Starting phenix.real_space_refine on Fri Aug 22 22:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iw7_35763/08_2025/8iw7_35763.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5310 2.51 5 N 1415 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8305 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1971 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 7, 'TRP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2437 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1839 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "S" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "Y" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 369 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8305 At special positions: 0 Unit cell: (105.448, 101.144, 120.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1532 8.00 N 1415 7.00 C 5310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 335.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 37 through 59 removed outlier: 4.501A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.627A pdb=" N LEU R 63 " --> pdb=" O PHE R 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS R 64 " --> pdb=" O LYS R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 60 through 64' Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.017A pdb=" N LEU R 70 " --> pdb=" O PRO R 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 4.214A pdb=" N PHE R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 116 removed outlier: 4.517A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 136 removed outlier: 3.826A pdb=" N PHE R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 163 removed outlier: 3.696A pdb=" N ILE R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR R 163 " --> pdb=" O PHE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.810A pdb=" N TYR R 169 " --> pdb=" O PHE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 removed outlier: 3.788A pdb=" N VAL R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 3.805A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 4.176A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 269 removed outlier: 3.714A pdb=" N LYS R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE R 267 " --> pdb=" O ALA R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 280 removed outlier: 4.008A pdb=" N TYR R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 283 No H-bonds generated for 'chain 'R' and resid 281 through 283' Processing helix chain 'R' and resid 289 through 292 Processing helix chain 'R' and resid 293 through 311 removed outlier: 4.065A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.686A pdb=" N ARG R 319 " --> pdb=" O TYR R 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA R 321 " --> pdb=" O TRP R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 326 No H-bonds generated for 'chain 'R' and resid 324 through 326' Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.481A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.920A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.435A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 268 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.601A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.703A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.141A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'Y' and resid 10 through 24 Processing helix chain 'Y' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.787A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.040A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.580A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.321A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.578A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.010A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.582A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.685A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.548A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.601A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 148 through 149 removed outlier: 3.717A pdb=" N GLU S 247 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU S 246 " --> pdb=" O GLY S 226 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 1598 1.46 - 1.58: 4147 1.58 - 1.70: 0 1.70 - 1.81: 64 Bond restraints: 8485 Sorted by residual: bond pdb=" N GLN A 390 " pdb=" CA GLN A 390 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.66e+00 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" CA ASN R 307 " pdb=" C ASN R 307 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.26e-02 6.30e+03 2.91e+00 bond pdb=" N PEA R 401 " pdb=" C1 PEA R 401 " ideal model delta sigma weight residual 1.486 1.452 