Starting phenix.real_space_refine on Sun Aug 24 14:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ojq_20092/08_2025/6ojq_20092.map" } resolution = 3.67 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2420 atoms to isotropic. 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 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 5760 2.51 5 N 1570 2.21 5 O 1784 1.98 5 H 8878 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18055 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6561 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6597 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4831 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 8, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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} 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} Time building chain proxies: 3.28, per 1000 atoms: 0.18 Number of scatterers: 18055 At special positions: 0 Unit cell: (76.7, 106.6, 110.5, 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 55 16.00 P 6 15.00 Mg 2 11.99 O 1784 8.00 N 1570 7.00 C 5760 6.00 H 8878 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=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 636.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 50.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.291A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.333A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.677A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.132A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.513A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.622A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.633A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 383 through 400 removed outlier: 3.988A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 412 removed outlier: 4.643A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 412 " --> pdb=" O TYR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.811A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.694A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.064A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.577A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' 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 127 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.251A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.818A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.872A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.074A 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: 3.847A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.564A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.511A pdb=" N ASN A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.719A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.845A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.968A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.702A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 removed outlier: 3.906A pdb=" N ASN K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 66 removed outlier: 3.790A pdb=" N VAL K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 74 Processing helix chain 'K' and resid 90 through 96 removed outlier: 3.544A pdb=" N GLU K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 120 removed outlier: 3.621A pdb=" N TYR K 120 " --> pdb=" O PHE K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 189 removed outlier: 4.033A pdb=" N ASN K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 removed outlier: 3.593A pdb=" N THR K 241 " --> pdb=" O LYS K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 270 removed outlier: 3.556A pdb=" N ASP K 249 " --> pdb=" O GLY K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 279 removed outlier: 3.993A pdb=" N ASP K 279 " --> pdb=" O PRO K 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 276 through 279' Processing helix chain 'K' and resid 280 through 285 Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 308 through 324 removed outlier: 3.673A pdb=" N SER K 314 " --> pdb=" O SER K 310 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA K 322 " --> pdb=" O PHE K 318 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS K 323 " --> pdb=" O GLY K 319 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR K 324 " --> pdb=" O GLN K 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.061A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.719A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 172 removed outlier: 7.686A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 273 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.716A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 168 " --> pdb=" O CYS A 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.782A pdb=" N CYS A 376 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 318 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 316 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 50 through 52 removed outlier: 9.432A pdb=" N ARG K 50 " --> pdb=" O ILE K 9 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL K 11 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE