Starting phenix.real_space_refine on Tue Feb 11 21:19:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gfy_29988/02_2025/8gfy_29988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gfy_29988/02_2025/8gfy_29988.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/8gfy_29988/02_2025/8gfy_29988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gfy_29988/02_2025/8gfy_29988.map" model { file = "/net/cci-nas-00/data/ceres_data/8gfy_29988/02_2025/8gfy_29988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gfy_29988/02_2025/8gfy_29988.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= 0.035 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 42 5.16 5 C 4278 2.51 5 N 1138 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 6670 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1742 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2426 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 348 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 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: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2103 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 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: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 19 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 4.55, per 1000 atoms: 0.68 Number of scatterers: 6670 At special positions: 0 Unit cell: (83.2992, 132.758, 100.653, 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 42 16.00 P 3 15.00 O 1209 8.00 N 1138 7.00 C 4278 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 48.5% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.613A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.506A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.665A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.558A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.666A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.500A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.767A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.786A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.534A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 37 through 61 Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.855A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.060A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 137 removed outlier: 3.649A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.584A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 163 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.623A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 3.824A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.575A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 241 No H-bonds generated for 'chain 'R' and resid 239 through 241' Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.742A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.174A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.804A 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: 4.542A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.696A 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: 6.622A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.930A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A 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: 7.151A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.859A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.122A 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: 6.911A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.650A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.868A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 999 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: 2.12 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2141 1.34 - 1.46: 1494 1.46 - 1.58: 3114 1.58 - 1.69: 5 1.69 - 1.81: 57 Bond restraints: 6811 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 7.00e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.538 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 6806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 9104 1.23 - 2.47: 152 2.47 - 3.70: 30 3.70 - 4.93: 12 4.93 - 6.17: 6 Bond angle restraints: 9304 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.56 109.97 4.59 1.27e+00 6.20e-01 1.31e+01 angle pdb=" CA ARG B 197 " pdb=" C ARG B 197 " pdb=" N LEU B 198 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.08e+00 angle pdb=" N PHE R 208 " pdb=" CA PHE R 208 " pdb=" C PHE R 208 " ideal model delta sigma weight residual 112.72 115.65 -2.93 1.28e+00 6.10e-01 5.26e+00 angle pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C4' GTP A 401 " ideal model delta sigma weight residual 111.00 104.83 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" CA ARG B 197 " pdb=" C ARG B 197 " pdb=" O ARG B 197 " ideal model delta sigma weight residual 118.55 120.76 -2.21 1.14e+00 7.69e-01 3.77e+00 ... (remaining 9299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 3845 28.59 - 57.17: 97 57.17 - 85.76: 8 85.76 - 114.34: 0 114.34 - 142.93: 2 Dihedral angle restraints: 3952 sinusoidal: 1354 harmonic: 2598 Sorted by residual: 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 -147.80 -142.93 1 2.00e+01 2.50e-03 4.31e+01 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 -9.93 114.52 1 2.00e+01 2.50e-03 3.40e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 3949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 732 0.034 - 0.068: 271 0.068 - 0.102: 75 0.102 - 0.136: 25 0.136 - 0.170: 1 Chirality restraints: 1104 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 2.57 -0.17 2.00e-01 2.50e+01 7.22e-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 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1101 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 332 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ILE R 205 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C THR R 281 " 0.020 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.007 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.007 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 976 2.76 - 3.29: 6033 3.29 - 3.83: 10567 3.83 - 4.36: 12046 4.36 - 4.90: 22332 Nonbonded interactions: 51954 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.306 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.322 3.040 ... (remaining 51949 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.060 Set scattering table: 0.060 Process input model: 19.