Starting phenix.real_space_refine on Fri Oct 23 10:20:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.map" model { file = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fin_31604/10_2026/7fin_31604.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 55 5.16 5 C 6081 2.51 5 N 1668 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9524 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3123 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 12, 'TRANS': 367} Chain breaks: 1 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1921 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" 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: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 196 Unusual residues: {'CLR': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GGL%COO:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9524 At special positions: 0 Unit cell: (97.461, 97.461, 157.437, 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 55 16.00 O 1720 8.00 N 1668 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.03 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 364.4 milliseconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 43.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 115 through 119 removed outlier: 3.593A pdb=" N CYS R 118 " --> pdb=" O HIS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 162 removed outlier: 3.796A pdb=" N PHE R 127 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 211 through 247 removed outlier: 3.532A pdb=" N LEU R 247 " --> pdb=" O SER R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 281 removed outlier: 3.570A pdb=" N TYR R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 329 removed outlier: 3.867A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.618A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 351 removed outlier: 3.522A pdb=" N TYR R 335 " --> pdb=" O ARG R 331 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 357 removed outlier: 3.865A pdb=" N VAL R 356 " --> pdb=" O VAL R 352 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 352 through 357' Processing helix chain 'R' and resid 361 through 366 Processing helix chain 'R' and resid 368 through 394 removed outlier: 3.902A pdb=" N ALA R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY R 375 " --> pdb=" O PHE R 371 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE R 376 " --> pdb=" O ALA R 372 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 415 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.234A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.967A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.750A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.727A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.881A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.721A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.146A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.720A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.554A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.734A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.037A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 78 through 83 removed outlier: 4.619A pdb=" N GLN R 102 " --> pdb=" O TRP R 112 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP R 112 " --> pdb=" O GLN R 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.110A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.995A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.056A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.584A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.801A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.409A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.581A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.197A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3026 1.34 - 1.46: 1968 1.46 - 1.58: 4675 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9743 Sorted by residual: bond pdb=" CA ILE R 272 " pdb=" C ILE R 272 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.39e+00 bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.47e+00 bond pdb=" CB PRO R 267 " pdb=" CG PRO R 267 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.90e+00 bond pdb=" C5 CLR R 606 " pdb=" C6 CLR R 606 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 ... (remaining 9738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12658 1.74 - 3.48: 470 3.48 - 5.22: 73 5.22 - 6.96: 25 