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.19e-02 7.06e+03 2.42e+00 ... (remaining 8480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11256 1.84 - 3.69: 250 3.69 - 5.53: 47 5.53 - 7.37: 9 7.37 - 9.22: 6 Bond angle restraints: 11568 Sorted by residual: angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" C GLN B 17 " ideal model delta sigma weight residual 111.14 103.58 7.56 1.08e+00 8.57e-01 4.90e+01 angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 111.90 107.50 4.40 8.10e-01 1.52e+00 2.95e+01 angle pdb=" N ASP R 112 " pdb=" CA ASP R 112 " pdb=" C ASP R 112 " ideal model delta sigma weight residual 111.03 105.07 5.96 1.11e+00 8.12e-01 2.88e+01 angle pdb=" N TYR R 301 " pdb=" CA TYR R 301 " pdb=" C TYR R 301 " ideal model delta sigma weight residual 112.23 107.14 5.09 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N LEU Y 50 " pdb=" CA LEU Y 50 " pdb=" C LEU Y 50 " ideal model delta sigma weight residual 114.04 109.03 5.01 1.24e+00 6.50e-01 1.63e+01 ... (remaining 11563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4396 17.73 - 35.47: 433 35.47 - 53.20: 88 53.20 - 70.94: 20 70.94 - 88.67: 5 Dihedral angle restraints: 4942 sinusoidal: 1667 harmonic: 3275 Sorted by residual: dihedral pdb=" CA PHE R 115 " pdb=" C PHE R 115 " pdb=" N CYS R 116 " pdb=" CA CYS R 116 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU R 205 " pdb=" C LEU R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 124.40 -31.40 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 924 0.038 - 0.077: 308 0.077 - 0.115: 103 0.115 - 0.153: 15 0.153 - 0.191: 4 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU Y 37 " pdb=" CB LEU Y 37 " pdb=" CD1 LEU Y 37 " pdb=" CD2 LEU Y 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ARG A 356 " pdb=" N ARG A 356 " pdb=" C ARG A 356 " pdb=" CB ARG A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1351 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO S 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 16 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASN B 16 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN B 16 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 17 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR B 87 " 0.034 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.011 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1205 2.75 - 3.29: 8046 3.29 - 3.83: 13179 3.83 - 4.36: 15482 4.36 - 4.90: 27059 Nonbonded interactions: 64971 Sorted by model distance: nonbonded pdb=" N GLU B 226 " pdb=" OE1 GLU B 226 " model vdw 2.214 3.120 nonbonded pdb=" N GLU Y 58 " pdb=" OE1 GLU Y 58 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.258 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.265 3.040 ... (remaining 64966 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8487 Z= 0.203 Angle : 0.705 9.218 11572 Z= 0.409 Chirality : 0.044 0.191 1354 Planarity : 0.004 0.070 1471 Dihedral : 15.117 88.670 2822 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.85 % Allowed : 23.24 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.24), residues: 1109 helix: -1.07 (0.26), residues: 369 sheet: -0.50 (0.34), residues: 246 loop : -1.61 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 181 TYR 0.020 0.001 TYR S 228 PHE 0.026 0.002 PHE R 159 TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8485) covalent geometry : angle 0.70521 (11568) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.89100 ( 4) hydrogen bonds : bond 0.25089 ( 360) hydrogen bonds : angle 8.20417 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.326 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 0.4174 time to fit residues: 66.1348 Evaluate side-chains 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN B 75 GLN B 225 HIS B 268 ASN A 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.141913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.108803 restraints weight = 12145.271| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.73 r_work: 0.3454 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8487 Z= 0.115 Angle : 0.559 9.106 11572 Z= 0.292 Chirality : 0.040 0.274 1354 Planarity : 0.004 0.055 1471 Dihedral : 5.104 55.673 1227 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.83 % Allowed : 22.00 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.25), residues: 1109 helix: 0.24 (0.28), residues: 378 sheet: -0.29 (0.34), residues: 255 loop : -1.62 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 92 TYR 0.018 0.001 TYR S 191 PHE 0.020 0.001 PHE R 159 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8485) covalent geometry : angle 0.55917 (11568) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.63612 ( 4) hydrogen bonds : bond 0.04663 ( 