Starting phenix.real_space_refine on Tue Aug 4 18:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.map" model { file = "/net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vpm_65254/08_2026/9vpm_65254.cif" } 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= -0.001 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 2846 2.51 5 N 1423 2.21 5 O 1424 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: 5693 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: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 1096 Classifications: {'peptide': 274} Incomplete info: {'backbone_only': 261} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1157 Unresolved non-hydrogen angles: 1703 Unresolved non-hydrogen dihedrals: 772 Unresolved non-hydrogen chiralities: 365 Planarities with less than four sites: {'TYR:plan': 15, 'PHE:plan': 22, 'ASN:plan1': 7, 'TRP:plan': 8, 'ARG:plan': 14, 'ASP:plan': 10, 'GLU:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 530 Time building chain proxies: 1.40, per 1000 atoms: 0.25 Number of scatterers: 5693 At special positions: 0 Unit cell: (107.88, 114.39, 125.55, 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 1424 8.00 N 1423 7.00 C 2846 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: 0.59 Conformation dependent library (CDL) restraints added in 430.0 milliseconds 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 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 48.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 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: 4.998A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.832A 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 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: 4.133A 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: 4.132A 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: 4.439A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.502A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 161 removed outlier: 3.983A pdb=" N ALA R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.758A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 removed outlier: 3.774A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) 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: 3.641A 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 54 Processing helix chain 'Q' and resid 62 through 80 removed outlier: 3.549A pdb=" N PHE Q 67 " --> pdb=" O SER Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'Q' and resid 97 through 132 removed outlier: 4.239A pdb=" N PHE Q 101 " --> pdb=" O PHE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 142 Processing helix chain 'Q' and resid 147 through 161 removed outlier: 3.736A pdb=" N LEU Q 153 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 190 through 210 removed outlier: 4.047A pdb=" N TRP Q 195 " --> pdb=" O VAL Q 191 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA Q 196 " --> pdb=" O SER Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 228 Processing helix chain 'Q' and resid 244 through 273 Proline residue: Q 263 - end of helix Processing helix chain 'Q' and resid 274 through 276 No H-bonds generated for 'chain 'Q' and resid 274 through 276' Processing helix chain 'Q' and resid 281 through 312 removed outlier: 4.529A pdb=" N LEU Q 285 " --> pdb=" O CYS Q 281 " (cutoff:3.500A) Proline residue: Q 292 - end of helix removed outlier: 4.211A pdb=" N SER Q 302 " --> pdb=" O SER Q 298 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS Q 303 " --> pdb=" O TYR Q 299 " (cutoff:3.500A) Proline residue: Q 306 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.406A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.089A 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: 6.788A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.862A 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: 3.929A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.540A 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: 7.058A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.533A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.573A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.733A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.747A 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: 3.580A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.508A 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: 6.711A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.549A 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: 4.517A 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: 5.240A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 6.275A 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: 3.563A 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 172 Processing sheet with id=AB8, first strand: chain 'Q' and resid 168 through 171 643 hydrogen bonds defined for protein. 