Starting phenix.real_space_refine on Tue Feb 11 23:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg2_29992/02_2025/8gg2_29992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg2_29992/02_2025/8gg2_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_29992/02_2025/8gg2_29992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg2_29992/02_2025/8gg2_29992.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg2_29992/02_2025/8gg2_29992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg2_29992/02_2025/8gg2_29992.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} 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, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} 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, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2} 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: 5.06, per 1000 atoms: 0.74 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: 1.67 Conformation dependent library (CDL) restraints added in 928.7 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: 0.73 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: 2.01 Time building geometry restraints manager: 1.93 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: 1.510 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.680 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- 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 6938 Z= 0.173 Angle : 0.477 6.844 9458 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.008 0.001 TRP R 105 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 234 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG G 27 *********************** 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 : 0.789 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 1.2948 time to fit residues: 130.8965 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 : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.133178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105018 restraints weight = 8579.600| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.22 r_work: 0.3075 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6938 Z= 0.221 Angle : 0.526 6.984 9458 Z= 0.278 Chirality : 0.042 0.136 1111 Planarity : 0.003 0.030 1185 Dihedral : 7.409 104.017 986 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.78 % Allowed : 7.73 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 878 helix: 1.73 (0.26), residues: 405 sheet: 0.47 (0.40), residues: 159 loop : -0.76 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.005 0.001 HIS R 296 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 185 ARG 0.003 0.000 ARG A 356 *********************** 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 95 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.727 Fit side-chains REVERT: A 17 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6752 (mtpp) REVERT: A 32 LYS cc_start: 0.7739 (mttt) cc_final: 0.7439 (mtpp) REVERT: R 65 GLN cc_start: 0.9014 (mt0) cc_final: 0.8363 (mp10) REVERT: R 284 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7614 (tp) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 1.3128 time to fit residues: 120.2877 Evaluate side-chains 82 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.131938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104475 restraints weight = 8750.550| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.12 r_work: 0.3065 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6938 Z= 0.188 Angle : 0.494 6.909 9458 Z= 0.260 Chirality : 0.041 0.135 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.303 102.208 986 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.93 % Allowed : 9.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 878 helix: 1.97 (0.27), residues: 405 sheet: 0.62 (0.41), residues: 159 loop : -0.79 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR R 185 ARG 0.003 0.000 ARG A 265 *********************** 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 89 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.711 Fit side-chains REVERT: A 17 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6370 (mttm) REVERT: A 32 LYS cc_start: 0.7244 (mttt) cc_final: 0.7013 (mtpp) REVERT: G 19 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7180 (tp) REVERT: R 65 GLN cc_start: 0.8863 (mt0) cc_final: 0.8108 (mp10) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 1.2915 time to fit residues: 110.5892 Evaluate side-chains 78 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 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 = 0.3524 r_free = 0.3524 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105140 restraints weight = 8872.144| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.08 r_work: 0.3071 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6938 Z= 0.162 Angle : 0.469 6.822 9458 Z= 0.247 Chirality : 0.040 0.134 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.179 100.167 986 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.93 % Allowed : 10.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 878 helix: 2.13 (0.27), residues: 405 sheet: 0.68 (0.41), residues: 159 loop : -0.78 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.013 0.001 TYR R 185 ARG 0.003 0.000 ARG A 265 *********************** 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: 13 poor density : 77 time to evaluate : 0.770 Fit side-chains REVERT: A 17 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6205 (mttm) REVERT: A 32 LYS cc_start: 0.7222 (mttt) cc_final: 0.6997 (mtpp) REVERT: G 19 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7227 (tp) REVERT: R 65 GLN cc_start: 0.8859 (mt0) cc_final: 0.8138 (mp10) REVERT: R 284 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7442 (tp) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 1.2319 time to fit residues: 106.7563 Evaluate side-chains 82 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106893 restraints weight = 8842.059| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.04 r_work: 0.3076 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.002 0.025 6938 Z= 0.161 Angle : 0.467 6.783 9458 Z= 0.246 Chirality : 0.040 0.133 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.108 100.084 986 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.78 % Allowed : 12.48 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 878 helix: 2.20 (0.27), residues: 405 sheet: 0.72 (0.41), residues: 159 loop : -0.76 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** 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 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.721 Fit side-chains REVERT: B 228 ASP cc_start: 0.8461 (m-30) cc_final: 0.8093 (m-30) REVERT: R 65 GLN cc_start: 0.8821 (mt0) cc_final: 0.8075 (mp10) REVERT: R 284 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7438 (tp) outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 1.2247 time to fit residues: 109.9062 Evaluate side-chains 81 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 82 MET 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 6 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 239 ASN B 340 ASN R 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102202 restraints