K 52 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS K 13 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE K 300 " --> pdb=" O MET K 12 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 32 through 34 Processing sheet with id=AB2, first strand: chain 'K' and resid 154 through 156 removed outlier: 4.389A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1209 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: 4.20 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 8855 1.05 - 1.26: 1580 1.26 - 1.48: 3803 1.48 - 1.69: 3918 1.69 - 1.91: 90 Bond restraints: 18246 Sorted by residual: bond pdb=" C1' G2P B 501 " pdb=" C2' G2P B 501 " ideal model delta sigma weight residual 1.537 1.261 0.276 2.00e-02 2.50e+03 1.91e+02 bond pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3' G2P B 501 " pdb=" C4' G2P B 501 " ideal model delta sigma weight residual 1.526 1.282 0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.283 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1' G2P B 501 " pdb=" O4' G2P B 501 " ideal model delta sigma weight residual 1.389 1.558 -0.169 2.00e-02 2.50e+03 7.12e+01 ... (remaining 18241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 32747 3.37 - 6.74: 100 6.74 - 10.12: 11 10.12 - 13.49: 3 13.49 - 16.86: 2 Bond angle restraints: 32863 Sorted by residual: angle pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" C8 GTP A 501 " ideal model delta sigma weight residual 126.00 109.14 16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" C4 GTP A 501 " ideal model delta sigma weight residual 126.00 142.14 -16.14 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 108.79 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 113.59 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 138.20 -10.28 3.00e+00 1.11e-01 1.17e+01 ... (remaining 32858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8491 35.32 - 70.63: 163 70.63 - 105.95: 2 105.95 - 141.26: 1 141.26 - 176.58: 3 Dihedral angle restraints: 8660 sinusoidal: 4699 harmonic: 3961 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 -114.15 -176.58 1 2.00e+01 2.50e-03 4.80e+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 -47.08 151.67 1 2.00e+01 2.50e-03 4.51e+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 274.12 125.64 148.48 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 8657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1082 0.050 - 0.099: 258 0.099 - 0.149: 53 0.149 - 0.199: 5 0.199 - 0.248: 2 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 1397 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 270 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 214 " -0.015 2.00e-02 2.50e+03 1.04e-02 3.26e+00 pdb=" CG PHE B 214 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 214 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 214 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 214 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 214 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 387 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C LEU B 387 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU B 387 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE B 388 " -0.010 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3030 2.29 - 2.87: 41689 2.87 - 3.45: 46489 3.45 - 4.02: 63494 4.02 - 4.60: 98372 Nonbonded interactions: 253074 Sorted by model distance: nonbonded pdb=" OG SER A 241 " pdb=" H VAL A 250 " model vdw 1.716 2.450 nonbonded pdb="HH22 ARG K 190 " pdb=" OD2 ASP K 231 " model vdw 1.723 2.450 nonbonded pdb=" HH TYR A 108 " pdb=" O ALA K 243 " model vdw 1.728 2.450 nonbonded pdb="HH12 ARG K 203 " pdb=" OE1 GLU K 236 " model vdw 1.738 2.450 nonbonded pdb=" OD2 ASP B 427 " pdb=" HE ARG K 278 " model vdw 1.740 2.450 ... (remaining 253069 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.130 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.390 Find NCS groups from input model: 0.070 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.009 0.276 9368 Z= 0.422 Angle : 0.783 16.860 12701 Z= 0.394 Chirality : 0.045 0.248 1400 Planarity : 0.004 0.049 1650 Dihedral : 10.579 176.576 3466 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.22), residues: 1154 helix: -1.03 (0.21), residues: 472 sheet: -3.13 (0.30), residues: 196 loop : -2.37 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 215 TYR 0.020 0.002 TYR A 432 PHE 0.031 0.002 PHE B 214 TRP 0.020 0.002 TRP A 21 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00861 ( 9368) covalent geometry : angle 0.78325 (12701) hydrogen bonds : bond 0.16588 ( 417) hydrogen bonds : angle 7.12257 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.518 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: B 103 TRP cc_start: 0.8154 (t60) cc_final: 0.7951 (t60) REVERT: B 179 ASP cc_start: 0.7358 (t70) cc_final: 0.6946 (t0) REVERT: B 205 ASP cc_start: 0.7599 (t70) cc_final: 0.7346 (t0) REVERT: B 278 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8186 (mmt180) REVERT: B 305 CYS cc_start: 0.7910 (m) cc_final: 0.7686 (p) REVERT: A 101 ASN cc_start: 0.8670 (t160) cc_final: 0.8395 (t0) REVERT: A 290 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 302 MET cc_start: 0.8599 (mmp) cc_final: 0.8039 (mmp) REVERT: K 113 GLN cc_start: 0.7453 (mt0) cc_final: 0.6546 (pp30) REVERT: K 185 GLU cc_start: 0.8790 (tt0) cc_final: 0.8406 (tm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3158 time to fit residues: 77.1956 Evaluate side-chains 89 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 192 HIS B 406 HIS B 426 ASN A 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087079 restraints weight = 49538.