Starting phenix.real_space_refine on Tue Aug 4 18:14:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vpn_65255/08_2026/9vpn_65255.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.036 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: 3 Type Number sf(0) Gaussians C 2884 2.51 5 N 1442 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5769 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 232 Classifications: {'peptide': 58} Incomplete info: {'backbone_only': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 872 Classifications: {'peptide': 218} Incomplete info: {'backbone_only': 209} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 916 Unresolved non-hydrogen angles: 1310 Unresolved non-hydrogen dihedrals: 596 Unresolved non-hydrogen chiralities: 268 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 16, 'ARG:plan': 8, 'ASN:plan1': 11, 'GLN:plan1': 5, 'HIS:plan': 5, 'PHE:plan': 15, 'TRP:plan': 2, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 435 Chain: "B" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 1329 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 304} Link IDs: {'PTRANS': 4, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1859 Unresolved non-hydrogen dihedrals: 805 Unresolved non-hydrogen chiralities: 395 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 29, 'GLN:plan1': 12, 'ARG:plan': 22, 'ASN:plan1': 14, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 8, 'PHE:plan': 11, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 639 Chain: "S" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 928 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1313 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 270 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 9, 'ARG:plan': 11, 'PHE:plan': 11, 'HIS:plan': 3, 'TRP:plan': 4, 'TYR:plan': 14, 'ASP:plan': 8, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 426 Chain: "R" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 1236 Classifications: {'peptide': 309} Incomplete info: {'backbone_only': 294} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1308 Unresolved non-hydrogen angles: 1914 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 403 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 16, 'ASP:plan': 11, 'TRP:plan': 9, 'PHE:plan': 23, 'ASN:plan1': 7, 'ARG:plan': 19, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 604 Chain: "Q" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 1172 Classifications: {'peptide': 293} Incomplete info: {'backbone_only': 279} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1255 Unresolved non-hydrogen angles: 1836 Unresolved non-hydrogen dihedrals: 845 Unresolved non-hydrogen chiralities: 385 Planarities with less than four sites: {'TRP:plan': 9, 'TYR:plan': 15, 'PHE:plan': 23, 'ASN:plan1': 6, 'ARG:plan': 18, 'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 579 Time building chain proxies: 1.71, per 1000 atoms: 0.30 Number of scatterers: 5769 At special positions: 0 Unit cell: (109.74, 117.18, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1443 8.00 N 1442 7.00 C 2884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.62 Conformation dependent library (CDL) restraints added in 482.3 milliseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 17 sheets defined 49.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.121A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.540A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.830A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.515A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.007A 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 'S' and resid 74 through 77 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'R' and resid 26 through 56 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.121A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 97 through 133 removed outlier: 4.509A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.897A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 161 removed outlier: 3.816A pdb=" N ALA R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.520A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 280 through 299 Proline residue: R 292 - end of helix removed outlier: 3.728A pdb=" N TYR R 299 " --> pdb=" O THR R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'Q' and resid 29 through 56 Processing helix chain 'Q' and resid 62 through 79 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'Q' and resid 97 through 132 removed outlier: 4.235A pdb=" N PHE Q 101 " --> pdb=" O PHE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 161 Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 193 through 210 Processing helix chain 'Q' and resid 210 through 232 Processing helix chain 'Q' and resid 236 through 278 removed outlier: 3.599A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG Q 245 " --> pdb=" O ARG Q 241 " (cutoff:3.500A) Proline residue: Q 263 - end of helix Processing helix chain 'Q' and resid 280 through 312 Proline residue: Q 292 - end of helix removed outlier: 3.667A pdb=" N SER Q 298 " --> pdb=" O CYS Q 294 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER Q 302 " --> pdb=" O SER Q 298 " (cutoff:3.500A) Proline residue: Q 306 - end of helix Processing helix chain 'Q' and resid 312 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.239A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.774A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.001A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.110A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.556A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.557A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.731A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.644A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.790A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.473A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 5.047A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.535A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AB8, first strand: chain 'Q' and resid 168 through 171 664 hydrogen bonds defined for protein. 