1797 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: 1.00 Time building geometry restraints manager: 0.74 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: 1424 1.28 - 1.35: 1404 1.35 - 1.42: 8 1.42 - 1.50: 1473 1.50 - 1.57: 1372 Bond restraints: 5681 Sorted by residual: bond pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 1.518 1.493 0.026 7.30e-03 1.88e+04 1.22e+01 bond pdb=" CA LEU S 20 " pdb=" C LEU S 20 " ideal model delta sigma weight residual 1.522 1.568 -0.046 1.34e-02 5.57e+03 1.16e+01 bond pdb=" CA TRP B 99 " pdb=" C TRP B 99 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.11e-02 8.12e+03 1.16e+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 1.13e+01 bond pdb=" CA PHE B 199 " pdb=" C PHE B 199 " ideal model delta sigma weight residual 1.523 1.484 0.040 1.18e-02 7.18e+03 1.12e+01 ... (remaining 5676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 6271 2.54 - 5.09: 688 5.09 - 7.63: 102 7.63 - 10.17: 16 10.17 - 12.71: 4 Bond angle restraints: 7081 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 97.82 12.71 1.32e+00 5.74e-01 9.28e+01 angle pdb=" C SER S 106 " pdb=" N PRO S 107 " pdb=" CA PRO S 107 " ideal model delta sigma weight residual 119.78 128.74 -8.96 1.03e+00 9.43e-01 7.57e+01 angle pdb=" C ASP G 48 " pdb=" N PRO G 49 " pdb=" CA PRO G 49 " ideal model delta sigma weight residual 119.56 128.16 -8.60 1.02e+00 9.61e-01 7.11e+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 97.01 12.51 1.55e+00 4.16e-01 6.51e+01 angle pdb=" N LYS B 280 " pdb=" CA LYS B 280 " pdb=" C LYS B 280 " ideal model delta sigma weight residual 111.28 118.87 -7.59 1.09e+00 8.42e-01 4.85e+01 ... (remaining 7076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.85: 949 3.85 - 7.70: 336 7.70 - 11.55: 99 11.55 - 15.40: 20 15.40 - 19.25: 8 Dihedral angle restraints: 1412 sinusoidal: 1 harmonic: 1411 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 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU B 70 " pdb=" C LEU B 70 " pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+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 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 1409 not shown) Chirality restraints: 0 Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+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 3.03e-02 9.18e+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 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 202 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C GLY B 202 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 202 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 203 " 0.017 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2589 2.84 - 3.36: 4148 3.36 - 3.87: 7160 3.87 - 4.39: 6928 4.39 - 4.90: 11413 Nonbonded interactions: 32238 Sorted by model distance: nonbonded pdb=" N ARG R 91 " pdb=" O ARG R 91 " model vdw 2.330 2.496 nonbonded pdb=" N ARG S 179 " pdb=" O ARG S 179 " model vdw 2.339 2.496 nonbonded pdb=" N PRO R 96 " pdb=" O PRO R 96 " model vdw 2.397 2.496 nonbonded pdb=" N GLY S 33 " pdb=" O GLY S 33 " model vdw 2.466 2.496 nonbonded pdb=" N GLY A 202 " pdb=" O GLY A 202 " model vdw 2.468 2.496 ... (remaining 32233 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 28 through 56 or resid 61 through 234 or resid 243 through \ 313)) } 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: 1.590 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.650 Find NCS groups from input model: 0.080 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 0.046 5681 Z= 0.814 Angle : 1.706 12.713 7081 Z= 1.253 Chirality : 0.000 0.000 0 Planarity : 0.008 0.037 1412 Dihedral : 4.494 19.254 1412 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.36 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.47 (0.22), residues: 1399 helix: 0.08 (0.19), residues: 633 sheet: 1.24 (0.31), residues: 257 loop : 0.38 (0.29), residues: 509 Details of bonding type rmsd/Z covalent geometry : bond 0.01037 / 0.81 ( 5681) covalent geometry : angle 1.70602 / 1.25 ( 7081) hydrogen bonds : bond 0.17554 / 13.52 ( 632) hydrogen bonds : angle 6.89390 / 5.54 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0156 time to fit residues: 1.4159 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.070777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058500 restraints weight = 45305.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059052 restraints weight = 34236.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059437 restraints weight = 28447.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.059626 restraints weight = 25219.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059846 restraints weight = 23337.907| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5681 Z= 0.165 Angle : 0.452 5.128 7081 Z= 0.296 Chirality : 0.000 0.000 0 Planarity : 0.003 0.012 1412 Dihedral : 4.072 22.357 1412 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.15 (0.23), residues: 1399 helix: 2.58 (0.20), residues: 646 sheet: 0.92 (0.31), residues: 238 loop : 0.23 (0.28), residues: 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.16 ( 5681) covalent geometry : angle 0.45166 / 0.30 ( 7081) hydrogen bonds : bond 0.03769 / 2.97 ( 632) hydrogen bonds : angle 4.15486 / 3.30 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0223 time to fit residues: 1.9995 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 overall best weight: 13.9794 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.064516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052638 restraints weight = 46183.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052840 restraints weight = 36787.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053068 restraints weight = 31353.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053135 restraints weight = 27359.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053164 restraints weight = 26083.785| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5681 Z= 0.392 Angle : 0.749 7.361 7081 Z= 0.500 Chirality : 0.000 0.000 0 Planarity : 0.005 0.024 1412 Dihedral : 6.116 28.921 1412 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.25 (0.22), residues: 1399 helix: 1.31 (0.20), residues: 628 sheet: -0.06 (0.32), residues: 239 loop : -1.07 (0.27), residues: 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.39 ( 5681) covalent geometry : angle 0.74909 / 0.50 ( 7081) hydrogen bonds : bond 0.05349 / 4.23 ( 632) hydrogen bonds : angle 5.91358 / 4.74 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.127 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0150 time to fit residues: 1.3511 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 109 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 104 optimal weight: 60.