Starting phenix.real_space_refine on Fri Nov 15 07:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/11_2024/8jhi_36266.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5454 2.51 5 N 1479 2.21 5 O 1566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8562 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1953 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 962 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2619 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 322, 2614 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "C" Number of residues, atoms: 322, 2614 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2680 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BALA R 392 " occ=0.33 ... (8 atoms not shown) pdb=" CB CALA R 392 " occ=0.67 Time building chain proxies: 6.30, per 1000 atoms: 0.74 Number of scatterers: 8562 At special positions: 0 Unit cell: (78.208, 98.176, 151.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1566 8.00 N 1479 7.00 C 5454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 45 " - pdb=" SG CYS N 119 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 130 " distance=2.03 Simple disulfide: pdb=" SG CYS R 165 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS R 286 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 458 " - pdb=" SG CYS R 465 " distance=2.03 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: 2.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 38.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 1 through 35 removed outlier: 4.146A pdb=" N MET A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.100A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.539A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.790A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.908A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.687A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'N' and resid 51 through 55 removed outlier: 3.757A pdb=" N TYR N 55 " --> pdb=" O PHE N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 88 removed outlier: 3.514A pdb=" N LYS N 88 " --> pdb=" O GLY N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 88' Processing helix chain 'N' and resid 110 through 114 removed outlier: 3.677A pdb=" N THR N 114 " --> pdb=" O PRO N 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 225 removed outlier: 4.313A pdb=" N ILE R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER R 215 " --> pdb=" O ILE R 211 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR R 217 " --> pdb=" O CYS R 213 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 236 Processing helix chain 'R' and resid 237 through 264 removed outlier: 3.941A pdb=" N VAL R 248 " --> pdb=" O CYS R 244 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 292 removed outlier: 3.909A pdb=" N THR R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET R 288 " --> pdb=" O LYS R 284 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 316 Processing helix chain 'R' and resid 324 through 326 No H-bonds generated for 'chain 'R' and resid 324 through 326' Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 336 through 341 Processing helix chain 'R' and resid 344 through 348 Processing helix chain 'R' and resid 375 through 408 removed outlier: 3.808A pdb=" N VAL R 400 " --> pdb=" O SER R 396 " (cutoff:3.500A) Proline residue: R 405 - end of helix Processing helix chain 'R' and resid 413 through 457 Proline residue: R 431 - end of helix removed outlier: 5.363A pdb=" N GLY R 447 " --> pdb=" O GLN R 443 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE R 448 " --> pdb=" O ALA R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 476 through 490 removed outlier: 3.512A pdb=" N PHE R 480 " --> pdb=" O ASP R 476 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 497 removed outlier: 3.772A pdb=" N PHE R 496 " --> pdb=" O ILE R 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.243A pdb=" N HIS A 36 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE A 222 " --> pdb=" O HIS A 36 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 38 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG A 37 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE A 245 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 39 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 247 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 41 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.505A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.913A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.128A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.940A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.710A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.664A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 26 through 30 Processing sheet with id=AB1, first strand: chain 'N' and resid 81 through 83 removed outlier: 3.669A pdb=" N SER N 82 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP N 70 " --> pdb=" O ARG N 61 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG N 61 " --> pdb=" O TRP N 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 352 through 354 376 hydrogen bonds defined for protein. 