1863 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: 1.03 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1443 1.28 - 1.35: 1425 1.35 - 1.42: 7 1.42 - 1.50: 1499 1.50 - 1.57: 1384 Bond restraints: 5758 Sorted by residual: bond pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 1.518 1.492 0.026 7.30e-03 1.88e+04 1.28e+01 bond pdb=" CA LEU S 20 " pdb=" C LEU S 20 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" CA PHE R 67 " pdb=" C PHE R 67 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.32e-02 5.74e+03 1.16e+01 bond pdb=" CA PHE B 199 " pdb=" C PHE B 199 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" CA ILE R 228 " pdb=" C ILE R 228 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.23e-02 6.61e+03 1.11e+01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 6390 2.54 - 5.07: 666 5.07 - 7.61: 103 7.61 - 10.15: 16 10.15 - 12.69: 4 Bond angle restraints: 7179 Sorted by residual: angle pdb=" N ARG R 91 " pdb=" CA ARG R 91 " pdb=" C ARG R 91 " ideal model delta sigma weight residual 110.53 97.84 12.69 1.32e+00 5.74e-01 9.24e+01 angle pdb=" C SER S 106 " pdb=" N PRO S 107 " pdb=" CA PRO S 107 " ideal model delta sigma weight residual 119.78 128.72 -8.94 1.03e+00 9.43e-01 7.54e+01 angle pdb=" N ARG S 179 " pdb=" CA ARG S 179 " pdb=" C ARG S 179 " ideal model delta sigma weight residual 109.52 96.97 12.55 1.55e+00 4.16e-01 6.56e+01 angle pdb=" N LYS B 280 " pdb=" CA LYS B 280 " pdb=" C LYS B 280 " ideal model delta sigma weight residual 111.28 118.83 -7.55 1.09e+00 8.42e-01 4.80e+01 angle pdb=" C ASP G 48 " pdb=" N PRO G 49 " pdb=" CA PRO G 49 " ideal model delta sigma weight residual 119.84 128.15 -8.31 1.25e+00 6.40e-01 4.42e+01 ... (remaining 7174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.22: 1058 4.22 - 8.44: 277 8.44 - 12.66: 70 12.66 - 16.87: 23 16.87 - 21.09: 4 Dihedral angle restraints: 1432 sinusoidal: 1 harmonic: 1431 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLN B 259 " pdb=" C GLN B 259 " pdb=" N GLU B 260 " pdb=" CA GLU B 260 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE Q 210 " pdb=" C PHE Q 210 " pdb=" N VAL Q 211 " pdb=" CA VAL Q 211 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 1429 not shown) Chirality restraints: 0 Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ASN B 340 " 0.065 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.023 2.00e-02 2.50e+03 pdb=" OXT ASN B 340 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 141 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C ARG R 141 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG R 141 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU R 142 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 202 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C GLY B 202 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY B 202 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 203 " 0.017 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2596 2.84 - 3.36: 4194 3.36 - 3.87: 7276 3.87 - 4.39: 6959 4.39 - 4.90: 11662 Nonbonded interactions: 32687 Sorted by model distance: nonbonded pdb=" N ARG R 91 " pdb=" O ARG R 91 " model vdw 2.326 2.496 nonbonded pdb=" N ARG S 179 " pdb=" O ARG S 179 " model vdw 2.327 2.496 nonbonded pdb=" N PRO R 96 " pdb=" O PRO R 96 " model vdw 2.401 2.496 nonbonded pdb=" N GLY S 33 " pdb=" O GLY S 33 " model vdw 2.467 2.496 nonbonded pdb=" N GLY A 202 " pdb=" O GLY A 202 " model vdw 2.468 2.496 ... (remaining 32682 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 Found NCS groups: ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 24 through 134 or resid 140 through 321)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.010 0.047 5758 Z= 0.798 Angle : 1.679 12.685 7179 Z= 1.227 Chirality : 0.000 0.000 0 Planarity : 0.008 0.038 1432 Dihedral : 4.404 21.091 1432 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1420 helix: 0.16 (0.19), residues: 649 sheet: 1.00 (0.32), residues: 252 loop : 0.49 (0.28), residues: 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01017 / 0.80 ( 5758) covalent geometry : angle 1.67871 / 1.23 ( 7179) hydrogen bonds : bond 0.17528 / 13.55 ( 653) hydrogen bonds : angle 7.11367 / 5.65 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0253 time to fit residues: 2.3545 Evaluate side-chains 43 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063486 restraints weight = 39643.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063437 restraints weight = 31775.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063756 restraints weight = 29772.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063831 restraints weight = 25614.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063866 restraints weight = 24599.968| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5758 Z= 0.201 Angle : 0.499 4.611 7179 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 1432 Dihedral : 4.299 22.876 1432 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.69 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.22), residues: 1420 helix: 2.60 (0.20), residues: 647 sheet: 0.49 (0.30), residues: 274 loop : 0.11 (0.29), residues: 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.20 ( 5758) covalent geometry : angle 0.49892 / 0.33 ( 7179) hydrogen bonds : bond 0.04601 / 3.57 ( 653) hydrogen bonds : angle 4.55399 / 3.58 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0181 time to fit residues: 1.6278 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 86 optimal weight: 0.0170 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 60 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 7.