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090661 restraints weight = 19257.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092737 restraints weight = 9691.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093940 restraints weight = 5863.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094727 restraints weight = 4178.196| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9368 Z= 0.274 Angle : 0.635 7.711 12701 Z= 0.335 Chirality : 0.045 0.209 1400 Planarity : 0.005 0.044 1650 Dihedral : 10.394 160.794 1309 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.80 % Allowed : 5.13 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.24), residues: 1154 helix: 0.03 (0.23), residues: 493 sheet: -2.89 (0.32), residues: 194 loop : -2.20 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.015 0.002 TYR A 24 PHE 0.012 0.002 PHE B 169 TRP 0.016 0.002 TRP A 21 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 9368) covalent geometry : angle 0.63509 (12701) hydrogen bonds : bond 0.04891 ( 417) hydrogen bonds : angle 5.50548 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.515 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: B 179 ASP cc_start: 0.7330 (t70) cc_final: 0.6948 (t0) REVERT: B 415 GLU cc_start: 0.5738 (tm-30) cc_final: 0.5518 (tm-30) REVERT: A 302 MET cc_start: 0.9145 (mmp) cc_final: 0.8902 (mmt) REVERT: K 50 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6943 (tpt90) REVERT: K 113 GLN cc_start: 0.7396 (mt0) cc_final: 0.6653 (pp30) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.2133 time to fit residues: 30.2543 Evaluate side-chains 75 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.088656 restraints weight = 49687.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092328 restraints weight = 18608.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094458 restraints weight = 9150.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095666 restraints weight = 5429.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096419 restraints weight = 3830.329| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9368 Z= 0.123 Angle : 0.513 6.483 12701 Z= 0.264 Chirality : 0.041 0.145 1400 Planarity : 0.004 0.045 1650 Dihedral : 9.716 153.195 1309 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.11 % Allowed : 5.43 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.25), residues: 1154 helix: 0.59 (0.24), residues: 491 sheet: -2.63 (0.33), residues: 193 loop : -1.98 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR A 172 PHE 0.020 0.001 PHE B 169 TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9368) covalent geometry : angle 0.51336 (12701) hydrogen bonds : bond 0.04356 ( 417) hydrogen bonds : angle 5.05606 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.400 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: B 55 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: B 179 ASP cc_start: 0.7324 (t70) cc_final: 0.6921 (t0) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.2178 time to fit residues: 25.2592 Evaluate side-chains 76 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.102229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088260 restraints weight = 49916.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091910 restraints weight = 19191.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094009 restraints weight = 9561.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095132 restraints weight = 5770.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095948 restraints weight = 4174.246| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9368 Z= 0.133 Angle : 0.496 6.157 12701 Z= 0.255 Chirality : 0.041 0.143 1400 Planarity : 0.003 0.035 1650 Dihedral : 9.367 146.767 1309 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.91 % Allowed : 6.14 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1154 helix: 0.89 (0.24), residues: 500 sheet: -2.33 (0.34), residues: 194 loop : -1.88 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.008 0.001 TYR A 108 PHE 0.016 0.001 PHE B 169 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9368) covalent geometry : angle 0.49642 (12701) hydrogen bonds : bond 0.03972 ( 417) hydrogen bonds : angle 4.77874 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.471 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: B 55 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: B 179 ASP cc_start: 0.7340 (t70) cc_final: 0.6920 (t0) REVERT: B 205 ASP cc_start: 0.7755 (t0) cc_final: 0.7514 (t0) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.1710 time to fit residues: 20.9876 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087365 restraints weight = 50195.