1054 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: 2.32 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2782 1.35 - 1.48: 2214 1.48 - 1.60: 3659 1.60 - 1.73: 0 1.73 - 1.86: 90 Bond restraints: 8745 Sorted by residual: bond pdb=" C ARG R 236 " pdb=" N PRO R 237 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 bond pdb=" CB ILE R 292 " pdb=" CG1 ILE R 292 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" CA ILE R 292 " pdb=" CB ILE R 292 " ideal model delta sigma weight residual 1.540 1.583 -0.043 2.70e-02 1.37e+03 2.48e+00 bond pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " ideal model delta sigma weight residual 1.808 1.856 -0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB CYS N 122 " pdb=" SG CYS N 122 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 8740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11476 1.79 - 3.57: 298 3.57 - 5.36: 36 5.36 - 7.14: 20 7.14 - 8.93: 4 Bond angle restraints: 11834 Sorted by residual: angle pdb=" CA CYS R 286 " pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " ideal model delta sigma weight residual 114.40 123.33 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" C LEU R 258 " pdb=" N GLU R 259 " pdb=" CA GLU R 259 " ideal model delta sigma weight residual 121.76 128.43 -6.67 2.19e+00 2.09e-01 9.27e+00 angle pdb=" C TYR R 461 " pdb=" N HIS R 462 " pdb=" CA HIS R 462 " ideal model delta sigma weight residual 121.54 127.35 -5.81 1.91e+00 2.74e-01 9.24e+00 angle pdb=" C LYS R 408 " pdb=" N GLU R 409 " pdb=" CA GLU R 409 " ideal model delta sigma weight residual 121.54 127.08 -5.54 1.91e+00 2.74e-01 8.42e+00 angle pdb=" N GLU B 10 " pdb=" CA GLU B 10 " pdb=" CB GLU B 10 " ideal model delta sigma weight residual 110.39 115.19 -4.80 1.66e+00 3.63e-01 8.35e+00 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4684 17.77 - 35.55: 439 35.55 - 53.32: 74 53.32 - 71.09: 15 71.09 - 88.87: 9 Dihedral angle restraints: 5221 sinusoidal: 2094 harmonic: 3127 Sorted by residual: dihedral pdb=" CB CYS N 122 " pdb=" SG CYS N 122 " pdb=" SG CYS N 130 " pdb=" CB CYS N 130 " ideal model delta sinusoidal sigma weight residual -86.00 -140.41 54.41 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS R 165 " pdb=" SG CYS R 165 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual -86.00 -137.85 51.85 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA SER R 215 " pdb=" C SER R 215 " pdb=" N ALA R 216 " pdb=" CA ALA R 216 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 823 0.037 - 0.074: 361 0.074 - 0.110: 100 0.110 - 0.147: 28 0.147 - 0.184: 5 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA TYR R 233 " pdb=" N TYR R 233 " pdb=" C TYR R 233 " pdb=" CB TYR R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1314 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 121 " 0.194 9.50e-02 1.11e+02 8.70e-02 4.70e+00 pdb=" NE ARG N 121 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG N 121 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG N 121 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 463 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO R 464 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 464 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 464 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 140 " 0.014 2.00e-02 2.50e+03 1.51e-02 4.54e+00 pdb=" CG TYR N 140 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR N 140 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR N 140 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR N 140 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 140 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR N 140 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 140 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 271 2.71 - 3.26: 8446 3.26 - 3.80: 14003 3.80 - 4.35: 17259 4.35 - 4.90: 28633 Nonbonded interactions: 68612 Sorted by model distance: nonbonded pdb=" OH TYR R 241 " pdb=" O VAL R 490 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.248 3.040 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 121 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.285 3.040 ... (remaining 68607 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=0.33 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8745 Z= 0.247 Angle : 0.707 8.929 11834 Z= 0.362 Chirality : 0.045 0.184 1317 Planarity : 0.006 0.087 1505 Dihedral : 14.305 88.867 3185 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1060 helix: 0.24 (0.27), residues: 361 sheet: 0.14 (0.35), residues: 219 loop : -1.55 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 453 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE R 480 TYR 0.037 0.002 TYR N 140 ARG 0.005 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.8762 (m-10) cc_final: 0.8512 (m-10) REVERT: B 292 PHE cc_start: 0.8266 (m-10) cc_final: 0.7893 (m-10) REVERT: C 41 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8419 (tm-30) REVERT: R 192 MET cc_start: 0.6198 (pmm) cc_final: 0.5666 (pmm) REVERT: R 298 MET cc_start: 0.7031 (mmp) cc_final: 0.6673 (mmm) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2542 time to fit residues: 78.2102 Evaluate side-chains 170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 220 GLN B 340 ASN N 105 GLN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8745 Z= 0.201 Angle : 0.624 7.139 11834 Z= 0.321 Chirality : 0.043 0.166 1317 Planarity : 