360) hydrogen bonds : angle 5.14111 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7377 (pp20) cc_final: 0.7150 (pp20) REVERT: B 59 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 75 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7707 (mp-120) REVERT: B 226 GLU cc_start: 0.8284 (pm20) cc_final: 0.7779 (pm20) outliers start: 31 outliers final: 11 residues processed: 153 average time/residue: 0.4161 time to fit residues: 68.7741 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain Y residue 22 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.142333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108910 restraints weight = 12063.942| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.75 r_work: 0.3464 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8487 Z= 0.109 Angle : 0.539 8.695 11572 Z= 0.278 Chirality : 0.040 0.299 1354 Planarity : 0.003 0.054 1471 Dihedral : 4.441 53.541 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.83 % Allowed : 24.97 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.26), residues: 1109 helix: 0.69 (0.29), residues: 363 sheet: -0.19 (0.34), residues: 255 loop : -1.63 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 181 TYR 0.014 0.001 TYR S 191 PHE 0.017 0.001 PHE R 144 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8485) covalent geometry : angle 0.53848 (11568) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.76253 ( 4) hydrogen bonds : bond 0.04071 ( 360) hydrogen bonds : angle 4.81911 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8140 (m) cc_final: 0.7879 (p) REVERT: B 75 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7566 (mp-120) REVERT: B 226 GLU cc_start: 0.8327 (pm20) cc_final: 0.7860 (pm20) REVERT: S 4 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7150 (pp) REVERT: S 180 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8301 (tm-30) outliers start: 31 outliers final: 13 residues processed: 148 average time/residue: 0.3432 time to fit residues: 55.4233 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107625 restraints weight = 12352.579| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.76 r_work: 0.3436 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8487 Z= 0.128 Angle : 0.549 8.751 11572 Z= 0.283 Chirality : 0.041 0.308 1354 Planarity : 0.003 0.051 1471 Dihedral : 4.455 51.547 1212 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 25.22 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.26), residues: 1109 helix: 0.83 (0.29), residues: 363 sheet: -0.16 (0.34), residues: 255 loop : -1.63 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 181 TYR 0.018 0.001 TYR B 59 PHE 0.028 0.002 PHE A 376 TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8485) covalent geometry : angle 0.54901 (11568) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.93738 ( 4) hydrogen bonds : bond 0.04039 ( 360) hydrogen bonds : angle 4.72015 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8065 (m) cc_final: 0.7860 (p) REVERT: B 10 GLU cc_start: 0.7344 (pp20) cc_final: 0.7011 (pp20) REVERT: B 124 TYR cc_start: 0.8247 (m-80) cc_final: 0.7962 (m-80) REVERT: B 226 GLU cc_start: 0.8343 (pm20) cc_final: 0.8125 (pm20) REVERT: A 365 CYS cc_start: 0.8277 (m) cc_final: 0.8069 (m) REVERT: S 4 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7069 (pp) REVERT: S 180 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8329 (tm-30) outliers start: 29 outliers final: 13 residues processed: 148 average time/residue: 0.4417 time to fit residues: 71.0541 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 105 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.142114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108866 restraints weight = 12345.176| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.81 r_work: 0.3450 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8487 Z= 0.111 Angle : 0.542 8.830 11572 Z= 0.275 Chirality : 0.041 0.299 1354 Planarity : 0.003 0.049 1471 Dihedral : 4.308 50.200 1212 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 27.32 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.26), residues: 1109 helix: 0.94 (0.29), residues: 363 sheet: -0.04 (0.35), residues: 242 loop : -1.58 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.014 0.001 TYR B 59 PHE 0.026 0.001 PHE A 376 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8485) covalent geometry : angle 0.54216 (11568) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.89033 ( 4) hydrogen bonds : bond 0.03690 ( 360) hydrogen bonds : angle 4.56029 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: R 106 LYS cc_start: 0.7795 (tptm) cc_final: 0.7586 (tppp) REVERT: R 127 SER cc_start: 0.8104 (m) cc_final: 0.7853 (p) REVERT: B 10 GLU cc_start: 0.7246 (pp20) cc_final: 0.6918 (pp20) REVERT: B 226 GLU cc_start: 0.8349 (pm20) cc_final: 0.8094 (pm20) REVERT: S 4 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7056 (pp) REVERT: S 180 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8240 (tm-30) outliers start: 21 outliers final: 11 residues processed: 139 average time/residue: 0.4387 time to fit residues: 66.2420 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN A 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.138947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105796 restraints weight = 12339.938| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.75 r_work: 0.3407 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8487 Z= 0.157 Angle : 0.573 9.588 11572 Z= 0.294 Chirality : 0.042 0.327 1354 Planarity : 0.004 0.047 1471 Dihedral : 4.509 49.965 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.33 % Allowed : 26.08 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.26), residues: 1109 helix: 0.84 (0.29), residues: 369 sheet: -0.18 (0.34), residues: 250 loop : -1.60 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 389 TYR 0.013 0.001 TYR B 59 PHE 0.022 0.002 PHE A 376 TRP 0.018 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8485) covalent geometry : angle 0.57314 (11568) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.15492 ( 4) hydrogen bonds : bond 0.04195 ( 360) hydrogen bonds : angle 4.69355 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8124 (m) cc_final: 0.7886 (p) REVERT: R 281 ASP cc_start: 0.7166 (m-30) cc_final: 0.6888 (m-30) REVERT: B 10 GLU cc_start: 0.7225 (pp20) cc_final: 0.6900 (pp20) REVERT: B 124 TYR cc_start: 0.8225 (m-80) cc_final: 0.7957 (m-80) REVERT: B 226 GLU cc_start: 0.8369 (pm20) cc_final: 0.8123 (pm20) REVERT: S 4 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7161 (pp) REVERT: S 180 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8294 (tm-30) outliers start: 35 outliers final: 15 residues processed: 145 average time/residue: 0.4441 time to fit residues: 69.9789 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106578 restraints weight = 12231.872| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.79 r_work: 0.3424 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8487 Z= 0.128 Angle : 0.568 11.022 11572 Z= 0.288 Chirality : 0.042 0.371 1354 Planarity : 0.003 0.046 1471 Dihedral : 4.440 49.338 1212 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.71 % Allowed : 27.07 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.26), residues: 1109 helix: 0.88 (0.29), residues: 369 sheet: -0.08 (0.35), residues: 237 loop : -1.58 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 181 TYR 0.011 0.001 TYR B 59 PHE 0.023 0.001 PHE A 376 TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8485) covalent geometry : angle 0.56764 (11568) SS BOND : bond 0.00278 ( 2) SS BOND : angle 1.10353 ( 4) hydrogen bonds : bond 0.03878 ( 360) hydrogen bonds : angle 4.61889 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: R 106 LYS cc_start: 0.7860 (tppp) cc_final: 0.7586 (tppp) REVERT: R 127 SER cc_start: 0.8100 (m) cc_final: 0.7863 (p) REVERT: B 10 GLU cc_start: 0.7204 (pp20) cc_final: 0.6970 (pp20) REVERT: B 59 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 75 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7713 (mp-120) REVERT: B 124 TYR cc_start: 0.8167 (m-80) cc_final: 0.7897 (m-80) REVERT: B 226 GLU cc_start: 0.8355 (pm20) cc_final: 0.8090 (pm20) REVERT: S 4 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7034 (pp) REVERT: S 180 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8145 (tm-30) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 0.4371 time to fit residues: 66.1529 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101272 restraints weight = 12301.588| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.75 r_work: 0.3344 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8487 Z= 0.267 Angle : 0.681 10.266 11572 Z= 0.353 Chirality : 0.047 0.361 1354 Planarity : 0.004 0.046 1471 Dihedral : 5.079 50.362 1212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.20 % Allowed : 26.58 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.25), residues: 1109 helix: 0.46 (0.28), residues: 369 sheet: -0.34 (0.33), residues: 253 loop : -1.72 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 232 TYR 0.018 0.002 TYR B 59 PHE 0.023 0.002 PHE R 144 TRP 0.029 0.002 TRP B 339 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8485) covalent geometry : angle 0.68016 (11568) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.61793 ( 4) hydrogen bonds : bond 0.05199 ( 360) hydrogen bonds : angle 5.10602 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.363 