6.96 - 8.70: 7 Bond angle restraints: 13233 Sorted by residual: angle pdb=" C LEU R 269 " pdb=" N PHE R 270 " pdb=" CA PHE R 270 " ideal model delta sigma weight residual 122.26 115.97 6.29 1.59e+00 3.96e-01 1.56e+01 angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 121.01 -7.11 1.80e+00 3.09e-01 1.56e+01 angle pdb=" N ALA R 358 " pdb=" CA ALA R 358 " pdb=" C ALA R 358 " ideal model delta sigma weight residual 109.81 117.13 -7.32 2.21e+00 2.05e-01 1.10e+01 angle pdb=" C ASP R 66 " pdb=" N MET R 67 " pdb=" CA MET R 67 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N AIB P 2 " pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 111.00 119.70 -8.70 2.80e+00 1.28e-01 9.67e+00 ... (remaining 13228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 5519 15.04 - 30.07: 167 30.07 - 45.11: 44 45.11 - 60.14: 0 60.14 - 75.18: 2 Dihedral angle restraints: 5732 sinusoidal: 2342 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 137.60 -44.60 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1324 0.089 - 0.178: 125 0.178 - 0.267: 8 0.267 - 0.355: 7 0.355 - 0.444: 7 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 1468 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 194 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO R 195 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO G 49 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 332 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.027 5.00e-02 4.00e+02 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1659 2.78 - 3.31: 8495 3.31 - 3.84: 15104 3.84 - 4.37: 17221 4.37 - 4.90: 30603 Nonbonded interactions: 73082 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.249 3.040 nonbonded pdb=" O ARG A 42 " pdb=" OG1 THR A 242 " model vdw 2.299 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OG1 THR A 285 " model vdw 2.325 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.336 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.336 3.040 ... (remaining 73077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.085 9750 Z= 0.213 Angle : 0.837 16.469 13245 Z= 0.445 Chirality : 0.063 0.444 1471 Planarity : 0.006 0.053 1657 Dihedral : 8.099 75.178 3526 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1149 helix: -0.09 (0.19), residues: 453 sheet: -0.51 (0.32), residues: 221 loop : -1.38 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 17 TYR 0.022 0.002 TYR R 141 PHE 0.024 0.002 PHE B 199 TRP 0.027 0.002 TRP A 281 HIS 0.013 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.20 ( 9743) covalent geometry : angle 0.80636 / 0.43 (13233) SS BOND : bond 0.00616 / 0.25 ( 6) SS BOND : angle 7.52679 / 4.53 ( 12) hydrogen bonds : bond 0.09300 / 5.98 ( 483) hydrogen bonds : angle 5.32175 / 3.73 ( 1398) Misc. bond : bond 0.07529 / 3.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 LEU cc_start: 0.7052 (mt) cc_final: 0.6625 (tp) REVERT: R 140 MET cc_start: 0.8733 (tmm) cc_final: 0.8475 (ttp) REVERT: R 153 LEU cc_start: 0.8755 (mt) cc_final: 0.8415 (mt) REVERT: R 304 LEU cc_start: 0.8424 (mt) cc_final: 0.8130 (pp) REVERT: R 389 SER cc_start: 0.9124 (t) cc_final: 0.8881 (p) REVERT: P 11 SER cc_start: 0.8043 (t) cc_final: 0.7736 (p) REVERT: A 220 HIS cc_start: 0.7503 (m-70) cc_final: 0.7064 (m-70) REVERT: A 296 LEU cc_start: 0.8048 (tp) cc_final: 0.7818 (tp) REVERT: A 378 ASP cc_start: 0.8444 (m-30) cc_final: 0.8122 (m-30) REVERT: B 35 ASN cc_start: 0.8200 (m-40) cc_final: 0.7755 (m110) REVERT: B 226 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7916 (mt-10) REVERT: N 60 TYR cc_start: 0.8935 (m-80) cc_final: 0.8577 (m-10) REVERT: N 73 ASP cc_start: 0.7648 (t0) cc_final: 0.7177 (t0) REVERT: N 90 ASP cc_start: 0.8383 (m-30) cc_final: 0.8119 (m-30) REVERT: N 113 THR cc_start: 0.9392 (m) cc_final: 0.9127 (p) REVERT: N 125 THR cc_start: 0.8473 (m) cc_final: 0.8083 (p) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1130 time to fit residues: 47.4123 Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 102 GLN R 173 HIS R 242 HIS P 1 HIS P 3 GLN P 20 GLN A 19 GLN A 23 ASN A 41 HIS A 220 HIS A 267 GLN B 88 ASN B 91 HIS B 268 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095349 restraints weight = 18445.883| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.27 r_work: 0.3287 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9750 Z= 0.113 Angle : 0.568 8.946 13245 Z= 0.295 Chirality : 0.040 0.144 1471 Planarity : 0.004 0.056 1657 Dihedral : 5.120 57.588 1363 