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060826 restraints weight = 39836.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060485 restraints weight = 32846.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060850 restraints weight = 30198.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060924 restraints weight = 26026.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060924 restraints weight = 25471.231| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.236 Angle : 0.532 7.244 7179 Z= 0.347 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 1432 Dihedral : 4.456 23.645 1432 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.23), residues: 1420 helix: 2.77 (0.20), residues: 643 sheet: -0.03 (0.30), residues: 280 loop : -0.40 (0.30), residues: 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.24 ( 5758) covalent geometry : angle 0.53205 / 0.35 ( 7179) hydrogen bonds : bond 0.04640 / 3.61 ( 653) hydrogen bonds : angle 4.78369 / 3.75 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0246 time to fit residues: 2.2989 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 104 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 chunk 103 optimal weight: 20.0000 chunk 113 optimal weight: 40.0000 chunk 130 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057678 restraints weight = 41713.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.057274 restraints weight = 41946.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057469 restraints weight = 36942.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057569 restraints weight = 32946.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057619 restraints weight = 30551.326| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5758 Z= 0.504 Angle : 0.893 9.063 7179 Z= 0.599 Chirality : 0.000 0.000 0 Planarity : 0.007 0.028 1432 Dihedral : 6.903 32.059 1432 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.96 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1420 helix: 0.36 (0.19), residues: 626 sheet: -0.67 (0.32), residues: 251 loop : -1.87 (0.26), residues: 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.50 ( 5758) covalent geometry : angle 0.89286 / 0.60 ( 7179) hydrogen bonds : bond 0.07029 / 5.44 ( 653) hydrogen bonds : angle 7.28120 / 5.74 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0248 time to fit residues: 2.2985 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 20.0000 chunk 89 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 75 optimal weight: 0.0470 chunk 122 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 78 optimal weight: 40.0000 overall best weight: 3.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060693 restraints weight = 40838.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060324 restraints weight = 33181.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.060432 restraints weight = 30592.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060516 restraints weight = 29971.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060624 restraints weight = 27321.506| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5758 Z= 0.134 Angle : 0.388 5.487 7179 Z= 0.249 Chirality : 0.000 0.000 0 Planarity : 0.002 0.013 1432 Dihedral : 4.181 23.522 1432 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1420 helix: 2.38 (0.20), residues: 644 sheet: -0.36 (0.33), residues: 244 loop : -1.37 (0.28), residues: 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.13 ( 5758) covalent geometry : angle 0.38803 / 0.25 ( 7179) hydrogen bonds : bond 0.03586 / 2.78 ( 653) hydrogen bonds : angle 4.82417 / 3.79 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0245 time to fit residues: 2.2832 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 4 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 69 optimal weight: 0.0570 chunk 123 optimal weight: 20.0000 chunk 75 optimal weight: 0.0030 chunk 80 optimal weight: 50.0000 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 4.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060530 restraints weight = 40592.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060097 restraints weight = 35718.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.060133 restraints weight = 33261.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060217 restraints weight = 33694.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060276 restraints weight = 30114.845| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5758 Z= 0.144 Angle : 0.375 5.128 7179 Z= 0.241 Chirality : 0.000 0.000 0 Planarity : 0.002 0.010 1432 Dihedral : 3.863 24.153 1432 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1420 helix: 2.96 (0.20), residues: 646 sheet: -0.22 (0.33), residues: 242 loop : -1.36 (0.28), residues: 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.14 ( 5758) covalent geometry : angle 0.37519 / 0.24 ( 7179) hydrogen bonds : bond 0.03577 / 2.77 ( 653) hydrogen bonds : angle 4.54498 / 3.56 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0244 time to fit residues: 2.2695 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.071371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058754 restraints weight = 41329.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058087 restraints weight = 45418.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058524 restraints weight = 37922.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058517 restraints weight = 32400.