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090926 restraints weight = 19367.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093022 restraints weight = 9733.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094127 restraints weight = 5874.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094952 restraints weight = 4260.686| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9368 Z= 0.142 Angle : 0.493 5.934 12701 Z= 0.253 Chirality : 0.041 0.140 1400 Planarity : 0.003 0.036 1650 Dihedral : 8.981 137.454 1309 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.11 % Allowed : 6.84 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.25), residues: 1154 helix: 1.06 (0.24), residues: 498 sheet: -2.15 (0.36), residues: 194 loop : -1.76 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 278 TYR 0.009 0.001 TYR K 274 PHE 0.013 0.001 PHE B 169 TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9368) covalent geometry : angle 0.49272 (12701) hydrogen bonds : bond 0.03895 ( 417) hydrogen bonds : angle 4.68465 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.574 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: B 55 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: B 145 THR cc_start: 0.7955 (m) cc_final: 0.7727 (m) REVERT: B 179 ASP cc_start: 0.7269 (t70) cc_final: 0.6833 (t0) REVERT: B 205 ASP cc_start: 0.7766 (t0) cc_final: 0.7439 (t0) outliers start: 11 outliers final: 10 residues processed: 83 average time/residue: 0.1745 time to fit residues: 22.5002 Evaluate side-chains 77 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086443 restraints weight = 49879.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090000 restraints weight = 19407.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092075 restraints weight = 9786.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093302 restraints weight = 5931.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094029 restraints weight = 4220.463| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9368 Z= 0.153 Angle : 0.499 7.071 12701 Z= 0.256 Chirality : 0.041 0.141 1400 Planarity : 0.003 0.031 1650 Dihedral : 8.796 131.011 1309 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 6.94 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.26), residues: 1154 helix: 1.19 (0.24), residues: 499 sheet: -2.12 (0.36), residues: 194 loop : -1.71 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.010 0.001 TYR K 118 PHE 0.012 0.001 PHE B 169 TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9368) covalent geometry : angle 0.49949 (12701) hydrogen bonds : bond 0.03871 ( 417) hydrogen bonds : angle 4.64199 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: B 145 THR cc_start: 0.7976 (m) cc_final: 0.7736 (m) REVERT: B 179 ASP cc_start: 0.7307 (t70) cc_final: 0.6862 (t0) REVERT: A 302 MET cc_start: 0.9185 (mmt) cc_final: 0.8949 (mmt) REVERT: K 185 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7304 (tm-30) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1737 time to fit residues: 20.8195 Evaluate side-chains 75 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 109 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083390 restraints weight = 50699.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087013 restraints weight = 19238.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089156 restraints weight = 9581.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090393 restraints weight = 5727.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090978 restraints weight = 4041.734| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9368 Z= 0.208 Angle : 0.539 7.058 12701 Z= 0.277 Chirality : 0.042 0.138 1400 Planarity : 0.004 0.032 1650 Dihedral : 8.829 128.842 1309 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.11 % Allowed : 7.85 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1154 helix: 1.14 (0.24), residues: 498 sheet: -2.22 (0.35), residues: 196 loop : -1.78 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.011 0.001 TYR K 274 PHE 0.013 0.001 PHE B 169 TRP 0.009 0.002 TRP A 21 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9368) covalent geometry : angle 0.53879 (12701) hydrogen bonds : bond 0.04115 ( 417) hydrogen bonds : angle 4.77884 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: B 145 THR cc_start: 0.7906 (m) cc_final: 0.7648 (m) REVERT: B 179 ASP cc_start: 0.7386 (t70) cc_final: 0.6925 (t0) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1668 time to fit residues: 19.2725 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084709 restraints weight = 49977.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088399 restraints weight = 18928.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090538 restraints weight = 9395.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091814 restraints weight = 5628.