 (mttt) cc_final: 0.7440 (mtpp) REVERT: A 221 MET cc_start: 0.8573 (ttm) cc_final: 0.8370 (ttp) REVERT: B 57 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8662 (pttp) REVERT: R 65 GLN cc_start: 0.8988 (mt0) cc_final: 0.8336 (mp10) REVERT: R 284 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7599 (tp) outliers start: 12 outliers final: 4 residues processed: 89 average time/residue: 0.5622 time to fit residues: 52.7071 Evaluate side-chains 83 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102994 restraints weight = 8700.875| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.11 r_work: 0.3046 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6939 Z= 0.151 Angle : 0.525 7.027 9460 Z= 0.276 Chirality : 0.042 0.138 1111 Planarity : 0.003 0.031 1185 Dihedral : 7.390 102.946 986 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.78 % Allowed : 9.36 % Favored : 88.86 % 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: 1.13 (0.29), residues: 878 helix: 1.96 (0.27), residues: 404 sheet: 0.50 (0.41), residues: 160 loop : -0.71 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.013 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6938) covalent geometry : angle 0.52470 ( 9458) SS BOND : bond 0.00399 ( 1) SS BOND : angle 1.26520 ( 2) hydrogen bonds : bond 0.05695 ( 351) hydrogen bonds : angle 4.14835 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.253 Fit side-chains REVERT: A 17 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6373 (mtpp) REVERT: A 32 LYS cc_start: 0.7253 (mttt) cc_final: 0.7014 (mtpp) REVERT: G 19 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7148 (tp) REVERT: R 65 GLN cc_start: 0.8910 (mt0) cc_final: 0.8115 (mp10) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.5718 time to fit residues: 48.7695 Evaluate side-chains 78 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103388 restraints weight = 8816.567| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.10 r_work: 0.3046 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6939 Z= 0.126 Angle : 0.490 6.881 9460 Z= 0.258 Chirality : 0.041 0.134 1111 Planarity : 0.003 0.030 1185 Dihedral : 7.297 101.358 986 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.08 % Allowed : 10.70 % Favored : 87.22 % 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: 1.17 (0.29), residues: 878 helix: 2.05 (0.27), residues: 405 sheet: 0.52 (0.41), residues: 160 loop : -0.78 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6938) covalent geometry : angle 0.48954 ( 9458) SS BOND : bond 0.00390 ( 1) SS BOND : angle 1.23066 ( 2) hydrogen bonds : bond 0.04988 ( 351) hydrogen bonds : angle 4.00182 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.276 Fit side-chains REVERT: A 17 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6269 (mttm) REVERT: A 32 LYS cc_start: 0.7321 (mttt) cc_final: 0.7074 (mtpp) REVERT: B 228 ASP cc_start: 0.8491 (m-30) cc_final: 0.8145 (m-30) REVERT: G 19 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7271 (tp) REVERT: R 65 GLN cc_start: 0.8902 (mt0) cc_final: 0.8168 (mp10) REVERT: R 284 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7457 (tp) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 0.5847 time to fit residues: 49.8282 Evaluate side-chains 79 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 16 ASN R 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105564 restraints weight = 9013.589| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.06 r_work: 0.3058 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6939 Z= 0.120 Angle : 0.483 6.848 9460 Z= 0.255 Chirality : 0.041 0.133 1111 Planarity : 0.003 0.030 1185 Dihedral : 7.224 100.856 986 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.53 % Allowed : 12.33 % Favored : 85.14 % 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: 1.29 (0.29), residues: 878 helix: 2.14 (0.27), residues: 404 sheet: 0.60 (0.41), residues: 160 loop : -0.72 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE B 241 TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6938) covalent geometry : angle 0.48308 ( 9458) SS BOND : bond 0.00342 ( 1) SS BOND : angle 1.13058 ( 2) hydrogen bonds : bond 0.04781 ( 351) hydrogen bonds : angle 3.92614 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.264 Fit side-chains REVERT: A 32 LYS cc_start: 0.7196 (mttt) cc_final: 0.6960 (mtpp) REVERT: B 59 