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058602 restraints weight = 29019.731| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5758 Z= 0.329 Angle : 0.609 6.726 7179 Z= 0.407 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 1432 Dihedral : 5.288 25.210 1432 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.94 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1420 helix: 1.78 (0.20), residues: 638 sheet: -0.31 (0.36), residues: 216 loop : -2.00 (0.26), residues: 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.33 ( 5758) covalent geometry : angle 0.60928 / 0.41 ( 7179) hydrogen bonds : bond 0.05277 / 4.09 ( 653) hydrogen bonds : angle 5.85389 / 4.59 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0242 time to fit residues: 2.2377 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 2 optimal weight: 40.0000 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 59 optimal weight: 40.0000 chunk 55 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 5.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059709 restraints weight = 40594.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059470 restraints weight = 36909.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059789 restraints weight = 32368.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059888 restraints weight = 27490.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059912 restraints weight = 26187.348| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5758 Z= 0.169 Angle : 0.411 5.442 7179 Z= 0.267 Chirality : 0.000 0.000 0 Planarity : 0.002 0.012 1432 Dihedral : 4.274 24.669 1432 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1420 helix: 2.50 (0.20), residues: 639 sheet: -0.51 (0.35), residues: 225 loop : -1.80 (0.26), residues: 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.17 ( 5758) covalent geometry : angle 0.41136 / 0.27 ( 7179) hydrogen bonds : bond 0.03855 / 2.99 ( 653) hydrogen bonds : angle 4.94395 / 3.87 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.298 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0238 time to fit residues: 2.2636 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 75 optimal weight: 0.0970 chunk 66 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 overall best weight: 12.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.071140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058562 restraints weight = 41207.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058434 restraints weight = 39680.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058636 restraints weight = 32906.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058644 restraints weight = 29584.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058624 restraints weight = 29581.227| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5758 Z= 0.343 Angle : 0.626 6.240 7179 Z= 0.418 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 1432 Dihedral : 5.434 26.165 1432 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.77 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1420 helix: 1.51 (0.20), residues: 637 sheet: -0.77 (0.35), residues: 212 loop : -2.26 (0.25), residues: 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.34 ( 5758) covalent geometry : angle 0.62582 / 0.42 ( 7179) hydrogen bonds : bond 0.05341 / 4.14 ( 653) hydrogen bonds : angle 6.02402 / 4.72 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0239 time to fit residues: 2.2314 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 81 optimal weight: 0.0270 chunk 11 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 overall best weight: 7.9848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059517 restraints weight = 41104.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059370 restraints weight = 39175.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059521 restraints weight = 32788.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059563 restraints weight = 30014.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059588 restraints weight = 28780.887| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5758 Z= 0.233 Angle : 0.483 5.406 7179 Z= 0.318 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 1432 Dihedral : 4.716 25.046 1432 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.31 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1420 helix: 1.88 (0.20), residues: 639 sheet: -1.07 (0.35), residues: 224 loop : -2.10 (0.26), residues: 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.23 ( 5758) covalent geometry : angle 0.48340 / 0.32 ( 7179) hydrogen bonds : bond 0.04339 / 3.37 ( 653) hydrogen bonds : angle 5.39760 / 4.23 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0237 time to fit residues: 2.2085 Evaluate side-chains 42 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 50.0000 chunk 53 optimal weight: 40.0000 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 chunk 119 optimal weight: 30.0000 chunk 1 optimal weight: 50.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057655 restraints weight = 40966.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057515 restraints weight = 35927.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057864 restraints weight = 29947.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057758 restraints weight = 28291.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057785 restraints weight = 27822.145| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.8422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5758 Z= 0.419 Angle : 0.725 6.888 7179 Z= 0.490 Chirality : 0.000 0.000 0 Planarity : 0.005 0.027 1432 Dihedral : 6.074 28.431 1432 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.32 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1420 helix: 0.65 (0.20), residues: 632 sheet: -1.27 (0.35), residues: 215 loop : -2.54 (0.25), residues: 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.42 ( 5758) covalent geometry : angle 0.72545 / 0.49 ( 7179) hydrogen bonds : bond 0.06068 / 4.71 ( 653) hydrogen bonds : angle 6.69616 / 5.25 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.43 seconds wall clock time: 18 minutes 8.29 seconds (1088.29 seconds total)