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092391 restraints weight = 3940.662| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9368 Z= 0.122 Angle : 0.487 7.265 12701 Z= 0.248 Chirality : 0.041 0.143 1400 Planarity : 0.003 0.032 1650 Dihedral : 8.597 124.117 1309 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.80 % Allowed : 8.05 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.26), residues: 1154 helix: 1.32 (0.24), residues: 498 sheet: -2.14 (0.36), residues: 196 loop : -1.66 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR K 274 PHE 0.010 0.001 PHE B 169 TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9368) covalent geometry : angle 0.48657 (12701) hydrogen bonds : bond 0.03785 ( 417) hydrogen bonds : angle 4.56853 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 THR cc_start: 0.7851 (m) cc_final: 0.7584 (m) REVERT: B 179 ASP cc_start: 0.7371 (t70) cc_final: 0.6900 (t0) REVERT: K 288 ASP cc_start: 0.7878 (p0) cc_final: 0.7631 (p0) outliers start: 8 outliers final: 8 residues processed: 77 average time/residue: 0.1822 time to fit residues: 21.5299 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.084538 restraints weight = 50306.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088152 restraints weight = 19762.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090236 restraints weight = 9993.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091433 restraints weight = 6094.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092206 restraints weight = 4374.024| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9368 Z= 0.164 Angle : 0.508 7.475 12701 Z= 0.260 Chirality : 0.041 0.140 1400 Planarity : 0.003 0.032 1650 Dihedral : 8.584 121.088 1309 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.11 % Allowed : 8.15 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.26), residues: 1154 helix: 1.32 (0.24), residues: 498 sheet: -2.05 (0.37), residues: 188 loop : -1.73 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.011 0.001 TYR K 274 PHE 0.011 0.001 PHE B 169 TRP 0.010 0.002 TRP A 21 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9368) covalent geometry : angle 0.50815 (12701) hydrogen bonds : bond 0.03888 ( 417) hydrogen bonds : angle 4.63733 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: B 145 THR cc_start: 0.7910 (m) cc_final: 0.7645 (m) REVERT: B 179 ASP cc_start: 0.7389 (t70) cc_final: 0.6922 (t0) REVERT: A 302 MET cc_start: 0.9256 (mmt) cc_final: 0.9041 (mmt) REVERT: K 288 ASP cc_start: 0.7912 (p0) cc_final: 0.7655 (p0) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.1838 time to fit residues: 21.5637 Evaluate side-chains 74 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085808 restraints weight = 49867.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089520 restraints weight = 18855.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091676 restraints weight = 9281.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092946 restraints weight = 5521.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093570 restraints weight = 3856.619| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9368 Z= 0.107 Angle : 0.479 7.594 12701 Z= 0.243 Chirality : 0.040 0.144 1400 Planarity : 0.003 0.032 1650 Dihedral : 8.416 118.530 1309 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.80 % Allowed : 8.45 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.26), residues: 1154 helix: 1.51 (0.24), residues: 499 sheet: -1.97 (0.36), residues: 196 loop : -1.58 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.009 0.001 TYR K 274 PHE 0.010 0.001 PHE B 169 TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9368) covalent geometry : angle 0.47858 (12701) hydrogen bonds : bond 0.03625 ( 417) hydrogen bonds : angle 4.45800 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 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 VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 THR cc_start: 0.7824 (m) cc_final: 0.7554 (m) REVERT: B 179 ASP cc_start: 0.7382 (t70) cc_final: 0.6899 (t0) REVERT: K 288 ASP cc_start: 0.7839 (p0) cc_final: 0.7630 (p0) outliers start: 8 outliers final: 8 residues processed: 74 average time/residue: 0.1987 time to fit residues: 21.8946 Evaluate side-chains 72 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085671 restraints weight = 50320.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089296 restraints weight = 19505.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091412 restraints weight = 9789.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092651 restraints weight = 5896.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093365 restraints weight = 4163.004| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9368 Z= 0.131 Angle : 0.489 7.907 12701 Z= 0.248 Chirality : 0.041 0.141 1400 Planarity : 0.003 0.036 1650 Dihedral : 8.424 119.304 1309 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.80 % Allowed : 8.65 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1154 helix: 1.56 (0.24), residues: 498 sheet: -1.94 (0.36), residues: 196 loop : -1.63 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.009 0.001 TYR K 274 PHE 0.010 0.001 PHE B 169 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9368) covalent geometry : angle 0.48898 (12701) hydrogen bonds : bond 0.03677 ( 417) hydrogen bonds : angle 4.45458 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.32 seconds wall clock time: 49 minutes 18.25 seconds (2958.25 seconds total)