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.12 % Allowed : 11.49 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1149 helix: 1.81 (0.23), residues: 457 sheet: -0.04 (0.33), residues: 229 loop : -0.85 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.028 0.002 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.022 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9743) covalent geometry : angle 0.56577 / 0.29 (13233) SS BOND : bond 0.00314 / 0.11 ( 6) SS BOND : angle 1.92249 / 1.28 ( 12) hydrogen bonds : bond 0.03840 / 2.47 ( 483) hydrogen bonds : angle 4.26455 / 2.96 ( 1398) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9147 (tm-30) REVERT: R 42 TYR cc_start: 0.7816 (t80) cc_final: 0.7196 (m-80) REVERT: R 137 LEU cc_start: 0.6977 (mt) cc_final: 0.6687 (tp) REVERT: R 138 GLN cc_start: 0.8026 (tt0) cc_final: 0.7727 (tm-30) REVERT: R 153 LEU cc_start: 0.8851 (mt) cc_final: 0.8553 (mt) REVERT: R 261 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7562 (tp) REVERT: R 304 LEU cc_start: 0.8534 (mt) cc_final: 0.8261 (pp) REVERT: P 9 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: P 25 TRP cc_start: 0.6231 (t60) cc_final: 0.5877 (t60) REVERT: A 15 GLU cc_start: 0.8382 (pp20) cc_final: 0.8155 (pp20) REVERT: A 339 TYR cc_start: 0.8671 (m-80) cc_final: 0.7936 (m-80) REVERT: A 343 ASP cc_start: 0.8189 (m-30) cc_final: 0.7629 (m-30) REVERT: A 365 CYS cc_start: 0.7673 (m) cc_final: 0.7385 (p) REVERT: A 378 ASP cc_start: 0.8486 (m-30) cc_final: 0.8230 (m-30) REVERT: B 8 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8340 (mtp85) REVERT: B 12 GLU cc_start: 0.8881 (tp30) cc_final: 0.8644 (tp30) REVERT: B 15 LYS cc_start: 0.9361 (mtmt) cc_final: 0.9041 (mmmm) REVERT: B 27 ASP cc_start: 0.8709 (t70) cc_final: 0.8243 (m-30) REVERT: B 32 GLN cc_start: 0.8002 (mt0) cc_final: 0.7770 (mt0) REVERT: B 226 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 239 ASN cc_start: 0.8460 (m-40) cc_final: 0.7940 (m110) REVERT: B 303 ASP cc_start: 0.7683 (m-30) cc_final: 0.7293 (p0) REVERT: G 13 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8554 (ttp80) REVERT: G 18 GLN cc_start: 0.8104 (tp40) cc_final: 0.7789 (tp40) REVERT: G 20 LYS cc_start: 0.8445 (mtmm) cc_final: 0.7989 (mtmm) REVERT: G 29 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7771 (ptmm) REVERT: G 36 ASP cc_start: 0.8275 (m-30) cc_final: 0.8021 (m-30) REVERT: G 52 THR cc_start: 0.7913 (t) cc_final: 0.7674 (p) REVERT: N 60 TYR cc_start: 0.9021 (m-80) cc_final: 0.8799 (m-80) REVERT: N 73 ASP cc_start: 0.8007 (t0) cc_final: 0.7496 (t0) REVERT: N 90 ASP cc_start: 0.8642 (m-30) cc_final: 0.8305 (m-30) REVERT: N 106 ASP cc_start: 0.7981 (p0) cc_final: 0.7770 (p0) REVERT: N 125 THR cc_start: 0.8398 (m) cc_final: 0.7983 (p) outliers start: 21 outliers final: 15 residues processed: 206 average time/residue: 0.1062 time to fit residues: 29.6896 Evaluate side-chains 172 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [87, 56, 106, 58, 17, 27, 34, 104, 23, 89, 15] chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 255 HIS B 13 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092368 restraints weight = 18356.058| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.32 r_work: 0.3226 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9750 Z= 0.115 Angle : 0.538 7.188 13245 Z= 0.278 Chirality : 0.040 0.319 1471 Planarity : 0.004 0.035 1657 Dihedral : 5.008 56.903 1363 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.23 % Allowed : 11.19 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1149 helix: 2.46 (0.23), residues: 456 sheet: 0.08 (0.33), residues: 236 loop : -0.63 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.027 0.002 TYR R 141 PHE 0.020 0.001 PHE R 270 TRP 0.021 0.001 TRP R 209 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9743) covalent geometry : angle 0.53513 / 0.28 (13233) SS BOND : bond 0.00163 / 0.08 ( 6) SS BOND : angle 1.86432 / 1.13 ( 12) hydrogen bonds : bond 0.03676 / 2.39 ( 483) hydrogen bonds : angle 4.02764 / 2.77 ( 1398) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9119 (tm-30) REVERT: R 42 TYR cc_start: 0.7934 (t80) cc_final: 0.7688 (t80) REVERT: R 138 GLN cc_start: 0.8025 (tt0) cc_final: 0.7731 (tm-30) REVERT: R 153 LEU cc_start: 0.8824 (mt) cc_final: 0.8552 (mt) REVERT: R 261 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7608 (tp) REVERT: R 293 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8787 (mtpt) REVERT: A 15 GLU cc_start: 0.8510 (pp20) cc_final: 0.8296 (pp20) REVERT: A 339 TYR cc_start: 0.8717 (m-80) cc_final: 0.7966 (m-80) REVERT: A 343 ASP cc_start: 0.8268 (m-30) cc_final: 0.7697 (m-30) REVERT: A 365 CYS cc_start: 0.7811 (m) cc_final: 0.7443 (p) REVERT: A 378 ASP cc_start: 0.8422 (m-30) cc_final: 0.8065 (m-30) REVERT: B 8 ARG cc_start: 0.8861 (mtp180) cc_final: 0.8508 (mtp85) REVERT: B 9 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8452 (mm110) REVERT: B 12 GLU cc_start: 0.8954 (tp30) cc_final: 0.8734 (tp30) REVERT: B 13 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: B 14 LEU cc_start: 0.8098 (mt) cc_final: 0.7875 (mt) REVERT: B 15 LYS cc_start: 0.9355 (mtmt) cc_final: 0.9066 (mmmm) REVERT: B 27 ASP cc_start: 0.8776 (t70) cc_final: 0.8405 (m-30) REVERT: B 226 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 239 ASN cc_start: 0.8488 (m-40) cc_final: 0.8125 (m-40) REVERT: B 301 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8219 (mmtt) REVERT: G 13 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8552 (ttp80) REVERT: G 29 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7735 (ptpp) REVERT: G 36 ASP cc_start: 0.8333 (m-30) cc_final: 0.8092 (m-30) REVERT: N 60 TYR cc_start: 0.9032 (m-80) cc_final: 0.8779 (m-80) REVERT: N 73 ASP cc_start: 0.7987 (t0) cc_final: 0.7468 (t0) REVERT: N 90 ASP cc_start: 0.8677 (m-30) cc_final: 0.8302 (m-30) REVERT: N 125 THR cc_start: 0.8464 (m) cc_final: 0.7999 (p) outliers start: 32 outliers final: 21 residues processed: 192 average time/residue: 0.1035 time to fit residues: 26.9942 Evaluate side-chains 168 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [35, 71, 49, 33, 55, 12, 108, 67, 113, 47, 44] chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 102 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090246 restraints weight = 18379.606| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.30 r_work: 0.3180 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9750 Z= 0.122 Angle : 0.538 7.290 13245 Z= 0.277 Chirality : 0.040 0.294 1471 Planarity : 0.003 0.035 1657 Dihedral : 4.961 58.574 1363 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.12 % Allowed : 11.69 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.25), residues: 1149 helix: 2.80 (0.24), residues: 456 sheet: 0.13 (0.33), residues: 234 loop : -0.57 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 356 TYR 0.026 0.001 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9743) covalent geometry : angle 0.53577 / 0.28 (13233) SS BOND : bond 0.00127 / 0.07 ( 6) SS BOND : angle 1.61664 / 1.05 ( 12) hydrogen bonds : bond 0.03634 / 2.35 ( 483) hydrogen bonds : angle 3.99346 / 2.75 ( 1398) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7947 (t80) cc_final: 0.7700 (t80) REVERT: R 138 GLN cc_start: 0.8105 (tt0) cc_final: 0.7791 (tm-30) REVERT: R 261 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 293 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8785 (mtpt) REVERT: R 403 ILE cc_start: 0.8861 (mm) cc_final: 0.8429 (pt) REVERT: A 15 GLU cc_start: 0.8542 (pp20) cc_final: 0.8323 (pp20) REVERT: A 343 ASP cc_start: 0.8369 (m-30) cc_final: 0.7787 (m-30) REVERT: A 365 CYS cc_start: 0.7794 (m) cc_final: 0.7421 (p) REVERT: A 378 ASP cc_start: 0.8463 (m-30) cc_final: 0.8122 (m-30) REVERT: B 9 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8468 (mm110) REVERT: B 12 GLU cc_start: 0.8932 (tp30) cc_final: 0.8578 (tp30) REVERT: B 14 LEU cc_start: 0.7940 (mt) cc_final: 0.7716 (mt) REVERT: B 15 LYS cc_start: 0.9338 (mtmt) cc_final: 0.8705 (tmtt) REVERT: B 27 ASP cc_start: 0.8796 (t70) cc_final: 0.8450 (m-30) REVERT: B 127 LYS cc_start: 0.8163 (tttt) cc_final: 0.7767 (tmtt) REVERT: B 226 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 239 ASN cc_start: 0.8539 (m-40) cc_final: 0.8182 (m-40) REVERT: B 301 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8477 (mmtm) REVERT: G 13 ARG cc_start: 0.8759 (mtt180) cc_final: 0.8506 (ttp80) REVERT: G 20 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8136 (ptpt) REVERT: G 29 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7724 (ptpp) REVERT: G 36 ASP cc_start: 0.8368 (m-30) cc_final: 0.8126 (m-30) REVERT: G 58 GLU cc_start: 0.8186 (pm20) cc_final: 0.7864 (pm20) REVERT: N 60 TYR cc_start: 0.9020 (m-80) cc_final: 0.8771 (m-80) REVERT: N 73 ASP cc_start: 0.7947 (t0) cc_final: 0.7483 (t0) REVERT: N 90 ASP cc_start: 0.8758 (m-30) cc_final: 0.8514 (m-30) REVERT: N 125 THR cc_start: 0.8499 (m) cc_final: 0.7984 (p) outliers start: 31 outliers final: 25 residues processed: 173 average time/residue: 0.0962 time to fit residues: 23.0283 Evaluate side-chains 166 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [40, 36, 63, 106, 73, 100, 56, 35, 0, 58, 60] chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 37 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089148 restraints weight = 18439.803| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.30 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9750 Z= 0.120 Angle : 0.537 9.205 13245 Z= 0.275 Chirality : 0.040 0.280 1471 Planarity : 0.003 0.036 1657 Dihedral : 4.826 55.092 1363 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.23 % Allowed : 13.00 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.25), residues: 1149 helix: 3.00 (0.24), residues: 457 sheet: 0.08 (0.33), residues: 236 loop : -0.43 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.025 0.001 TYR R 141 PHE 0.017 0.001 PHE R 270 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9743) covalent geometry : angle 0.53574 / 0.27 (13233) SS BOND : bond 0.00099 / 0.06 ( 6) SS BOND : angle 1.46147 / 0.93 ( 12) hydrogen bonds : bond 0.03581 / 2.33 ( 483) hydrogen bonds : angle 3.94430 / 2.72 ( 1398) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8028 (t80) cc_final: 0.7604 (t80) REVERT: R 138 GLN cc_start: 0.8110 (tt0) cc_final: 0.7716 (tm-30) REVERT: R 261 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7623 (tp) REVERT: R 304 LEU cc_start: 0.8458 (mm) cc_final: 0.8145 (pp) REVERT: A 15 GLU cc_start: 0.8564 (pp20) cc_final: 0.8325 (pp20) REVERT: A 343 ASP cc_start: 0.8391 (m-30) cc_final: 0.7839 (m-30) REVERT: A 365 CYS cc_start: 0.7742 (m) cc_final: 0.7394 (p) REVERT: A 378 ASP cc_start: 0.8427 (m-30) cc_final: 0.8054 (m-30) REVERT: B 12 GLU cc_start: 0.9041 (tp30) cc_final: 0.8715 (tp30) REVERT: B 15 LYS cc_start: 0.9348 (mtmt) cc_final: 0.8710 (tmtt) REVERT: B 27 ASP cc_start: 0.8797 (t70) cc_final: 0.8478 (m-30) REVERT: B 226 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 239 ASN cc_start: 0.8561 (m-40) cc_final: 0.8243 (m-40) REVERT: G 13 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8497 (ttp80) REVERT: G 20 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8173 (ptpt) REVERT: G 29 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7726 (ptpp) REVERT: G 36 ASP cc_start: 0.8357 (m-30) cc_final: 0.8126 (m-30) REVERT: N 73 ASP cc_start: 0.7903 (t0) cc_final: 0.7455 (t0) REVERT: N 90 ASP cc_start: 0.8812 (m-30) cc_final: 0.8572 (m-30) outliers start: 32 outliers final: 25 residues processed: 170 average time/residue: 0.1100 time to fit residues: 25.4203 Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [110, 64, 53, 91, 84, 76, 17, 54, 20, 86, 100] chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 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 = 0.3930 r_free = 0.3930 target = 0.128602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088484 restraints weight = 18448.055| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.29 r_work: 0.3148 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9750 Z= 0.126 Angle : 0.568 8.405 13245 Z= 0.288 Chirality : 0.040 0.279 1471 Planarity : 0.004 0.039 1657 Dihedral : 4.873 54.483 1363 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.43 % Allowed : 13.10 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1149 helix: 3.11 (0.24), residues: 457 sheet: 0.12 (0.33), residues: 236 loop : -0.38 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.024 0.001 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9743) covalent geometry : angle 0.56207 / 0.29 (13233) SS BOND : bond 0.00571 / 0.19 ( 6) SS BOND : angle 2.70350 / 1.55 ( 12) hydrogen bonds : bond 0.03595 / 2.33 ( 483) hydrogen bonds : angle 3.90344 / 2.70 ( 1398) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8074 (t80) cc_final: 0.7647 (t80) REVERT: R 138 GLN cc_start: 0.8116 (tt0) cc_final: 0.7723 (tm-30) REVERT: R 261 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7620 (tp) REVERT: A 15 GLU cc_start: 0.8578 (pp20) cc_final: 0.8258 (pp20) REVERT: A 343 ASP cc_start: 0.8418 (m-30) cc_final: 0.7841 (m-30) REVERT: A 378 ASP cc_start: 0.8434 (m-30) cc_final: 0.8074 (m-30) REVERT: B 12 GLU cc_start: 0.9041 (tp30) cc_final: 0.8734 (tp30) REVERT: B 15 LYS cc_start: 0.9355 (mtmt) cc_final: 0.8712 (tmtt) REVERT: B 27 ASP cc_start: 0.8850 (t70) cc_final: 0.8545 (m-30) REVERT: B 134 ARG cc_start: 0.7342 (ptt180) cc_final: 0.6746 (mmp80) REVERT: B 226 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 262 MET cc_start: 0.8733 (tpp) cc_final: 0.8101 (tpp) REVERT: G 13 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8503 (ttp80) REVERT: G 20 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8121 (ptpp) REVERT: G 22 GLU cc_start: 0.8450 (tp30) cc_final: 0.8140 (tp30) REVERT: G 29 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7780 (ptpp) REVERT: G 36 ASP cc_start: 0.8366 (m-30) cc_final: 0.8128 (m-30) REVERT: G 58 GLU cc_start: 0.8346 (pm20) cc_final: 0.8128 (pm20) REVERT: N 73 ASP cc_start: 0.7959 (t0) cc_final: 0.7567 (t0) REVERT: N 90 ASP cc_start: 0.8833 (m-30) cc_final: 0.8576 (m-30) outliers start: 34 outliers final: 28 residues processed: 163 average time/residue: 0.1066 time to fit residues: 23.2644 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [21, 7, 33, 93, 71, 110, 99, 40, 48, 61, 53] chunk 21 optimal weight: 0.0570 chunk 7 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.127912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087630 restraints weight = 18274.231| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.27 r_work: 0.3128 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9750 Z= 0.130 Angle : 0.568 8.369 13245 Z= 0.289 Chirality : 0.040 0.270 1471 Planarity : 0.004 0.040 1657 Dihedral : 4.832 53.889 1363 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.43 % Allowed : 13.41 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1149 helix: 3.09 (0.24), residues: 457 sheet: 0.13 (0.33), residues: 236 loop : -0.36 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.024 0.001 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9743) covalent geometry : angle 0.56355 / 0.29 (13233) SS BOND : bond 0.00107 / 0.06 ( 6) SS BOND : angle 2.35749 / 1.37 ( 12) hydrogen bonds : bond 0.03643 / 2.35 ( 483) hydrogen bonds : angle 3.90136 / 2.69 ( 1398) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8059 (t80) cc_final: 0.7637 (t80) REVERT: R 138 GLN cc_start: 0.8129 (tt0) cc_final: 0.7732 (tm-30) REVERT: R 261 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7631 (tp) REVERT: R 387 LEU cc_start: 0.8570 (mp) cc_final: 0.8239 (tp) REVERT: A 15 GLU cc_start: 0.8570 (pp20) cc_final: 0.8335 (pp20) REVERT: A 343 ASP cc_start: 0.8410 (m-30) cc_final: 0.7841 (m-30) REVERT: A 378 ASP cc_start: 0.8458 (m-30) cc_final: 0.8104 (m-30) REVERT: B 12 GLU cc_start: 0.9033 (tp30) cc_final: 0.8750 (tp30) REVERT: B 15 LYS cc_start: 0.9359 (mtmt) cc_final: 0.8715 (tmtt) REVERT: B 27 ASP cc_start: 0.8819 (t70) cc_final: 0.8520 (m-30) REVERT: B 134 ARG cc_start: 0.7413 (ptt180) cc_final: 0.6831 (mmp80) REVERT: B 226 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8249 (mt-10) REVERT: G 13 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8479 (ttp80) REVERT: G 20 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8059 (ptpp) REVERT: G 22 GLU cc_start: 0.8517 (tp30) cc_final: 0.8281 (tp30) REVERT: G 29 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7804 (ptpp) REVERT: G 36 ASP cc_start: 0.8382 (m-30) cc_final: 0.8145 (m-30) REVERT: G 58 GLU cc_start: 0.8299 (pm20) cc_final: 0.8037 (pm20) REVERT: N 73 ASP cc_start: 0.7971 (t0) cc_final: 0.7562 (t0) REVERT: N 90 ASP cc_start: 0.8860 (m-30) cc_final: 0.8613 (m-30) REVERT: N 113 THR cc_start: 0.9421 (m) cc_final: 0.9192 (p) REVERT: N 120 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8755 (mm-40) REVERT: N 125 THR cc_start: 0.8534 (m) cc_final: 0.7923 (p) outliers start: 34 outliers final: 27 residues processed: 166 average time/residue: 0.1083 time to fit residues: 24.3321 Evaluate side-chains 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [30, 53, 109, 60, 89, 34, 38, 26, 43, 103, 13] chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088753 restraints weight = 18316.477| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.31 r_work: 0.3150 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9750 Z= 0.111 Angle : 0.556 8.487 13245 Z= 0.283 Chirality : 0.040 0.267 1471 Planarity : 0.004 0.042 1657 Dihedral : 4.787 53.498 1363 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.92 % Allowed : 14.01 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1149 helix: 3.09 (0.24), residues: 457 sheet: 0.12 (0.33), residues: 230 loop : -0.31 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.023 0.001 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.031 0.001 TRP R 209 