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.064995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052994 restraints weight = 45501.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053133 restraints weight = 36430.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053429 restraints weight = 31582.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053434 restraints weight = 27710.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053467 restraints weight = 26260.550| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5681 Z= 0.271 Angle : 0.548 5.729 7081 Z= 0.365 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 1412 Dihedral : 5.031 22.776 1412 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.38 (0.23), residues: 1399 helix: 1.71 (0.20), residues: 627 sheet: -0.02 (0.33), residues: 235 loop : -1.41 (0.27), residues: 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.27 ( 5681) covalent geometry : angle 0.54764 / 0.37 ( 7081) hydrogen bonds : bond 0.04126 / 3.27 ( 632) hydrogen bonds : angle 5.08362 / 4.04 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0175 time to fit residues: 1.5387 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 126 optimal weight: 40.0000 chunk 43 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 overall best weight: 10.3996 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.064414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052587 restraints weight = 46667.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052914 restraints weight = 36526.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053103 restraints weight = 31046.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053181 restraints weight = 27032.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053213 restraints weight = 25954.525| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5681 Z= 0.286 Angle : 0.585 5.576 7081 Z= 0.390 Chirality : 0.000 0.000 0 Planarity : 0.004 0.018 1412 Dihedral : 5.408 25.909 1412 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.10 (0.23), residues: 1399 helix: 1.49 (0.21), residues: 619 sheet: -0.41 (0.34), residues: 233 loop : -1.77 (0.26), residues: 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.29 ( 5681) covalent geometry : angle 0.58532 / 0.39 ( 7081) hydrogen bonds : bond 0.04510 / 3.58 ( 632) hydrogen bonds : angle 5.49711 / 4.39 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0186 time to fit residues: 1.7621 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 138 optimal weight: 30.0000 chunk 38 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 0.0980 chunk 2 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 overall best weight: 10.0192 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.064494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052406 restraints weight = 46381.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052858 restraints weight = 35970.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053028 restraints weight = 30222.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053346 restraints weight = 27266.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053424 restraints weight = 25229.233| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5681 Z= 0.271 Angle : 0.544 5.371 7081 Z= 0.363 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 1412 Dihedral : 5.208 23.850 1412 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.21 (0.23), residues: 1399 helix: 1.63 (0.21), residues: 621 sheet: -0.78 (0.33), residues: 243 loop : -2.01 (0.26), residues: 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.27 ( 5681) covalent geometry : angle 0.54403 / 0.36 ( 7081) hydrogen bonds : bond 0.04244 / 3.37 ( 632) hydrogen bonds : angle 5.30707 / 4.23 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0172 time to fit residues: 1.6176 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 71 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 50.0000 chunk 106 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 overall best weight: 15.9996 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.063120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050956 restraints weight = 46033.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051256 restraints weight = 36172.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051566 restraints weight = 31111.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051858 restraints weight = 27336.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051967 restraints weight = 25466.066| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.8347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5681 Z= 0.413 Angle : 0.749 7.305 7081 Z= 0.507 Chirality : 0.000 0.000 0 Planarity : 0.005 0.022 1412 Dihedral : 6.545 29.527 1412 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.50 (0.22), residues: 1399 helix: 0.51 (0.20), residues: 607 sheet: -1.03 (0.35), residues: 214 loop : -2.68 (0.24), residues: 578 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.41 ( 5681) covalent geometry : angle 0.74886 / 0.51 ( 7081) hydrogen bonds : bond 0.05550 / 4.40 ( 632) hydrogen bonds : angle 6.58470 / 5.29 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0146 time to fit residues: 1.3769 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 103 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.062174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050349 restraints weight = 46305.