weight = 8833.486| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.06 r_work: 0.3032 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6938 Z= 0.254 Angle : 0.528 6.917 9458 Z= 0.277 Chirality : 0.042 0.138 1111 Planarity : 0.003 0.032 1185 Dihedral : 7.270 101.799 986 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.23 % Allowed : 13.52 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 878 helix: 2.10 (0.27), residues: 404 sheet: 0.67 (0.41), residues: 159 loop : -0.69 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.002 PHE B 151 TYR 0.014 0.001 TYR A 339 ARG 0.003 0.000 ARG A 356 *********************** 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 89 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.777 Fit side-chains REVERT: B 16 ASN cc_start: 0.7140 (m-40) cc_final: 0.6777 (m110) REVERT: B 228 ASP cc_start: 0.8503 (m-30) cc_final: 0.8145 (m-30) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 1.2402 time to fit residues: 108.9811 Evaluate side-chains 81 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.132896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106413 restraints weight = 8782.649| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.06 r_work: 0.3077 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6938 Z= 0.146 Angle : 0.466 6.670 9458 Z= 0.245 Chirality : 0.040 0.132 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.037 102.371 986 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.93 % Allowed : 14.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 878 helix: 2.22 (0.27), residues: 405 sheet: 0.76 (0.41), residues: 158 loop : -0.76 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE R 49 TYR 0.010 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** 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 92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.766 Fit side-chains REVERT: B 16 ASN cc_start: 0.7129 (m-40) cc_final: 0.6765 (m110) REVERT: B 59 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: B 228 ASP cc_start: 0.8468 (m-30) cc_final: 0.8097 (m-30) REVERT: R 65 GLN cc_start: 0.8895 (mt0) cc_final: 0.8304 (mp10) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 1.3500 time to fit residues: 124.3053 Evaluate side-chains 83 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET 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 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.0010 chunk 76 optimal weight: 2.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.130077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103577 restraints weight = 8859.410| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.06 r_work: 0.3055 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6938 Z= 0.193 Angle : 0.493 6.696 9458 Z= 0.259 Chirality : 0.041 0.136 1111 Planarity : 0.003 0.030 1185 Dihedral : 7.072 103.456 986 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.78 % Allowed : 15.16 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 878 helix: 2.20 (0.27), residues: 404 sheet: 0.73 (0.41), residues: 158 loop : -0.71 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE R 49 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** 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: 12 poor density : 72 time to evaluate : 0.731 Fit side-chains REVERT: B 16 ASN cc_start: 0.7104 (m-40) cc_final: 0.6733 (m110) REVERT: B 228 ASP cc_start: 0.8488 (m-30) cc_final: 0.8116 (m-30) REVERT: R 65 GLN cc_start: 0.8920 (mt0) cc_final: 0.8310 (mp10) REVERT: R 284 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7428 (tp) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 1.2189 time to fit residues: 101.7486 Evaluate side-chains 83 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103891 restraints weight = 8875.428| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.07 r_work: 0.3057 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6938 Z= 0.185 Angle : 0.488 6.564 9458 Z= 0.257 Chirality : 0.041 0.134 1111 Planarity : 0.003 0.029 1185 Dihedral : 7.008 104.288 986 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.63 % Allowed : 15.30 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 878 helix: 2.19 (0.27), residues: 405 sheet: 0.73 (0.41), residues: 158 loop : -0.79 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE R 49 TYR 0.011 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 *********************** 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 85 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.762 Fit side-chains REVERT: B 16 ASN cc_start: 0.7114 (m-40) cc_final: 0.6744 (m110) REVERT: B 57 LYS cc_start: 0.8930 (pttp) cc_final: 0.8475 (pttp) REVERT: B 228 ASP cc_start: 0.8490 (m-30) cc_final: 0.8118 (m-30) REVERT: R 65 GLN cc_start: 0.8902 (mt0) cc_final: 0.8320 (mp10) REVERT: R 284 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7424 (tp) outliers start: 11 outliers final: 10 residues processed: 81 average time/residue: 1.1565 time to fit residues: 99.1535 Evaluate side-chains 84 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.0000 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106445 restraints weight = 9044.473| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.09 r_work: 0.3078 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 0.020 6938 Z= 0.153 Angle : 0.470 6.391 9458 Z= 0.247 Chirality : 0.040 0.133 1111 Planarity : 0.003 0.029 1185 Dihedral : 6.839 104.253 986 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.78 % Allowed : 15.45 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 878 helix: 2.25 (0.27), residues: 405 sheet: 0.76 (0.40), residues: 158 loop : -0.77 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE R 49 TYR 0.009 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 ********************** 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 89 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.742 Fit side-chains REVERT: B 16 ASN cc_start: 0.7150 (m-40) cc_final: 0.6764 (m110) REVERT: B 228 ASP cc_start: 0.8487 (m-30) cc_final: 0.8166 (m-30) REVERT: R 65 GLN cc_start: 0.8882 (mt0) cc_final: 0.8325 (mp10) REVERT: R 284 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7474 (tp) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 1.2210 time to fit residues: 109.5155 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 75 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 = 0.3547 r_free = 0.3547 target = 0.133980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107362 restraints weight = 8898.946| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.08 r_work: 0.3087 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6938 Z= 0.140 Angle : 0.462 6.230 9458 Z= 0.243 Chirality : 0.040 0.132 1111 Planarity : 0.003 0.029 1185 Dihedral : 6.593 101.259 986 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.63 % Allowed : 15.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 878 helix: 2.44 (0.27), residues: 398 sheet: 0.76 (0.40), residues: 158 loop : -0.76 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE R 49 TYR 0.009 0.001 TYR A 339 ARG 0.004 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4759.15 seconds wall clock time: 84 minutes 56.01 seconds (5096.01 seconds total)