0.005 0.049 1505 Dihedral : 4.603 30.764 1183 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.48 % Allowed : 11.43 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1060 helix: 0.81 (0.29), residues: 359 sheet: 0.15 (0.36), residues: 213 loop : -1.38 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 453 HIS 0.003 0.001 HIS A 357 PHE 0.044 0.002 PHE R 219 TYR 0.020 0.001 TYR R 241 ARG 0.006 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 GLN cc_start: 0.8107 (mp10) cc_final: 0.7801 (mp10) REVERT: B 111 TYR cc_start: 0.8818 (m-10) cc_final: 0.8582 (m-10) REVERT: B 262 MET cc_start: 0.7373 (tpp) cc_final: 0.7011 (tpp) REVERT: B 292 PHE cc_start: 0.8312 (m-10) cc_final: 0.7961 (m-10) REVERT: C 41 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 51 ARG cc_start: 0.6632 (mtt180) cc_final: 0.6386 (mtm180) REVERT: R 298 MET cc_start: 0.7219 (mmp) cc_final: 0.6974 (mmm) outliers start: 23 outliers final: 17 residues processed: 194 average time/residue: 0.2338 time to fit residues: 61.1120 Evaluate side-chains 186 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8745 Z= 0.203 Angle : 0.606 8.516 11834 Z= 0.309 Chirality : 0.043 0.157 1317 Planarity : 0.004 0.051 1505 Dihedral : 4.456 29.802 1183 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.59 % Allowed : 14.46 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1060 helix: 0.99 (0.29), residues: 360 sheet: 0.16 (0.36), residues: 213 loop : -1.35 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 453 HIS 0.002 0.001 HIS R 181 PHE 0.034 0.002 PHE R 219 TYR 0.020 0.001 TYR R 241 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 61 MET cc_start: 0.8069 (ppp) cc_final: 0.7716 (ppp) REVERT: B 262 MET cc_start: 0.7389 (tpp) cc_final: 0.7070 (tpp) REVERT: B 289 TYR cc_start: 0.8945 (m-80) cc_final: 0.8643 (m-80) REVERT: C 41 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8464 (tm-30) outliers start: 24 outliers final: 21 residues processed: 191 average time/residue: 0.2251 time to fit residues: 57.6786 Evaluate side-chains 195 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8745 Z= 0.287 Angle : 0.632 7.992 11834 Z= 0.324 Chirality : 0.043 0.150 1317 Planarity : 0.004 0.049 1505 Dihedral : 4.533 30.448 1183 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.13 % Allowed : 16.07 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1060 helix: 1.08 (0.29), residues: 360 sheet: 0.08 (0.37), residues: 204 loop : -1.33 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.042 0.002 PHE R 219 TYR 0.019 0.002 TYR R 241 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.8230 (ppp) cc_final: 0.7859 (ppp) REVERT: B 262 MET cc_start: 0.7431 (tpp) cc_final: 0.7002 (tpp) REVERT: C 41 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8514 (tm-30) REVERT: R 298 MET cc_start: 0.7377 (mmp) cc_final: 0.7001 (mmm) outliers start: 29 outliers final: 24 residues processed: 187 average time/residue: 0.2245 time to fit residues: 57.5810 Evaluate side-chains 185 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 387 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 GLN ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8745 Z= 0.288 Angle : 0.625 8.218 11834 Z= 0.322 Chirality : 0.043 0.150 1317 Planarity : 0.004 0.048 1505 Dihedral : 4.522 30.205 1183 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.45 % Allowed : 17.26 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1060 helix: 1.05 (0.28), residues: 367 sheet: -0.14 (0.35), residues: 212 loop : -1.31 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.033 0.002 PHE R 219 TYR 0.014 0.002 TYR R 245 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.010 Fit side-chains REVERT: A 28 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7525 (mt-10) REVERT: B 61 MET cc_start: 0.8267 (ppp) cc_final: 0.7906 (ppp) REVERT: B 273 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 41 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8540 (tm-30) REVERT: R 184 ASP cc_start: 0.7145 (t0) cc_final: 0.6695 (t70) outliers start: 32 outliers final: 28 residues processed: 188 average time/residue: 0.2134 time to fit residues: 55.4107 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 433 LEU Chi-restraints excluded: chain R residue 486 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8745 Z= 0.194 Angle : 0.611 9.797 11834 Z= 0.306 Chirality : 0.042 0.166 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.404 28.982 1183 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.13 % Allowed : 18.55 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1060 helix: 1.16 (0.29), residues: 367 sheet: -0.09 (0.36), residues: 212 loop : -1.25 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS B 225 PHE 0.041 0.001 PHE R 219 TYR 0.015 0.001 TYR R 428 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7596 (mt-10) REVERT: B 105 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8033 (t80) REVERT: C 41 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 53 LYS cc_start: 0.8619 (tptt) cc_final: 0.8410 (tptt) REVERT: R 184 ASP cc_start: 0.7142 (t0) cc_final: 0.6693 (t70) REVERT: R 298 MET cc_start: 0.7283 (mmp) cc_final: 0.6989 (mmm) outliers start: 29 outliers final: 25 residues processed: 199 average time/residue: 0.2126 time to fit residues: 58.6317 Evaluate