Starting phenix.real_space_refine on Thu Mar 5 02:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2b_14460/03_2026/7z2b_14460_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 5723 2.51 5 N 1575 2.21 5 O 1754 1.98 5 H 8797 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17921 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 4772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4772 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 4 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6569 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 6482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6482 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.04, per 1000 atoms: 0.17 Number of scatterers: 17921 At special positions: 0 Unit cell: (98.7, 95.55, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 60 16.00 P 9 15.00 Mg 3 11.99 O 1754 8.00 N 1575 7.00 C 5723 6.00 H 8797 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 647.1 milliseconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 53.2% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'K' and resid 16 through 23 Processing helix chain 'K' and resid 70 through 78 Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 103 through 109 Processing helix chain 'K' and resid 116 through 133 Processing helix chain 'K' and resid 157 through 160 Processing helix chain 'K' and resid 185 through 199 Processing helix chain 'K' and resid 259 through 287 Processing helix chain 'K' and resid 295 through 298 Processing helix chain 'K' and resid 299 through 310 removed outlier: 4.431A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 342 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.609A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.079A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.524A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.408A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.996A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.601A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.511A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 412 removed outlier: 4.324A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.911A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.428A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.487A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.275A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 removed outlier: 3.666A pdb=" N GLY H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.544A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.813A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.602A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 282' Processing helix chain 'H' and resid 287 through 297 removed outlier: 3.548A pdb=" N ASP H 297 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.206A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.122A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 4.070A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.424A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.424A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.278A pdb=" N MET K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 110 through 111 Processing sheet with id=AA5, first strand: chain 'K' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.815A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1509 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: 3.20 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8771 1.03 - 1.23: 482 1.23 - 1.43: 3449 1.43 - 1.62: 5302 1.62 - 1.82: 98 Bond restraints: 18102 Sorted by residual: bond pdb=" N3B ANP K 401 " pdb=" PG ANP K 401 " ideal model delta sigma weight residual 1.795 1.611 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" O3A ANP K 401 " pdb=" PB ANP K 401 " ideal model delta sigma weight residual 1.700 1.574 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C GLY A 412 " pdb=" O GLY A 412 " ideal model delta sigma weight residual 1.235 1.308 -0.073 1.35e-02 5.49e+03 2.91e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" O2A G2P H 501 " pdb=" PA G2P H 501 " ideal model delta sigma weight residual 1.513 1.610 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 18097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.57: 32361 5.57 - 11.15: 231 11.15 - 16.72: 7 16.72 - 22.29: 3 22.29 - 27.86: 2 Bond angle restraints: 32604 Sorted by residual: angle pdb=" C3' ANP K 401 " pdb=" C4' ANP K 401 " pdb=" C5' ANP K 401 " ideal model delta sigma weight residual 116.03 88.17 27.86 3.00e+00 1.11e-01 8.63e+01 angle pdb=" O2A ANP K 401 " pdb=" PA ANP K 401 " pdb=" O5' ANP K 401 " ideal model delta sigma weight residual 108.82 85.68 23.14 3.00e+00 1.11e-01 5.95e+01 angle pdb=" O3A ANP K 401 " pdb=" PA ANP K 401 " pdb=" O5' ANP K 401 " ideal model delta sigma weight residual 98.09 77.63 20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.56 126.24 -6.68 1.01e+00 9.80e-01 4.37e+01 angle pdb=" N ILE K 173 " pdb=" CA ILE K 173 " pdb=" C ILE K 173 " ideal model delta sigma weight residual 108.12 117.58 -9.46 1.44e+00 4.82e-01 4.32e+01 ... (remaining 32599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 8260 34.65 - 69.30: 314 69.30 - 103.95: 17 103.95 - 138.61: 0 138.61 - 173.26: 4 Dihedral angle restraints: 8595 sinusoidal: 4670 harmonic: 3925 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.68 -168.05 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.76 156.35 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 134.43 139.70 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 8592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1133 0.114 - 0.228: 242 0.228 - 0.343: 26 0.343 - 0.457: 2 0.457 - 0.571: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C4' ANP K 401 " pdb=" C3' ANP K 401 " pdb=" C5' ANP K 401 " pdb=" O4' ANP K 401 " both_signs ideal model delta sigma weight residual False -2.45 -3.02 0.57 2.00e-01 2.50e+01 8.15e+00 chirality pdb=" CA HIS A 197 " pdb=" N HIS A 197 " pdb=" C HIS A 197 " pdb=" CB HIS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE K 126 " pdb=" N PHE K 126 " pdb=" C PHE K 126 " pdb=" CB PHE K 126 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1401 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 333 " 0.100 2.00e-02 2.50e+03 1.06e-01 1.68e+02 pdb=" CG ASN K 333 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN K 333 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN K 333 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN K 333 " 0.160 2.00e-02 2.50e+03 pdb="HD22 ASN K 333 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 266 " -0.084 2.00e-02 2.50e+03 9.00e-02 1.21e+02 pdb=" CG ASN K 266 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN K 266 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN K 266 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN K 266 " -0.136 2.00e-02 2.50e+03 pdb="HD22 ASN K 266 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 75 " 0.055 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR K 75 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR K 75 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR K 75 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR K 75 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR K 75 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 75 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TYR K 75 " -0.039 2.00e-02 2.50e+03 pdb=" HD2 TYR K 75 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TYR K 75 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR K 75 " -0.030 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.78: 13 1.78 - 2.48: 11800 2.48 - 3.19: 55937 3.19 - 3.89: 72093 3.89 - 4.60: 115459 Nonbonded interactions: 255302 Sorted by model distance: nonbonded pdb=" NZ LYS K 171 " pdb=" OG SER H 423 " model vdw 1.073 2.950 nonbonded pdb=" NZ LYS K 336 " pdb=" OG SER A 419 " model vdw 1.165 2.950 nonbonded pdb=" HZ2 LYS K 171 " pdb=" OG SER H 423 " model vdw 1.348 2.450 nonbonded pdb=" NZ LYS K 336 " pdb=" HB3 SER A 419 " model vdw 1.458 2.770 nonbonded pdb=" NZ LYS K 336 " pdb=" CB SER A 419 " model vdw 1.576 3.250 ... (remaining 255297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.730 Find NCS groups from input model: 0.060 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 : 0.012 0.200 9306 Z= 0.777 Angle : 1.720 27.864 12618 Z= 1.132 Chirality : 0.092 0.571 1404 Planarity : 0.008 0.074 1625 Dihedral : 15.625 173.258 3450 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 0.62 % Allowed : 6.06 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.23), residues: 1146 helix: 0.50 (0.21), residues: 499 sheet: -0.24 (0.36), residues: 214 loop : -0.85 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 250 TYR 0.045 0.005 TYR K 97 PHE 0.037 0.003 PHE K 61 TRP 0.018 0.003 TRP A 21 HIS 0.014 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.01225 ( 9305) covalent geometry : angle 1.72018 (12618) hydrogen bonds : bond 0.18487 ( 489) hydrogen bonds : angle 7.93485 ( 1509) Misc. bond : bond 0.19985 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.6057 (pttt) outliers start: 6 outliers final: 1 residues processed: 227 average time/residue: 0.2785 time to fit residues: 81.4885 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain A residue 326 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 26 ASN K 197 ASN K 325 HIS A 197 HIS A 226 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.071573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053252 restraints weight = 88627.350| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.42 r_work: 0.3079 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9306 Z= 0.201 Angle : 0.697 6.934 12618 Z= 0.382 Chirality : 0.044 0.143 1404 Planarity : 0.005 0.055 1625 Dihedral : 12.457 171.122 1339 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 1.13 % Allowed : 12.64 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.24), residues: 1146 helix: 1.45 (0.22), residues: 511 sheet: -0.53 (0.35), residues: 203 loop : -0.62 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 340 TYR 0.023 0.002 TYR K 337 PHE 0.022 0.002 PHE K 144 TRP 0.012 0.002 TRP A 21 HIS 0.007 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9305) covalent geometry : angle 0.69662 (12618) hydrogen bonds : bond 0.06433 ( 489) hydrogen bonds : angle 5.93360 ( 1509) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: K 144 PHE cc_start: 0.7487 (t80) cc_final: 0.7206 (t80) REVERT: K 218 LEU cc_start: 0.9377 (tp) cc_final: 0.9175 (tp) REVERT: A 116 ASP cc_start: 0.8763 (p0) cc_final: 0.8538 (m-30) REVERT: A 155 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9070 (mt-10) REVERT: A 168 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: A 237 SER cc_start: 0.9108 (m) cc_final: 0.8857 (p) REVERT: H 12 CYS cc_start: 0.8090 (t) cc_final: 0.7752 (t) REVERT: H 145 THR cc_start: 0.8189 (m) cc_final: 0.7847 (m) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 0.2274 time to fit residues: 45.9550 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain H residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 26 ASN K 194 HIS A 15 GLN A 101 ASN A 192 HIS ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.067466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049367 restraints weight = 91679.993| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.22 r_work: 0.2976 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9306 Z= 0.295 Angle : 0.681 6.437 12618 Z= 0.376 Chirality : 0.044 0.160 1404 Planarity : 0.005 0.036 1625 Dihedral : 11.970 179.337 1335 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 1.95 % Allowed : 12.44 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.12 (0.24), residues: 1146 helix: 1.25 (0.22), residues: 515 sheet: -1.17 (0.34), residues: 204 loop : -0.60 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 340 TYR 0.020 0.002 TYR K 75 PHE 0.030 0.002 PHE A 255 TRP 0.012 0.002 TRP A 21 HIS 0.008 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9305) covalent geometry : angle 0.68069 (12618) hydrogen bonds : bond 0.05492 ( 489) hydrogen bonds : angle 5.71660 ( 1509) Misc. bond : bond 0.00167 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 35 MET cc_start: 0.9293 (mmm) cc_final: 0.9000 (tpt) REVERT: K 119 MET cc_start: 0.9485 (tpp) cc_final: 0.8715 (tpp) REVERT: A 35 GLN cc_start: 0.9567 (tt0) cc_final: 0.8955 (tm-30) REVERT: A 168 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: A 237 SER cc_start: 0.9071 (m) cc_final: 0.8848 (p) REVERT: H 12 CYS cc_start: 0.8270 (t) cc_final: 0.7925 (t) REVERT: H 37 HIS cc_start: 0.8619 (m90) cc_final: 0.8398 (m90) REVERT: H 332 MET cc_start: 0.8953 (mmp) cc_final: 0.8699 (mmp) outliers start: 19 outliers final: 16 residues processed: 139 average time/residue: 0.2098 time to fit residues: 40.2076 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 68 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050063 restraints weight = 90748.107| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.19 r_work: 0.2993 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9306 Z= 0.174 Angle : 0.596 7.339 12618 Z= 0.319 Chirality : 0.041 0.150 1404 Planarity : 0.004 0.039 1625 Dihedral : 11.665 174.194 1335 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 2.16 % Allowed : 14.18 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.41 (0.25), residues: 1146 helix: 