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 6811 Z= 0.169 Angle : 0.464 6.167 9304 Z= 0.248 Chirality : 0.040 0.170 1104 Planarity : 0.003 0.048 1164 Dihedral : 12.901 142.927 2261 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.86 (0.28), residues: 873 helix: 1.49 (0.27), residues: 389 sheet: 0.59 (0.40), residues: 165 loop : -0.53 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE B 234 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.788 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 97 average time/residue: 1.1684 time to fit residues: 119.7876 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.095381 restraints weight = 8845.057| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.68 r_work: 0.2893 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6811 Z= 0.208 Angle : 0.509 6.277 9304 Z= 0.272 Chirality : 0.042 0.192 1104 Planarity : 0.003 0.042 1164 Dihedral : 8.152 144.490 978 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.24 % Allowed : 8.85 % Favored : 89.91 % 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: 0.90 (0.28), residues: 873 helix: 1.63 (0.27), residues: 391 sheet: 0.56 (0.42), residues: 159 loop : -0.62 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.774 Fit side-chains REVERT: A 330 GLU cc_start: 0.7437 (tt0) cc_final: 0.7033 (tt0) REVERT: B 262 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8620 (ttp) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 1.2187 time to fit residues: 112.1995 Evaluate side-chains 81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 51 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098331 restraints weight = 8931.102| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.73 r_work: 0.2936 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6811 Z= 0.122 Angle : 0.436 6.200 9304 Z= 0.233 Chirality : 0.040 0.130 1104 Planarity : 0.003 0.037 1164 Dihedral : 7.553 145.918 976 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.55 % Allowed : 10.71 % Favored : 87.73 % 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: 1.13 (0.28), residues: 873 helix: 1.82 (0.27), residues: 393 sheet: 0.68 (0.42), residues: 159 loop : -0.53 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.751 Fit side-chains REVERT: A 34 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7819 (ttpt) REVERT: A 330 GLU cc_start: 0.7191 (tt0) cc_final: 0.6688 (tt0) outliers start: 10 outliers final: 1 residues processed: 85 average time/residue: 1.1062 time to fit residues: 99.8109 Evaluate side-chains 78 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 340 ASN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101931 restraints weight = 8955.356| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.63 r_work: 0.2935 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6811 Z= 0.151 Angle : 0.455 6.299 9304 Z= 0.242 Chirality : 0.040 0.131 1104 Planarity : 0.003 0.032 1164 Dihedral : 7.552 146.638 976 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.17 % Allowed : 11.49 % Favored : 86.34 % 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: 1.16 (0.28), residues: 873 helix: 1.88 (0.27), residues: 392 sheet: 0.69 (0.42), residues: 159 loop : -0.55 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.003 0.001 HIS R 178 PHE 0.011 0.001 PHE A 212 TYR 0.008 0.001 TYR R 132 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.805 Fit side-chains REVERT: A 330 GLU cc_start: 0.7228 (tt0) cc_final: 0.6699 (tt0) REVERT: B 175 GLN cc_start: 0.8455 (mm110) cc_final: 0.8239 (tp40) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: R 65 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8118 (mt0) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 1.1811 time to fit residues: 106.3616 Evaluate side-chains 84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 340 ASN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.096528 restraints weight = 8972.357| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.74 r_work: 0.2918 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6811 Z= 0.281 Angle : 0.532 6.407 9304 Z= 0.282 Chirality : 0.043 0.141 1104 Planarity : 0.003 0.041 1164 Dihedral : 7.726 147.980 976 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 12.58 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 873 helix: 1.65 (0.27), residues: 392 sheet: 0.56 (0.41), residues: 166 loop : -0.60 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.005 0.001 HIS R 178 PHE 0.014 0.002 PHE A 212 TYR 0.012 0.001 TYR R 132 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.798 Fit side-chains REVERT: A 330 GLU cc_start: 0.7200 (tt0) cc_final: 0.6755 (tt0) REVERT: B 234 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: R 65 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: R 228 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7379 (ttm170) outliers start: 17 outliers final: 7 residues processed: 87 average time/residue: 1.0769 time to fit residues: 99.7692 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 228 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098365 restraints weight = 8830.417| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.69 r_work: 0.2957 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6811 Z= 0.171 Angle : 0.471 6.264 9304 Z= 0.252 Chirality : 0.041 0.135 1104 Planarity : 0.003 0.034 1164 Dihedral : 7.675 148.175 976 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.48 % Allowed : 13.66 % Favored : 83.85 % 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: 