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9743) covalent geometry : angle 0.55251 / 0.28 (13233) SS BOND : bond 0.00085 / 0.05 ( 6) SS BOND : angle 2.05925 / 1.19 ( 12) hydrogen bonds : bond 0.03498 / 2.26 ( 483) hydrogen bonds : angle 3.84508 / 2.66 ( 1398) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8059 (t80) cc_final: 0.7683 (t80) REVERT: R 138 GLN cc_start: 0.8039 (tt0) cc_final: 0.7664 (tm-30) REVERT: R 261 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7653 (tp) REVERT: R 387 LEU cc_start: 0.8521 (mp) cc_final: 0.8220 (tp) REVERT: A 15 GLU cc_start: 0.8589 (pp20) cc_final: 0.8295 (pp20) REVERT: A 343 ASP cc_start: 0.8393 (m-30) cc_final: 0.7821 (m-30) REVERT: A 378 ASP cc_start: 0.8408 (m-30) cc_final: 0.7982 (m-30) REVERT: B 12 GLU cc_start: 0.9040 (tp30) cc_final: 0.8762 (tp30) REVERT: B 15 LYS cc_start: 0.9379 (mtmt) cc_final: 0.8707 (tmtt) REVERT: B 27 ASP cc_start: 0.8815 (t70) cc_final: 0.8536 (m-30) REVERT: B 32 GLN cc_start: 0.7592 (mt0) cc_final: 0.7224 (mp10) REVERT: B 45 MET cc_start: 0.8951 (mtt) cc_final: 0.8617 (mtm) REVERT: B 134 ARG cc_start: 0.7443 (ptt180) cc_final: 0.6814 (mmp80) REVERT: B 217 MET cc_start: 0.8399 (ppp) cc_final: 0.8130 (ppp) REVERT: B 226 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 266 HIS cc_start: 0.8201 (t70) cc_final: 0.7868 (t-90) REVERT: G 20 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8060 (ptpp) REVERT: G 29 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7848 (ptpp) REVERT: G 36 ASP cc_start: 0.8356 (m-30) cc_final: 0.8121 (m-30) REVERT: G 58 GLU cc_start: 0.8290 (pm20) cc_final: 0.8008 (pm20) REVERT: N 73 ASP cc_start: 0.7921 (t0) cc_final: 0.7515 (t0) REVERT: N 90 ASP cc_start: 0.8847 (m-30) cc_final: 0.8582 (m-30) REVERT: N 113 THR cc_start: 0.9415 (m) cc_final: 0.9192 (p) REVERT: N 125 THR cc_start: 0.8548 (m) cc_final: 0.7924 (p) outliers start: 29 outliers final: 25 residues processed: 160 average time/residue: 0.1127 time to fit residues: 24.3035 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [32, 98, 65, 7, 93, 113, 56, 74, 81, 50, 92] chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 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 = 0.3923 r_free = 0.3923 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087672 restraints weight = 18319.482| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.29 r_work: 0.3137 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9750 Z= 0.122 Angle : 0.563 9.590 13245 Z= 0.286 Chirality : 0.040 0.264 1471 Planarity : 0.004 0.040 1657 Dihedral : 4.696 52.603 1363 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.52 % Allowed : 14.31 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.25), residues: 1149 helix: 3.10 (0.24), residues: 458 sheet: 0.05 (0.33), residues: 233 loop : -0.24 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 356 TYR 0.023 0.001 TYR R 141 PHE 0.018 0.001 PHE R 270 TRP 0.021 0.001 TRP R 209 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9743) covalent geometry : angle 0.56050 / 0.29 (13233) SS BOND : bond 0.00083 / 0.05 ( 6) SS BOND : angle 1.91592 / 1.12 ( 12) hydrogen bonds : bond 0.03533 / 2.29 ( 483) hydrogen bonds : angle 3.81960 / 2.64 ( 1398) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8054 (t80) cc_final: 0.7678 (t80) REVERT: R 138 GLN cc_start: 0.8102 (tt0) cc_final: 0.7707 (tm-30) REVERT: R 261 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7672 (tp) REVERT: A 15 GLU cc_start: 0.8542 (pp20) cc_final: 0.8309 (pp20) REVERT: A 35 GLN cc_start: 0.8433 (mp10) cc_final: 0.8090 (mp10) REVERT: A 343 ASP cc_start: 0.8422 (m-30) cc_final: 0.7854 (m-30) REVERT: A 378 ASP cc_start: 0.8446 (m-30) cc_final: 0.8032 (m-30) REVERT: B 8 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8469 (ttt180) REVERT: B 12 GLU cc_start: 0.9041 (tp30) cc_final: 0.8771 (tp30) REVERT: B 15 LYS cc_start: 0.9378 (mtmt) cc_final: 0.8705 (tmtt) REVERT: B 27 ASP cc_start: 0.8753 (t70) cc_final: 0.8405 (m-30) REVERT: B 32 GLN cc_start: 0.7522 (mt0) cc_final: 0.7188 (mp10) REVERT: B 134 ARG cc_start: 0.7500 (ptt180) cc_final: 0.6821 (mmp80) REVERT: B 226 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 266 HIS cc_start: 0.8331 (t70) cc_final: 0.7908 (t-90) REVERT: G 13 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8470 (ttp80) REVERT: G 20 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8042 (ptpp) REVERT: G 22 GLU cc_start: 0.8285 (tp30) cc_final: 0.7892 (tp30) REVERT: G 30 VAL cc_start: 