Fit side-chains REVERT: R 127 SER cc_start: 0.8163 (m) cc_final: 0.7861 (p) REVERT: B 75 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7834 (mp-120) REVERT: B 124 TYR cc_start: 0.8277 (m-80) cc_final: 0.8015 (m-80) REVERT: B 226 GLU cc_start: 0.8349 (pm20) cc_final: 0.8101 (pm20) REVERT: S 4 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7184 (pp) REVERT: S 180 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8195 (tm-30) outliers start: 34 outliers final: 20 residues processed: 141 average time/residue: 0.4713 time to fit residues: 71.8958 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104654 restraints weight = 12234.478| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.78 r_work: 0.3394 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8487 Z= 0.149 Angle : 0.618 10.177 11572 Z= 0.313 Chirality : 0.043 0.340 1354 Planarity : 0.004 0.045 1471 Dihedral : 4.775 49.883 1212 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 27.69 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.26), residues: 1109 helix: 0.69 (0.28), residues: 369 sheet: -0.28 (0.33), residues: 258 loop : -1.65 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 280 TYR 0.009 0.001 TYR B 124 PHE 0.021 0.001 PHE A 376 TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8485) covalent geometry : angle 0.61795 (11568) SS BOND : bond 0.00610 ( 2) SS BOND : angle 1.16391 ( 4) hydrogen bonds : bond 0.04176 ( 360) hydrogen bonds : angle 4.79591 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.416 Fit side-chains REVERT: R 127 SER cc_start: 0.8165 (m) cc_final: 0.7921 (p) REVERT: B 96 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7733 (ttp-170) REVERT: B 124 TYR cc_start: 0.8223 (m-80) cc_final: 0.7965 (m-80) REVERT: B 226 GLU cc_start: 0.8342 (pm20) cc_final: 0.8097 (pm20) REVERT: S 4 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7049 (pp) REVERT: S 180 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8246 (tm-30) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.4241 time to fit residues: 61.7228 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 0.0970 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 259 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 = 0.3979 r_free = 0.3979 target = 0.140797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107376 restraints weight = 12010.659| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.77 r_work: 0.3439 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8487 Z= 0.117 Angle : 0.594 11.953 11572 Z= 0.297 Chirality : 0.042 0.367 1354 Planarity : 0.004 0.053 1471 Dihedral : 4.519 48.685 1212 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.35 % Allowed : 28.18 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1109 helix: 0.87 (0.29), residues: 368 sheet: -0.06 (0.35), residues: 241 loop : -1.56 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 280 TYR 0.010 0.001 TYR S 191 PHE 0.021 0.001 PHE R 115 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8485) covalent geometry : angle 0.59432 (11568) SS BOND : bond 0.00418 ( 2) SS BOND : angle 0.93526 ( 4) hydrogen bonds : bond 0.03691 ( 360) hydrogen bonds : angle 4.59324 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.312 Fit side-chains REVERT: R 127 SER cc_start: 0.8154 (m) cc_final: 0.7935 (p) REVERT: R 186 CYS cc_start: 0.8995 (m) cc_final: 0.8635 (p) REVERT: B 124 TYR cc_start: 0.8184 (m-80) cc_final: 0.7935 (m-80) REVERT: B 226 GLU cc_start: 0.8359 (pm20) cc_final: 0.8109 (pm20) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 0.3992 time to fit residues: 58.9315 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.136742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103048 restraints weight = 12316.024| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.78 r_work: 0.3371 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8487 Z= 0.205 Angle : 0.666 11.650 11572 Z= 0.339 Chirality : 0.046 0.390 1354 Planarity : 0.004 0.048 1471 Dihedral : 4.952 49.545 1212 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.35 % Allowed : 28.18 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.25), residues: 1109 helix: 0.57 (0.28), residues: 369 sheet: -0.30 (0.33), residues: 253 loop : -1.66 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.010 0.002 TYR S 95 PHE 0.026 0.002 PHE B 292 TRP 0.027 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8485) covalent geometry : angle 0.66568 (11568) SS BOND : bond 0.00645 ( 2) SS BOND : angle 1.33686 ( 4) hydrogen bonds : bond 0.04701 ( 360) hydrogen bonds : angle 4.90966 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.16 seconds wall clock time: 50 minutes 36.66 seconds (3036.66 seconds total)