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050756 restraints weight = 35280.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050910 restraints weight = 29677.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051268 restraints weight = 26947.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051383 restraints weight = 24728.694| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.8901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5681 Z= 0.509 Angle : 0.876 8.305 7081 Z= 0.595 Chirality : 0.000 0.000 0 Planarity : 0.006 0.026 1412 Dihedral : 7.476 37.393 1412 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.58 (0.21), residues: 1399 helix: -0.50 (0.20), residues: 598 sheet: -1.24 (0.40), residues: 173 loop : -3.13 (0.23), residues: 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.51 ( 5681) covalent geometry : angle 0.87552 / 0.60 ( 7081) hydrogen bonds : bond 0.06364 / 5.04 ( 632) hydrogen bonds : angle 7.41096 / 5.94 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.166 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0158 time to fit residues: 1.4161 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 9 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 128 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 0.0170 chunk 111 optimal weight: 10.0000 overall best weight: 7.2032 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.064501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.052400 restraints weight = 45084.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052762 restraints weight = 35027.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053129 restraints weight = 29585.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053305 restraints weight = 26554.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053306 restraints weight = 24740.542| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5681 Z= 0.203 Angle : 0.481 4.359 7081 Z= 0.318 Chirality : 0.000 0.000 0 Planarity : 0.003 0.015 1412 Dihedral : 5.327 25.049 1412 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.23), residues: 1399 helix: 1.14 (0.21), residues: 599 sheet: -1.44 (0.35), residues: 224 loop : -2.66 (0.25), residues: 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.20 ( 5681) covalent geometry : angle 0.48126 / 0.32 ( 7081) hydrogen bonds : bond 0.03905 / 3.10 ( 632) hydrogen bonds : angle 5.49339 / 4.39 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0188 time to fit residues: 1.6630 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 chunk 136 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 28 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.063194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051222 restraints weight = 46648.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051719 restraints weight = 35509.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052087 restraints weight = 29354.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052249 restraints weight = 26029.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052370 restraints weight = 24120.581| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.8863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5681 Z= 0.356 Angle : 0.661 6.402 7081 Z= 0.447 Chirality : 0.000 0.000 0 Planarity : 0.004 0.019 1412 Dihedral : 6.262 31.139 1412 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.78 (0.22), residues: 1399 helix: 0.57 (0.21), residues: 603 sheet: -1.33 (0.39), residues: 185 loop : -3.06 (0.23), residues: 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.36 ( 5681) covalent geometry : angle 0.66076 / 0.45 ( 7081) hydrogen bonds : bond 0.05106 / 4.05 ( 632) hydrogen bonds : angle 6.38100 / 5.11 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0176 time to fit residues: 1.6238 Evaluate side-chains 42 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 30.0000 chunk 59 optimal weight: 40.0000 chunk 88 optimal weight: 0.2980 chunk 121 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 57 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 overall best weight: 11.4592 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.063686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051765 restraints weight = 44919.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052136 restraints weight = 35176.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052363 restraints weight = 29901.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052570 restraints weight = 27152.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052667 restraints weight = 25303.275| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5681 Z= 0.304 Angle : 0.595 5.731 7081 Z= 0.400 Chirality : 0.000 0.000 0 Planarity : 0.004 0.019 1412 Dihedral : 5.882 29.645 1412 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.15 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.58 (0.22), residues: 1399 helix: 0.81 (0.21), residues: 605 sheet: -1.12 (0.40), residues: 177 loop : -3.07 (0.23), residues: 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.30 ( 5681) covalent geometry : angle 0.59505 / 0.40 ( 7081) hydrogen bonds : bond 0.04637 / 3.68 ( 632) hydrogen bonds : angle 6.02389 / 4.82 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 729.46 seconds wall clock time: 13 minutes 2.15 seconds (782.15 seconds total)