0.8576 (t) cc_final: 0.8258 (p) REVERT: G 36 ASP cc_start: 0.8388 (m-30) cc_final: 0.8140 (m-30) REVERT: G 58 GLU cc_start: 0.8333 (pm20) cc_final: 0.8039 (pm20) REVERT: N 73 ASP cc_start: 0.7961 (t0) cc_final: 0.7567 (t0) REVERT: N 90 ASP cc_start: 0.8885 (m-30) cc_final: 0.8635 (m-30) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.1112 time to fit residues: 23.1525 Evaluate side-chains 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [19, 33, 29, 14, 112, 63, 21, 34, 106, 50, 57] chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 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 = 0.3908 r_free = 0.3908 target = 0.127309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086384 restraints weight = 18333.880| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.31 r_work: 0.3114 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9750 Z= 0.141 Angle : 0.591 10.287 13245 Z= 0.299 Chirality : 0.041 0.265 1471 Planarity : 0.004 0.058 1657 Dihedral : 4.759 52.131 1363 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1149 helix: 3.08 (0.24), residues: 458 sheet: -0.05 (0.33), residues: 237 loop : -0.23 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 356 TYR 0.023 0.001 TYR R 141 PHE 0.019 0.001 PHE R 270 TRP 0.021 0.001 TRP R 209 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9743) covalent geometry : angle 0.58738 / 0.30 (13233) SS BOND : bond 0.00297 / 0.11 ( 6) SS BOND : angle 2.15547 / 1.23 ( 12) hydrogen bonds : bond 0.03646 / 2.36 ( 483) hydrogen bonds : angle 3.86718 / 2.67 ( 1398) Misc. bond : bond 0.00031 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8057 (t80) cc_final: 0.7680 (t80) REVERT: R 138 GLN cc_start: 0.8075 (tt0) cc_final: 0.7691 (tm-30) REVERT: R 261 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7703 (tp) REVERT: R 304 LEU cc_start: 0.8363 (mm) cc_final: 0.8117 (pp) REVERT: A 15 GLU cc_start: 0.8645 (pp20) cc_final: 0.8356 (pp20) REVERT: A 35 GLN cc_start: 0.8422 (mp10) cc_final: 0.8048 (mp10) REVERT: A 343 ASP cc_start: 0.8443 (m-30) cc_final: 0.7839 (m-30) REVERT: A 378 ASP cc_start: 0.8482 (m-30) cc_final: 0.8075 (m-30) REVERT: B 12 GLU cc_start: 0.9040 (tp30) cc_final: 0.8502 (tp30) REVERT: B 15 LYS cc_start: 0.9383 (mtmt) cc_final: 0.8721 (tmtt) REVERT: B 134 ARG cc_start: 0.7620 (ptt180) cc_final: 0.6814 (mmp80) REVERT: B 226 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8178 (mt-10) REVERT: B 266 HIS cc_start: 0.8414 (t70) cc_final: 0.7951 (t-90) REVERT: G 13 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8473 (ttp80) REVERT: G 20 LYS cc_start: 0.8286 (mtmm) cc_final: 0.8009 (ptpp) REVERT: G 36 ASP cc_start: 0.8432 (m-30) cc_final: 0.8189 (m-30) REVERT: G 58 GLU cc_start: 0.8299 (pm20) cc_final: 0.8004 (pm20) REVERT: N 73 ASP cc_start: 0.7937 (t0) cc_final: 0.7532 (t0) REVERT: N 90 ASP cc_start: 0.8939 (m-30) cc_final: 0.8690 (m-30) outliers start: 23 outliers final: 22 residues processed: 151 average time/residue: 0.1125 time to fit residues: 22.8716 Evaluate side-chains 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [16, 86, 42, 110, 31, 83, 0, 14, 45, 99, 68] chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 110 optimal weight: 0.0270 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 117 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 = 0.3923 r_free = 0.3923 target = 0.128269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088159 restraints weight = 18267.523| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.27 r_work: 0.3139 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9750 Z= 0.112 Angle : 0.567 10.190 13245 Z= 0.287 Chirality : 0.040 0.253 1471 Planarity : 0.003 0.038 1657 Dihedral : 4.668 52.241 1363 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.52 % Allowed : 14.82 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1149 helix: 3.10 (0.24), residues: 458 sheet: 0.00 (0.33), residues: 236 loop : -0.17 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.022 0.001 TYR R 141 PHE 0.019 0.001 PHE R 270 TRP 0.022 0.001 TRP R 209 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9743) covalent geometry : angle 0.56481 / 0.29 (13233) SS BOND : bond 0.00084 / 0.04 ( 6) SS BOND : angle 1.86374 / 1.08 ( 12) hydrogen bonds : bond 0.03483 / 2.26 ( 483) hydrogen bonds : angle 3.79447 / 2.63 ( 1398) Misc. bond : bond 0.00027 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.57 seconds wall clock time: 43 minutes 34.85 seconds (2614.85 seconds total)