1.56 (0.22), residues: 519 sheet: -1.16 (0.33), residues: 206 loop : -0.49 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 340 TYR 0.014 0.001 TYR K 75 PHE 0.020 0.002 PHE A 255 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9305) covalent geometry : angle 0.59568 (12618) hydrogen bonds : bond 0.04875 ( 489) hydrogen bonds : angle 5.39808 ( 1509) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 243 ILE cc_start: 0.9556 (mp) cc_final: 0.8931 (tp) REVERT: K 337 TYR cc_start: 0.8554 (t80) cc_final: 0.8056 (t80) REVERT: A 168 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 237 SER cc_start: 0.9092 (m) cc_final: 0.8866 (p) REVERT: H 12 CYS cc_start: 0.8175 (t) cc_final: 0.7845 (t) REVERT: H 26 ASP cc_start: 0.9519 (t0) cc_final: 0.9081 (m-30) REVERT: H 37 HIS cc_start: 0.8583 (m90) cc_final: 0.8350 (m90) REVERT: H 120 ASP cc_start: 0.8811 (m-30) cc_final: 0.8391 (m-30) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.1786 time to fit residues: 32.3241 Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 123 GLN Chi-restraints excluded: chain K residue 193 ILE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.0000 chunk 74 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.067940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049721 restraints weight = 90391.573| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.17 r_work: 0.2987 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9306 Z= 0.196 Angle : 0.584 6.558 12618 Z= 0.313 Chirality : 0.041 0.149 1404 Planarity : 0.004 0.040 1625 Dihedral : 11.494 174.610 1335 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 2.57 % Allowed : 13.16 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.25), residues: 1146 helix: 1.56 (0.22), residues: 521 sheet: -1.27 (0.33), residues: 206 loop : -0.40 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 340 TYR 0.013 0.001 TYR K 75 PHE 0.021 0.002 PHE A 255 TRP 0.012 0.002 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9305) covalent geometry : angle 0.58445 (12618) hydrogen bonds : bond 0.04646 ( 489) hydrogen bonds : angle 5.29416 ( 1509) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 243 ILE cc_start: 0.9574 (mp) cc_final: 0.9023 (tp) REVERT: K 337 TYR cc_start: 0.8662 (t80) cc_final: 0.8152 (t80) REVERT: A 168 GLU cc_start: 0.8538 (pt0) cc_final: 0.8198 (mt-10) REVERT: A 237 SER cc_start: 0.9098 (m) cc_final: 0.8867 (p) REVERT: H 12 CYS cc_start: 0.8188 (t) cc_final: 0.7850 (t) REVERT: H 26 ASP cc_start: 0.9515 (t0) cc_final: 0.9081 (m-30) REVERT: H 37 HIS cc_start: 0.8562 (m90) cc_final: 0.8303 (m90) REVERT: H 120 ASP cc_start: 0.8835 (m-30) cc_final: 0.8402 (m-30) REVERT: H 259 MET cc_start: 0.9141 (mmm) cc_final: 0.8796 (mmm) REVERT: H 290 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8653 (mt-10) outliers start: 25 outliers final: 18 residues processed: 127 average time/residue: 0.1814 time to fit residues: 33.1013 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 123 GLN Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 279 ASN A 133 GLN H 59 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.066590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048845 restraints weight = 90790.122| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.01 r_work: 0.2956 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9306 Z= 0.231 Angle : 0.599 6.160 12618 Z= 0.321 Chirality : 0.041 0.151 1404 Planarity : 0.004 0.040 1625 Dihedral : 11.337 174.585 1335 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 14.49 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.24 (0.25), residues: 1146 helix: 1.44 (0.22), residues: 522 sheet: -1.52 (0.32), residues: 206 loop : -0.45 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 340 TYR 0.014 0.001 TYR A 172 PHE 0.023 0.002 PHE A 255 TRP 0.011 0.002 TRP A 21 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9305) covalent geometry : angle 0.59881 (12618) hydrogen bonds : bond 0.04595 ( 489) hydrogen bonds : angle 5.30642 ( 1509) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 337 TYR cc_start: 0.8697 (t80) cc_final: 0.8196 (t80) REVERT: A 168 GLU cc_start: 0.8547 (pt0) cc_final: 0.8176 (mt-10) REVERT: A 237 SER cc_start: 0.9096 (m) cc_final: 0.8840 (p) REVERT: H 12 CYS cc_start: 0.8221 (t) cc_final: 0.7872 (t) REVERT: H 26 ASP cc_start: 0.9474 (t0) cc_final: 0.9032 (m-30) REVERT: H 59 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (p0) REVERT: H 120 ASP cc_start: 0.8837 (m-30) cc_final: 0.8420 (m-30) REVERT: H 259 MET cc_start: 0.9134 (mmm) cc_final: 0.8783 (mmm) REVERT: H 290 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8347 (tp30) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.1921 time to fit residues: 34.1722 Evaluate side-chains 124 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 193 ILE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 8 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.066957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049180 restraints weight = 89935.682| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.03 r_work: 0.2970 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9306 Z= 0.172 Angle : 0.584 9.031 12618 Z= 0.308 Chirality : 0.041 0.153 1404 Planarity : 0.004 0.039 1625 Dihedral : 11.178 172.767 1335 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.40 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 14.90 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.40 (0.25), residues: 1146 helix: 1.61 (0.23), residues: 523 sheet: -1.54 (0.32), residues: 204 loop : -0.39 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 340 TYR 0.010 0.001 TYR A 172 PHE 0.021 0.001 PHE A 255 TRP 0.013 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9305) covalent geometry : angle 0.58413 (12618) hydrogen bonds : bond 0.04421 ( 489) hydrogen bonds : angle 5.20923 ( 1509) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 337 TYR cc_start: 0.8645 (t80) cc_final: 0.8125 (t80) REVERT: A 168 GLU cc_start: 0.8540 (pt0) cc_final: 0.8167 (mt-10) REVERT: A 237 SER cc_start: 0.9098 (m) cc_final: 0.8843 (p) REVERT: H 12 CYS cc_start: 0.8149 (t) cc_final: 0.7803 (t) REVERT: H 26 ASP cc_start: 0.9469 (t0) cc_final: 0.9026 (m-30) REVERT: H 59 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8430 (p0) REVERT: H 120 ASP cc_start: 0.8820 (m-30) cc_final: 0.8320 (m-30) REVERT: H 149 MET cc_start: 0.9318 (tpp) cc_final: 0.8802 (tpp) REVERT: H 259 MET cc_start: 0.9104 (mmm) cc_final: 0.8751 (mmm) REVERT: H 290 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8310 (tp30) outliers start: 23 outliers final: 19 residues processed: 120 average time/residue: 0.1900 time to fit residues: 32.9608 Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 119 MET Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.067121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.049728 restraints weight = 89138.616| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.98 r_work: 0.2974 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9306 Z= 0.175 Angle : 0.581 7.795 12618 Z= 0.307 Chirality : 0.041 0.144 1404 Planarity : 0.004 0.039 1625 Dihedral : 11.116 172.357 1335 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 14.90 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.25), residues: 1146 helix: 1.66 (0.23), residues: 527 sheet: -1.54 (0.32), residues: 204 loop : -0.34 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 340 TYR 0.009 0.001 TYR A 172 PHE 0.022 0.001 PHE A 255 TRP 0.012 0.001 TRP A 21 HIS 0.009 0.001 HIS K 215 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9305) covalent geometry : angle 0.58080 (12618) hydrogen bonds : bond 0.04379 ( 489) hydrogen bonds : angle 5.13515 ( 1509) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 142 CYS cc_start: 0.8878 (m) cc_final: 0.8671 (m) REVERT: K 337 TYR cc_start: 0.8649 (t80) cc_final: 0.8150 (t80) REVERT: A 168 GLU cc_start: 0.8531 (pt0) cc_final: 0.8155 (mt-10) REVERT: A 237 SER cc_start: 0.9105 (m) cc_final: 0.8847 (p) REVERT: H 12 CYS cc_start: 0.8157 (t) cc_final: 0.7808 (t) REVERT: H 26 ASP cc_start: 0.9462 (t0) cc_final: 0.9028 (m-30) REVERT: H 120 ASP cc_start: 0.8812 (m-30) cc_final: 0.8311 (m-30) REVERT: H 259 MET cc_start: 0.9078 (mmm) cc_final: 0.8746 (mmm) REVERT: H 290 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8303 (tp30) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.1855 time to fit residues: 32.8144 Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 59 ASN H 136 GLN H 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048998 restraints weight = 90097.615| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.00 r_work: 0.2962 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9306 Z= 0.189 Angle : 0.577 7.375 12618 Z= 0.306 Chirality : 0.041 0.149 1404 Planarity : 0.004 0.092 1625 Dihedral : 11.125 171.565 1335 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.36 % Allowed : 15.31 