Starting phenix.real_space_refine on Fri Jul 19 16:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/07_2024/8jhi_36266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/07_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_36266/07_2024/8jhi_36266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/07_2024/8jhi_36266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/07_2024/8jhi_36266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhi_36266/07_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.27, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 3.54 Conformation dependent library (CDL) restraints added in 1.9 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: 0.84 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: 2.19 Time building geometry restraints manager: 3.80 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: 97.52 - 104.83: 116 104.83 - 112.14: 4234 112.14 - 119.46: 3063 119.46 - 126.77: 4290 126.77 - 134.09: 131 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 2.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.248 2.440 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 121 " model vdw 2.270 2.520 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.285 2.440 ... (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 ========== 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: 1.570 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.220 Find NCS groups from input model: 0.090 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.016 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: 0.2496 time to fit residues: 76.5244 Evaluate side-chains 170 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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: 1.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** R 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8745 Z= 0.272 Angle : 0.626 7.258 11834 Z= 0.322 Chirality : 0.043 0.165 1317 Planarity : 0.005 0.051 1505 Dihedral : 4.601 31.595 1183 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.02 % Allowed : 12.19 % Favored : 84.79 % 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: -0.42 (0.27), residues: 1060 helix: 0.83 (0.29), residues: 357 sheet: 0.23 (0.36), residues: 218 loop : -1.37 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 453 HIS 0.003 0.001 HIS R 332 PHE 0.034 0.002 PHE R 219 TYR 0.017 0.002 TYR N 140 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 215 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 61 MET cc_start: 0.8129 (ppp) cc_final: 0.7789 (ppp) REVERT: C 41 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8469 (tm-30) REVERT: C 51 ARG cc_start: 0.6906 (mtt180) cc_final: 0.6680 (mtm180) outliers start: 28 outliers final: 21 residues processed: 194 average time/residue: 0.2152 time to fit residues: 56.4938 Evaluate side-chains 187 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 325 THR 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 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 C residue 76 THR 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 76 optimal weight: 6.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7746 moved from start: 0.1699 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= 0.162 Angle : 0.587 8.979 11834 Z= 0.294 Chirality : 0.042 0.160 1317 Planarity : 0.004 0.049 1505 Dihedral : 4.405 29.821 1183 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.27 % Allowed : 15.86 % Favored : 81.88 % 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 (0.27), residues: 1060 helix: 1.06 (0.29), residues: 360 sheet: 0.17 (0.36), residues: 213 loop : -1.28 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 453 HIS 0.002 0.000 HIS R 462 PHE 0.033 0.001 PHE R 219 TYR 0.017 0.001 TYR R 204 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 205 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.263 Fit side-chains REVERT: A 28 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7969 (mm-30) REVERT: A 220 HIS cc_start: 0.7787 (m-70) cc_final: 0.7513 (m-70) REVERT: B 61 MET cc_start: 0.8062 (ppp) cc_final: 0.7694 (ppp) REVERT: B 111 TYR cc_start: 0.8750 (m-80) cc_final: 0.8500 (m-10) REVERT: B 292 PHE cc_start: 0.8211 (m-80) cc_final: 0.7863 (m-10) REVERT: C 41 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8458 (tm-30) REVERT: N 110 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7657 (ptpp) REVERT: N 112 GLU cc_start: 0.8420 (pm20) cc_final: 0.8075 (pm20) REVERT: R 298 MET cc_start: 0.7351 (mmp) cc_final: 0.6947 (mmm) outliers start: 21 outliers final: 16 residues processed: 188 average time/residue: 0.2227 time to fit residues: 56.0535 Evaluate side-chains 188 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 302 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 84 SER 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 339 TRP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 110 LYS 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: 0.8980 chunk 71 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8745 Z= 0.163 Angle : 0.563 7.940 11834 Z= 0.284 Chirality : 0.041 0.155 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.241 29.218 1183 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.48 % Allowed : 17.26 % Favored : 80.26 % 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: -0.18 (0.27), residues: 1060 helix: 1.21 (0.29), residues: 360 sheet: 0.08 (0.35), residues: 217 loop : -1.24 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.002 0.000 HIS R 462 PHE 0.044 0.001 PHE R 219 TYR 0.014 0.001 TYR R 204 ARG 0.003 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 199 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 220 HIS cc_start: 0.7752 (m-70) cc_final: 0.7479 (m-70) REVERT: B 61 MET cc_start: 0.8075 (ppp) cc_final: 0.7736 (ppp) REVERT: B 111 TYR cc_start: 0.8750 (m-80) cc_final: 0.8544 (m-80) REVERT: B 292 PHE cc_start: 0.8206 (m-80) cc_final: 0.7825 (m-10) REVERT: C 41 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8449 (tm-30) REVERT: N 42 ARG cc_start: 0.8303 (ttt180) cc_final: 0.8084 (tpt170) outliers start: 23 outliers final: 20 residues processed: 182 average time/residue: 0.2159 time to fit residues: 53.2382 Evaluate side-chains 193 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 306 SER 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 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 339 TRP 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 N residue 130 CYS 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 486 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8745 Z= 0.278 Angle : 0.611 9.422 11834 Z= 0.309 Chirality : 0.042 0.158 1317 Planarity : 0.004 0.047 1505 Dihedral : 4.361 30.315 1183 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.88 % Allowed : 16.61 % Favored : 79.50 % 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: -0.19 (0.27), residues: 1060 helix: 1.15 (0.29), residues: 368 sheet: 0.02 (0.35), residues: 226 loop : -1.23 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS B 225 PHE 0.040 0.002 PHE R 219 TYR 0.019 0.002 TYR R 245 ARG 0.003 0.000 ARG R 236 *********************** 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 212 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8270 (ppp) cc_final: 0.7894 (ppp) REVERT: N 100 ASN cc_start: 0.7615 (t0) cc_final: 0.7226 (t0) REVERT: N 110 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7748 (ptpp) outliers start: 36 outliers final: 28 residues processed: 188 average time/residue: 0.2086 time to fit residues: 53.4874 Evaluate side-chains 196 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain A residue 325 THR 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 146 LEU 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 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 C residue 76 THR 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 110 LYS 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 418 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8745 Z= 0.220 Angle : 0.597 8.529 11834 Z= 0.299 Chirality : 0.042 0.164 1317 Planarity : 0.004 0.046 1505 Dihedral : 4.329 29.847 1183 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.24 % Allowed : 18.02 % Favored : 78.75 % 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: -0.12 (0.27), residues: 1060 helix: 1.32 (0.29), residues: 361 sheet: -0.02 (0.36), residues: 211 loop : -1.18 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS A 357 PHE 0.030 0.001 PHE R 219 TYR 0.015 0.001 TYR R 241 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 205 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7536 (mt-10) REVERT: B 61 MET cc_start: 0.8275 (ppp) cc_final: 0.7890 (ppp) REVERT: C 41 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 53 LYS cc_start: 0.8598 (tptt) cc_final: 0.8393 (tptt) REVERT: N 100 ASN cc_start: 0.7644 (t0) cc_final: 0.7233 (t0) REVERT: R 184 ASP cc_start: 0.7147 (t0) cc_final: 0.6748 (t70) REVERT: R 221 PHE cc_start: 0.6543 (m-80) cc_final: 0.6178 (m-80) REVERT: R 298 MET cc_start: 0.7336 (mmp) cc_final: 0.6948 (mmm) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.2078 time to fit residues: 52.6066 Evaluate side-chains 196 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 325 THR 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP 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 B residue 339 TRP 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 130 CYS 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 418 MET 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: 0.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8745 Z= 0.203 Angle : 0.594 8.290 11834 Z= 0.297 Chirality : 0.042 0.187 1317 Planarity : 0.004 0.044 1505 Dihedral : 4.297 29.492 1183 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.34 % Allowed : 18.34 % 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: -0.09 (0.27), residues: 1060 helix: 1.36 (0.29), residues: 366 sheet: 0.01 (0.35), residues: 216 loop : -1.21 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.000 HIS A 357 PHE 0.021 0.001 PHE R 219 TYR 0.015 0.001 TYR R 245 ARG 0.003 0.000 ARG B 197 *********************** 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 206 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7511 (mt-10) REVERT: B 61 MET cc_start: 0.8260 (ppp) cc_final: 0.7877 (ppp) REVERT: B 292 PHE cc_start: 0.8538 (m-10) cc_final: 0.8153 (m-80) REVERT: C 41 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 53 LYS cc_start: 0.8616 (tptt) cc_final: 0.8407 (tptt) REVERT: N 100 ASN cc_start: 0.7713 (t0) cc_final: 0.7453 (t0) REVERT: R 184 ASP cc_start: 0.7140 (t0) cc_final: 0.6730 (t70) REVERT: R 298 MET cc_start: 0.7284 (mmp) cc_final: 0.6898 (mmm) outliers start: 31 outliers final: 25 residues processed: 188 average time/residue: 0.2183 time to fit residues: 56.3199 Evaluate side-chains 195 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 325 THR 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 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 B residue 339 TRP 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 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 Chi-restraints excluded: chain R residue 433 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: 0.0770 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 96 optimal weight: 0.0170 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8745 Z= 0.171 Angle : 0.590 9.387 11834 Z= 0.295 Chirality : 0.041 0.177 1317 Planarity : 0.004 0.042 1505 Dihedral : 4.233 28.562 1183 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.91 % Allowed : 19.42 % Favored : 77.67 % 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: -0.03 (0.27), residues: 1060 helix: 1.37 (0.29), residues: 366 sheet: 0.02 (0.36), residues: 210 loop : -1.12 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.002 0.000 HIS R 181 PHE 0.018 0.001 PHE R 219 TYR 0.014 0.001 TYR R 428 ARG 0.005 0.000 ARG N 90 *********************** 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 209 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7567 (mt-10) REVERT: B 292 PHE cc_start: 0.8455 (m-10) cc_final: 0.8101 (m-80) REVERT: C 41 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8488 (tm-30) REVERT: N 100 ASN cc_start: 0.7736 (t0) cc_final: 0.7481 (t0) REVERT: R 184 ASP cc_start: 0.7089 (t0) cc_final: 0.6675 (t70) REVERT: R 298 MET cc_start: 0.7266 (mmp) cc_final: 0.6896 (mmm) outliers start: 27 outliers final: 24 residues processed: 194 average time/residue: 0.2043 time to fit residues: 54.0438 Evaluate side-chains 195 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR 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 B residue 339 TRP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 76 THR 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 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 356 ASN Chi-restraints excluded: chain R residue 371 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** ** A 279 ASN ** 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: 0.7752 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8745 Z= 0.177 Angle : 0.608 9.583 11834 Z= 0.302 Chirality : 0.042 0.205 1317 Planarity : 0.004 0.042 1505 Dihedral : 4.195 28.250 1183 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.02 % Allowed : 19.63 % Favored : 77.35 % 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: 0.01 (0.27), residues: 1060 helix: 1.42 (0.29), residues: 366 sheet: 0.09 (0.35), residues: 210 loop : -1.13 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS A 357 PHE 0.029 0.001 PHE R 219 TYR 0.014 0.001 TYR R 241 ARG 0.003 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 205 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8020 (mmp80) cc_final: 0.7281 (mpt180) REVERT: A 28 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 105 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 262 MET cc_start: 0.7151 (tpp) cc_final: 0.6888 (tpp) REVERT: B 292 PHE cc_start: 0.8430 (m-10) cc_final: 0.8078 (m-80) REVERT: C 41 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8483 (tm-30) REVERT: N 100 ASN cc_start: 0.7734 (t0) cc_final: 0.7486 (t0) REVERT: N 109 LEU cc_start: 0.8225 (tt) cc_final: 0.7877 (mp) REVERT: R 184 ASP cc_start: 0.7107 (t0) cc_final: 0.6678 (t70) REVERT: R 298 MET cc_start: 0.7288 (mmp) cc_final: 0.6899 (mmm) outliers start: 28 outliers final: 25 residues processed: 188 average time/residue: 0.2109 time to fit residues: 54.1239 Evaluate side-chains 200 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 270 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP 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 B residue 339 TRP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain N residue 43 LEU 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 130 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.0670 chunk 96 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8524 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8745 Z= 0.205 Angle : 0.640 10.662 11834 Z= 0.316 Chirality : 0.042 0.215 1317 Planarity : 0.004 0.050 1505 Dihedral : 4.182 28.519 1183 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.02 % Allowed : 19.74 % Favored : 77.24 % 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: 0.02 (0.27), residues: 1060 helix: 1.46 (0.29), residues: 366 sheet: 0.04 (0.35), residues: 217 loop : -1.16 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.002 0.000 HIS A 357 PHE 0.027 0.001 PHE R 219 TYR 0.017 0.001 TYR R 245 ARG 0.002 0.000 ARG B 42 ********************** 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 197 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7578 (mt-10) REVERT: B 105 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.7984 (t80) REVERT: B 292 PHE cc_start: 0.8561 (m-10) cc_final: 0.8159 (m-80) REVERT: N 100 ASN cc_start: 0.7769 (t0) cc_final: 0.7535 (t0) REVERT: N 109 LEU cc_start: 0.8265 (tt) cc_final: 0.7982 (mp) REVERT: R 184 ASP cc_start: 0.7158 (t0) cc_final: 0.6734 (t70) REVERT: R 298 MET cc_start: 0.7283 (mmp) cc_final: 0.6893 (mmm) outliers start: 28 outliers final: 26 residues processed: 180 average time/residue: 0.2087 time to fit residues: 51.4055 Evaluate side-chains 195 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 325 THR 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP 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 B residue 339 TRP Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain N residue 43 LEU 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 130 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118794 restraints weight = 13331.110| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.38 r_work: 0.3459 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8745 Z= 0.183 Angle : 0.629 9.665 11834 Z= 0.312 Chirality : 0.042 0.210 1317 Planarity : 0.004 0.046 1505 Dihedral : 4.150 28.154 1183 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.91 % Allowed : 20.28 % Favored : 76.81 % 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: 0.07 (0.27), residues: 1060 helix: 1.44 (0.29), residues: 366 sheet: 0.09 (0.35), residues: 220 loop : -1.07 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.002 0.000 HIS A 357 PHE 0.022 0.001 PHE R 219 TYR 0.014 0.001 TYR R 245 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: 2259.20 seconds wall clock time: 40 minutes 46.33 seconds (2446.33 seconds total)