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: B 228 ASP cc_start: 0.8466 (m-30) cc_final: 0.8100 (m-30) REVERT: G 19 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7183 (tp) REVERT: R 65 GLN cc_start: 0.8843 (mt0) cc_final: 0.8088 (mp10) REVERT: R 284 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7398 (tp) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.5328 time to fit residues: 48.3051 Evaluate side-chains 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103583 restraints weight = 8963.591| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.08 r_work: 0.3035 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6939 Z= 0.145 Angle : 0.509 6.879 9460 Z= 0.268 Chirality : 0.042 0.137 1111 Planarity : 0.003 0.032 1185 Dihedral : 7.270 101.562 986 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.38 % Allowed : 13.97 % Favored : 83.66 % 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: 1.22 (0.29), residues: 878 helix: 2.08 (0.27), residues: 404 sheet: 0.56 (0.41), residues: 160 loop : -0.73 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.013 0.001 TYR A 339 PHE 0.012 0.001 PHE B 241 TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6938) covalent geometry : angle 0.50913 ( 9458) SS BOND : bond 0.00436 ( 1) SS BOND : angle 1.14206 ( 2) hydrogen bonds : bond 0.05283 ( 351) hydrogen bonds : angle 3.98854 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.182 Fit side-chains REVERT: A 32 LYS cc_start: 0.7248 (mttt) cc_final: 0.6999 (mtpp) REVERT: B 16 ASN cc_start: 0.7166 (m-40) cc_final: 0.6800 (m110) REVERT: B 57 LYS cc_start: 0.8868 (pttp) cc_final: 0.8485 (pttp) REVERT: B 59 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: B 228 ASP cc_start: 0.8507 (m-30) cc_final: 0.8149 (m-30) REVERT: G 19 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7230 (tp) REVERT: R 284 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7435 (tp) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.5768 time to fit residues: 50.9571 Evaluate side-chains 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106534 restraints weight = 8902.849| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.08 r_work: 0.3077 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6939 Z= 0.100 Angle : 0.458 6.674 9460 Z= 0.241 Chirality : 0.040 0.131 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.049 102.540 986 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.93 % Allowed : 14.86 % Favored : 83.21 % 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: 1.32 (0.29), residues: 878 helix: 2.20 (0.27), residues: 405 sheet: 0.67 (0.41), residues: 159 loop : -0.79 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE B 241 TRP 0.006 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6938) covalent geometry : angle 0.45735 ( 9458) SS BOND : bond 0.00293 ( 1) SS BOND : angle 1.06089 ( 2) hydrogen bonds : bond 0.04166 ( 351) hydrogen bonds : angle 3.83482 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.259 Fit side-chains REVERT: A 32 LYS cc_start: 0.7216 (mttt) cc_final: 0.7007 (ttmm) REVERT: B 16 ASN cc_start: 0.7173 (m-40) cc_final: 0.6805 (m110) REVERT: B 59 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 228 ASP cc_start: 0.8481 (m-30) cc_final: 0.8113 (m-30) REVERT: R 65 GLN cc_start: 0.8947 (mt0) cc_final: 0.8495 (mp10) REVERT: R 284 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7479 (tp) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.5319 time to fit residues: 49.8059 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.0010 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107997 restraints weight = 8967.600| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.08 r_work: 0.3099 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6939 Z= 0.090 Angle : 0.447 6.540 9460 Z= 0.236 Chirality : 0.040 0.130 1111 Planarity : 0.003 0.029 1185 Dihedral : 6.841 101.386 986 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.49 % Allowed : 15.90 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.29), residues: 878 helix: 2.49 (0.27), residues: 397 sheet: 0.71 (0.40), residues: 164 loop : -0.71 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.008 0.001 TYR R 209 PHE 0.012 0.001 PHE R 101 TRP 0.005 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 6938) covalent geometry : angle 0.44692 ( 9458) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.85273 ( 2) hydrogen bonds : bond 0.03780 ( 351) hydrogen bonds : angle 3.74540 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.198 Fit side-chains REVERT: B 16 ASN cc_start: 0.7067 (m-40) cc_final: 0.6681 (m110) REVERT: B 228 ASP cc_start: 0.8458 (m-30) cc_final: 0.8122 (m-30) REVERT: R 65 GLN cc_start: 0.8889 (mt0) cc_final: 0.8255 (mp10) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.5707 time to fit residues: 48.7097 Evaluate side-chains 78 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105989 restraints weight = 8934.908| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.09 r_work: 0.3069 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6939 Z= 0.115 Angle : 0.473 6.519 9460 Z= 0.249 Chirality : 0.040 0.133 1111 Planarity : 0.003 0.030 1185 Dihedral : 6.843 102.030 986 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.63 % Allowed : 15.90 % Favored : 82.47 % 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: 1.49 (0.29), residues: 878 helix: 2.44 (0.27), residues: 397 sheet: 0.73 (0.41), residues: 158 loop : -0.76 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.012 0.001 TYR R 219 PHE 0.011 0.001 PHE B 241 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6938) covalent geometry : angle 0.47276 ( 9458) SS BOND : bond 0.00346 ( 1) SS BOND : angle 0.92119 ( 2) hydrogen bonds : bond 0.04383 ( 351) hydrogen bonds : angle 3.82012 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.241 Fit side-chains REVERT: B 16 ASN cc_start: 0.7162 (m-40) cc_final: 0.6776 (m110) REVERT: B 57 LYS cc_start: 0.8917 (pttp) cc_final: 0.8369 (pttp) REVERT: B 228 ASP cc_start: 0.8501 (m-30) cc_final: 0.8142 (m-30) REVERT: R 65 GLN cc_start: 0.8919 (mt0) cc_final: 0.8290 (mp10) REVERT: R 284 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7466 (tp) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.5185 time to fit residues: 45.3406 Evaluate side-chains 83 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105274 restraints weight = 8916.648| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.09 r_work: 0.3056 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6939 Z= 0.119 Angle : 0.483 6.375 9460 Z= 0.254 Chirality : 0.041 0.134 1111 Planarity : 0.003 0.030 1185 Dihedral : 6.791 102.379 986 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.63 % Allowed : 16.05 % Favored : 82.32 % 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: 1.44 (0.29), residues: 878 helix: 2.40 (0.27), residues: 397 sheet: 0.69 (0.40), residues: 158 loop : -0.77 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.012 0.001 TYR R 219 PHE 0.011 0.001 PHE B 241 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6938) covalent geometry : angle 0.48242 ( 9458) SS BOND : bond 0.00339 ( 1) SS BOND : angle 0.92943 ( 2) hydrogen bonds : bond 0.04578 ( 351) hydrogen bonds : angle 3.87206 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.180 Fit side-chains REVERT: B 16 ASN cc_start: 0.7136 (m-40) cc_final: 0.6750 (m110) REVERT: B 228 ASP cc_start: 0.8483 (m-30) cc_final: 0.8138 (m-30) REVERT: R 65 GLN cc_start: 0.8913 (mt0) cc_final: 0.8279 (mp10) REVERT: R 284 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7579 (tp) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.5258 time to fit residues: 46.5328 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105834 restraints weight = 8931.116| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.08 r_work: 0.3070 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6939 Z= 0.114 Angle : 0.479 6.271 9460 Z= 0.252 Chirality : 0.041 0.134 1111 Planarity : 0.003 0.029 1185 Dihedral : 6.690 101.817 986 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.78 % Allowed : 15.90 % Favored : 82.32 % 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: 1.44 (0.29), residues: 878 helix: 2.40 (0.27), residues: 397 sheet: 0.69 (0.40), residues: 158 loop : -0.77 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.012 0.001 TYR R 219 PHE 0.014 0.001 PHE R 101 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6938) covalent geometry : angle 0.47917 ( 9458) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.93243 ( 2) hydrogen bonds : bond 0.04454 ( 351) hydrogen bonds : angle 3.85323 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.78 seconds wall clock time: 40 minutes 31.94 seconds (2431.94 seconds total)