side-chains 194 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 8745 Z= 0.206 Angle : 0.645 8.983 11834 Z= 0.320 Chirality : 0.043 0.184 1317 Planarity : 0.004 0.046 1505 Dihedral : 4.343 28.420 1183 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.67 % Allowed : 19.74 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 1060 helix: 1.25 (0.29), residues: 367 sheet: -0.14 (0.36), residues: 212 loop : -1.28 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.002 0.001 HIS R 181 PHE 0.037 0.001 PHE R 219 TYR 0.024 0.001 TYR R 441 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7589 (mt-10) REVERT: B 105 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 273 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7861 (mp) REVERT: C 53 LYS cc_start: 0.8656 (tptt) cc_final: 0.8421 (tptt) REVERT: R 184 ASP cc_start: 0.7196 (t0) cc_final: 0.6743 (t70) REVERT: R 298 MET cc_start: 0.7341 (mmp) cc_final: 0.6997 (mmm) outliers start: 34 outliers final: 28 residues processed: 187 average time/residue: 0.2190 time to fit residues: 56.3859 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 110 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8745 Z= 0.328 Angle : 0.697 8.877 11834 Z= 0.350 Chirality : 0.045 0.234 1317 Planarity : 0.004 0.044 1505 Dihedral : 4.538 29.414 1183 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.99 % Allowed : 19.85 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1060 helix: 1.23 (0.29), residues: 368 sheet: -0.28 (0.35), residues: 212 loop : -1.36 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.003 0.001 HIS A 357 PHE 0.043 0.002 PHE R 219 TYR 0.024 0.002 TYR R 441 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 273 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7982 (mp) REVERT: R 184 ASP cc_start: 0.7334 (t0) cc_final: 0.6843 (t70) outliers start: 37 outliers final: 29 residues processed: 182 average time/residue: 0.2152 time to fit residues: 54.0433 Evaluate side-chains 193 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 0.0270 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8745 Z= 0.194 Angle : 0.659 8.879 11834 Z= 0.329 Chirality : 0.043 0.212 1317 Planarity : 0.004 0.043 1505 Dihedral : 4.440 27.999 1183 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.13 % Allowed : 20.93 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1060 helix: 1.30 (0.29), residues: 366 sheet: -0.22 (0.35), residues: 212 loop : -1.31 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.041 0.001 PHE R 219 TYR 0.018 0.001 TYR R 441 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7947 (mmp80) cc_final: 0.7156 (mpt180) REVERT: A 28 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7575 (mt-10) REVERT: B 105 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8024 (t80) REVERT: R 184 ASP cc_start: 0.7139 (t0) cc_final: 0.6687 (t70) REVERT: R 195 ARG cc_start: 0.7420 (ppt170) cc_final: 0.7111 (ppt170) REVERT: R 298 MET cc_start: 0.7227 (mmp) cc_final: 0.6927 (mmm) outliers start: 29 outliers final: 26 residues processed: 184 average time/residue: 0.2148 time to fit residues: 54.3404 Evaluate side-chains 196 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8745 Z= 0.246 Angle : 0.680 10.428 11834 Z= 0.340 Chirality : 0.043 0.224 1317 Planarity : 0.004 0.043 1505 Dihedral : 4.422 28.461 1183 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.24 % Allowed : 21.25 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1060 helix: 1.34 (0.29), residues: 366 sheet: -0.25 (0.35), residues: 212 loop : -1.31 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.002 0.001 HIS R 181 PHE 0.048 0.002 PHE R 219 TYR 0.021 0.002 TYR R 441 ARG 0.006 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7571 (mt-10) REVERT: B 105 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8038 (t80) REVERT: B 273 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 41 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8395 (tm-30) REVERT: R 184 ASP cc_start: 0.7162 (t0) cc_final: 0.6700 (t70) REVERT: R 298 MET cc_start: 0.7345 (mmp) cc_final: 0.6984 (mmm) outliers start: 30 outliers final: 27 residues processed: 175 average time/residue: 0.2357 time to fit residues: 58.3774 Evaluate side-chains 190 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain R residue 283 ASN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 443 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 = 0.4096 r_free = 0.4096 target = 0.154456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113588 restraints weight = 13373.114| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.52 r_work: 0.3439 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8745 Z= 0.204 Angle : 0.677 11.342 11834 Z= 0.338 Chirality : 0.043 0.215 1317 Planarity : 0.004 0.043 1505 Dihedral : 4.378 27.960 1183 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.13 % Allowed : 21.57 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1060 helix: 1.38 (0.29), residues: 366 sheet: -0.16 (0.36), residues: 207 loop : -1.33 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.001 HIS R 181 PHE 0.050 0.001 PHE R 219 TYR 0.019 0.001 TYR R 441 ARG 0.003 0.000 ARG A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.63 seconds wall clock time: 43 minutes 4.97 seconds (2584.97 seconds total)