0.99 (0.28), residues: 873 helix: 1.74 (0.27), residues: 390 sheet: 0.66 (0.42), residues: 160 loop : -0.66 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.010 0.001 TYR A 339 ARG 0.001 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.763 Fit side-chains REVERT: B 175 GLN cc_start: 0.8229 (mm110) cc_final: 0.8029 (tp40) REVERT: B 234 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: R 65 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8231 (mt0) outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 1.1117 time to fit residues: 100.5083 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 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 239 ASN B 340 ASN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.098894 restraints weight = 8885.947| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.70 r_work: 0.2971 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6811 Z= 0.155 Angle : 0.459 6.226 9304 Z= 0.245 Chirality : 0.041 0.206 1104 Planarity : 0.003 0.034 1164 Dihedral : 7.580 148.056 976 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.02 % Allowed : 14.44 % Favored : 83.54 % 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: 1.07 (0.28), residues: 873 helix: 1.78 (0.27), residues: 394 sheet: 0.72 (0.42), residues: 159 loop : -0.61 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR A 339 ARG 0.001 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.761 Fit side-chains REVERT: B 175 GLN cc_start: 0.8226 (mm110) cc_final: 0.8021 (tp40) REVERT: B 234 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: R 65 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8207 (mt0) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 1.0355 time to fit residues: 92.5731 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098372 restraints weight = 8931.208| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.74 r_work: 0.2944 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6811 Z= 0.202 Angle : 0.483 6.304 9304 Z= 0.257 Chirality : 0.041 0.135 1104 Planarity : 0.003 0.037 1164 Dihedral : 7.587 148.309 976 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.86 % Allowed : 14.91 % Favored : 83.23 % 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: 1.00 (0.28), residues: 873 helix: 1.72 (0.27), residues: 393 sheet: 0.69 (0.42), residues: 160 loop : -0.67 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.744 Fit side-chains REVERT: B 175 GLN cc_start: 0.8230 (mm110) cc_final: 0.8027 (tp40) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: R 65 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8249 (mt0) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 1.0433 time to fit residues: 91.0904 Evaluate side-chains 78 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3403 r_free = 0.3403 target = 0.124497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101387 restraints weight = 8888.499| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.74 r_work: 0.2989 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6811 Z= 0.123 Angle : 0.441 6.190 9304 Z= 0.236 Chirality : 0.040 0.219 1104 Planarity : 0.003 0.031 1164 Dihedral : 7.436 147.560 976 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.40 % Allowed : 15.68 % Favored : 82.92 % 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 (0.28), residues: 873 helix: 1.86 (0.27), residues: 393 sheet: 0.88 (0.42), residues: 156 loop : -0.68 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.727 Fit side-chains REVERT: B 175 GLN cc_start: 0.8242 (mm110) cc_final: 0.8024 (tp40) REVERT: B 234 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: R 65 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8177 (mt0) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 1.1040 time to fit residues: 96.4388 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 65 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3427 r_free = 0.3427 target = 0.126507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103298 restraints weight = 9020.785| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.76 r_work: 0.3003 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6811 Z= 0.105 Angle : 0.424 6.181 9304 Z= 0.226 Chirality : 0.039 0.133 1104 Planarity : 0.003 0.030 1164 Dihedral : 7.318 146.317 976 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.24 % Allowed : 15.53 % Favored : 83.23 % 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: 1.27 (0.28), residues: 873 helix: 1.99 (0.27), residues: 394 sheet: 0.86 (0.42), residues: 157 loop : -0.61 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.007 0.001 TYR A 339 ARG 0.001 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.804 Fit side-chains REVERT: B 175 GLN cc_start: 0.8218 (mm110) cc_final: 0.8008 (tp40) REVERT: R 65 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8136 (mt0) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 1.0112 time to fit residues: 90.5948 Evaluate side-chains 79 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain R residue 65 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** 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 = 0.3382 r_free = 0.3382 target = 0.122741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099692 restraints weight = 8878.393| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.71 r_work: 0.2965 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6811 Z= 0.159 Angle : 0.461 6.315 9304 Z= 0.245 Chirality : 0.041 0.164 1104 Planarity : 0.003 0.035 1164 Dihedral : 7.363 146.549 976 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.78 % Allowed : 16.15 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.28), residues: 873 helix: 1.93 (0.27), residues: 398 sheet: 0.86 (0.42), residues: 156 loop : -0.58 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE B 292 TYR 0.008 0.001 TYR R 132 ARG 0.001 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4430.27 seconds wall clock time: 79 minutes 13.44 seconds (4753.44 seconds total)