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.44 (0.25), residues: 1146 helix: 1.62 (0.22), residues: 528 sheet: -1.61 (0.32), residues: 204 loop : -0.29 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 166 TYR 0.009 0.001 TYR K 75 PHE 0.023 0.002 PHE A 255 TRP 0.011 0.002 TRP A 21 HIS 0.006 0.001 HIS K 215 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9305) covalent geometry : angle 0.57742 (12618) hydrogen bonds : bond 0.04313 ( 489) hydrogen bonds : angle 5.09142 ( 1509) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8500 (pt0) cc_final: 0.8166 (mt-10) REVERT: H 12 CYS cc_start: 0.8181 (t) cc_final: 0.7811 (t) REVERT: H 26 ASP cc_start: 0.9470 (t0) cc_final: 0.9031 (m-30) REVERT: H 59 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (p0) REVERT: H 120 ASP cc_start: 0.8801 (m-30) cc_final: 0.8304 (m-30) REVERT: H 259 MET cc_start: 0.9044 (mmm) cc_final: 0.8765 (mmm) REVERT: H 290 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8283 (tp30) outliers start: 23 outliers final: 20 residues processed: 117 average time/residue: 0.1651 time to fit residues: 29.2480 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048926 restraints weight = 89734.428| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.98 r_work: 0.2963 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 9306 Z= 0.251 Angle : 0.870 59.199 12618 Z= 0.521 Chirality : 0.042 0.419 1404 Planarity : 0.004 0.088 1625 Dihedral : 11.122 171.528 1335 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.26 % Allowed : 15.42 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.44 (0.25), residues: 1146 helix: 1.63 (0.22), residues: 528 sheet: -1.61 (0.32), residues: 204 loop : -0.30 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 166 TYR 0.009 0.001 TYR K 75 PHE 0.022 0.001 PHE A 255 TRP 0.011 0.002 TRP A 21 HIS 0.005 0.001 HIS K 215 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9305) covalent geometry : angle 0.87041 (12618) hydrogen bonds : bond 0.04316 ( 489) hydrogen bonds : angle 5.09335 ( 1509) Misc. bond : bond 0.00053 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 4 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue SER 212 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue THR 302 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue MET 398 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 86 is missing expected H atoms. Skipping. Residue VAL 257 is missing expected H atoms. Skipping. Residue MET 325 is missing expected H atoms. Skipping. Residue SER 423 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8514 (pt0) cc_final: 0.8176 (mt-10) REVERT: H 12 CYS cc_start: 0.8192 (t) cc_final: 0.7816 (t) REVERT: H 26 ASP cc_start: 0.9467 (t0) cc_final: 0.9028 (m-30) REVERT: H 120 ASP cc_start: 0.8797 (m-30) cc_final: 0.8299 (m-30) REVERT: H 259 MET cc_start: 0.9037 (mmm) cc_final: 0.8758 (mmm) REVERT: H 290 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8282 (tp30) outliers start: 22 outliers final: 21 residues processed: 113 average time/residue: 0.1631 time to fit residues: 27.9102 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 95 PHE Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 290 GLU Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 107 optimal weight: 0.0870 chunk 77 optimal weight: 30.0000 chunk 105 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 84 optimal weight: 0.0070 chunk 104 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048914 restraints weight = 90145.189| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.99 r_work: 0.2962 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 9306 Z= 0.251 Angle : 0.870 59.199 12618 Z= 0.521 Chirality : 0.042 0.419 1404 Planarity : 0.004 0.088 1625 Dihedral : 11.122 171.528 1335 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.26 % Allowed : 15.31 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.44 (0.25), residues: 1146 helix: 1.63 (0.22), residues: 528 sheet: -1.61 (0.32), residues: 204 loop : -0.30 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 166 TYR 0.009 0.001 TYR K 75 PHE 0.022 0.001 PHE A 255 TRP 0.011 0.002 TRP A 21 HIS 0.005 0.001 HIS K 215 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9305) covalent geometry : angle 0.87041 (12618) hydrogen bonds : bond 0.04316 ( 489) hydrogen bonds : angle 5.09335 ( 1509) Misc. bond : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4688.28 seconds wall clock time: 80 minutes 50.60 seconds (4850.60 seconds total)