Starting phenix.real_space_refine on Thu Jul 2 15:47:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.map" model { file = "/net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvg_62593/07_2026/9kvg_62593.cif" } resolution = 2.63 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= 0.061 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 65 5.16 5 C 5693 2.51 5 N 1501 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1790 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2548 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain: "E" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1780 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Chain: "R" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'CHO': 1, 'J40': 1, 'Y01': 1, 'YFW': 1} Classifications: {'undetermined': 4, 'water': 6} Link IDs: {None: 9} Time building chain proxies: 1.54, per 1000 atoms: 0.17 Number of scatterers: 8935 At special positions: 0 Unit cell: (102.2, 116.07, 128.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 2 15.00 O 1674 8.00 N 1501 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.04 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS R 371 " - pdb=" SG CYS R 375 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 314.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 40.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.619A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.611A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.178A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.918A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.656A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.922A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.544A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.023A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.550A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.612A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'R' and resid 35 through 64 removed outlier: 3.664A pdb=" N GLU R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 99 removed outlier: 4.198A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.796A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 326 through 371 Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 378 through 401 removed outlier: 4.049A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.287A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.515A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.954A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.567A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.114A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 4.034A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.586A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.021A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 7.057A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.614A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.749A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1236 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: 1.11 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1441 1.31 - 1.44: 2477 1.44 - 1.57: 5101 1.57 - 1.69: 3 1.69 - 1.82: 93 Bond restraints: 9115 Sorted by residual: bond pdb=" C18 J40 R 504 " pdb=" C19 J40 R 504 " ideal model delta sigma weight residual 1.330 1.538 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C15 J40 R 504 " pdb=" C16 J40 R 504 " ideal model delta sigma weight residual 1.329 1.536 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C21 J40 R 504 " pdb=" C22 J40 R 504 " ideal model delta sigma weight residual 1.332 1.532 -0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" C24 J40 R 504 " pdb=" C25 J40 R 504 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.30e+01 bond pdb=" C11 J40 R 504 " pdb=" O18 J40 R 504 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 9110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 12289 3.30 - 6.60: 45 6.60 - 9.90: 8 9.90 - 13.20: 3 13.20 - 16.50: 7 Bond angle restraints: 12352 Sorted by residual: angle pdb=" O1 J40 R 504 " pdb=" P1 J40 R 504 " pdb=" O13 J40 R 504 " ideal model delta sigma weight residual 92.86 109.36 -16.50 3.00e+00 1.11e-01 3.02e+01 angle pdb=" C24 J40 R 504 " pdb=" C25 J40 R 504 " pdb=" C26 J40 R 504 " ideal model delta sigma weight residual 127.60 112.63 14.97 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C23 J40 R 504 " pdb=" C24 J40 R 504 " pdb=" C25 J40 R 504 " ideal model delta sigma weight residual 127.40 112.67 14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C21 J40 R 504 " pdb=" C22 J40 R 504 " pdb=" C23 J40 R 504 " ideal model delta sigma weight residual 126.99 112.36 14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C20 J40 R 504 " pdb=" C21 J40 R 504 " pdb=" C22 J40 R 504 " ideal model delta sigma weight residual 126.79 112.59 14.20 3.00e+00 1.11e-01 2.24e+01 ... (remaining 12347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 5420 23.25 - 46.49: 109 46.49 - 69.74: 26 69.74 - 92.98: 5 92.98 - 116.23: 3 Dihedral angle restraints: 5563 sinusoidal: 2302 harmonic: 3261 Sorted by residual: dihedral pdb=" CAT Y01 R 503 " pdb=" CAR Y01 R 503 " pdb=" CBC Y01 R 503 " pdb=" CAV Y01 R 503 " ideal model delta sinusoidal sigma weight residual 58.10 -58.13 116.23 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" CAT Y01 R 503 " pdb=" CAR Y01 R 503 " pdb=" CBC Y01 R 503 " pdb=" OAW Y01 R 503 " ideal model delta sinusoidal sigma weight residual 178.96 63.57 115.39 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" CBC Y01 R 503 " pdb=" CAR Y01 R 503 " pdb=" CAT Y01 R 503 " pdb=" CBH Y01 R 503 " ideal model delta sinusoidal sigma weight residual -57.13 43.82 -100.95 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 5560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1141 0.041 - 0.082: 177 0.082 - 0.123: 79 0.123 - 0.165: 7 0.165 - 0.206: 1 Chirality restraints: 1405 Sorted by residual: chirality pdb=" C3 J40 R 504 " pdb=" C2 J40 R 504 " pdb=" C4 J40 R 504 " pdb=" O3 J40 R 504 " both_signs ideal model delta sigma weight residual False -2.31 -2.52 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C17 CHO R 502 " pdb=" C13 CHO R 502 " pdb=" C16 CHO R 502 " pdb=" C20 CHO R 502 " both_signs ideal model delta sigma weight residual False 2.56 2.41 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1402 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 504 " 0.150 2.00e-02 2.50e+03 2.70e-01 7.30e+02 pdb=" C21 J40 R 504 " -0.352 2.00e-02 2.50e+03 pdb=" C22 J40 R 504 " 0.351 2.00e-02 2.50e+03 pdb=" C23 J40 R 504 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 504 " 0.144 2.00e-02 2.50e+03 2.51e-01 6.28e+02 pdb=" C24 J40 R 504 " -0.324 2.00e-02 2.50e+03 pdb=" C25 J40 R 504 " 0.324 2.00e-02 2.50e+03 pdb=" C26 J40 R 504 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 J40 R 504 " 0.088 2.00e-02 2.50e+03 8.75e-02 7.65e+01 pdb=" C18 J40 R 504 " -0.089 2.00e-02 2.50e+03 pdb=" C19 J40 R 504 " -0.086 2.00e-02 2.50e+03 pdb=" C20 J40 R 504 " 0.087 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 15 2.38 - 3.01: 5264 3.01 - 3.64: 13388 3.64 - 4.27: 20653 4.27 - 4.90: 35099 Nonbonded interactions: 74419 Sorted by model distance: nonbonded pdb=" OH TYR R 215 " pdb=" O HOH R 601 " model vdw 1.744 3.040 nonbonded pdb=" O PHE R 403 " pdb=" O2 J40 R 504 " model vdw 2.084 3.040 nonbonded pdb=" OH TYR R 400 " pdb=" O HOH R 601 " model vdw 2.086 3.040 nonbonded pdb=" O THR B 91 " pdb=" OG1 THR B 92 " model vdw 2.168 3.040 nonbonded pdb=" OE1 GLU A 318 " pdb=" NZ LYS A 345 " model vdw 2.170 3.120 ... (remaining 74414 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: 1.910 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 : 0.005 0.208 9118 Z= 0.265 Angle : 0.677 16.497 12358 Z= 0.312 Chirality : 0.038 0.206 1405 Planarity : 0.010 0.270 1547 Dihedral : 10.617 116.227 3450 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.73 % Allowed : 3.45 % Favored : 95.82 % 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: 2.10 (0.26), residues: 1107 helix: 3.38 (0.27), residues: 391 sheet: 0.96 (0.33), residues: 253 loop : -0.10 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 71 TYR 0.011 0.001 TYR E 235 PHE 0.007 0.001 PHE R 362 TRP 0.004 0.001 TRP B 104 HIS 0.001 0.000 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.26 ( 9115) covalent geometry : angle 0.67739 / 0.31 (12352) SS BOND : bond 0.00357 / 0.19 ( 3) SS BOND : angle 0.79425 / 0.39 ( 6) hydrogen bonds : bond 0.17346 / 11.66 ( 445) hydrogen bonds : angle 6.02035 / 4.30 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.6363 (m-30) cc_final: 0.6113 (m-30) REVERT: B 237 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6063 (pp) REVERT: R 223 ARG cc_start: 0.5053 (tpt170) cc_final: 0.4637 (ttm-80) outliers start: 7 outliers final: 1 residues processed: 190 average time/residue: 0.4128 time to fit residues: 84.1756 Evaluate side-chains 116 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 299 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 93 ASN B 130 ASN B 244 ASN B 298 ASN R 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.230101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185577 restraints weight = 10489.835| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.25 r_work: 0.4124 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9118 Z= 0.146 Angle : 0.628 8.136 12358 Z= 0.323 Chirality : 0.045 0.277 1405 Planarity : 0.004 0.047 1547 Dihedral : 9.639 99.200 1443 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.35 % Allowed : 11.51 % Favored : 85.15 % 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: 1.67 (0.26), residues: 1107 helix: 2.88 (0.26), residues: 384 sheet: 0.92 (0.32), residues: 257 loop : -0.30 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 139 TYR 0.017 0.002 TYR B 269 PHE 0.016 0.002 PHE B 156 TRP 0.021 0.002 TRP E 46 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9115) covalent geometry : angle 0.62631 / 0.32 (12352) SS BOND : bond 0.00762 / 0.39 ( 3) SS BOND : angle 2.24977 / 1.36 ( 6) hydrogen bonds : bond 0.04026 / 2.65 ( 445) hydrogen bonds : angle 4.83319 / 3.39 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7640 (pttm) REVERT: A 229 ASP cc_start: 0.6754 (m-30) cc_final: 0.6079 (m-30) REVERT: A 272 ASP cc_start: 0.6161 (m-30) cc_final: 0.5836 (m-30) REVERT: B 239 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: B 282 SER cc_start: 0.7298 (m) cc_final: 0.7093 (t) REVERT: B 298 ASN cc_start: 0.7395 (m-40) cc_final: 0.7082 (p0) REVERT: B 319 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6357 (tpp80) REVERT: E 92 MET cc_start: 0.6335 (ptm) cc_final: 0.5740 (ttp) REVERT: E 220 GLU cc_start: 0.6072 (mp0) cc_final: 0.5715 (mp0) REVERT: G 20 MET cc_start: -0.1730 (OUTLIER) cc_final: -0.3989 (pp-130) REVERT: R 220 ARG cc_start: 0.5605 (mtm180) cc_final: 0.4420 (ppt90) REVERT: R 223 ARG cc_start: 0.5504 (tpt170) cc_final: 0.4630 (ttm-80) REVERT: R 377 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5702 (mpp) outliers start: 32 outliers final: 12 residues processed: 165 average time/residue: 0.3958 time to fit residues: 70.4074 Evaluate side-chains 139 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 377 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 0.0670 chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 0.0030 chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 244 ASN R 54 ASN R 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.226124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.180702 restraints weight = 10262.209| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.90 r_work: 0.4043 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9118 Z= 0.143 Angle : 0.615 12.002 12358 Z= 0.315 Chirality : 0.044 0.229 1405 Planarity : 0.004 0.057 1547 Dihedral : 9.018 94.193 1440 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.93 % Allowed : 15.27 % Favored : 81.80 % 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 (0.26), residues: 1107 helix: 2.63 (0.26), residues: 383 sheet: 0.75 (0.32), residues: 257 loop : -0.39 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.018 0.002 TYR B 269 PHE 0.013 0.002 PHE A 196 TRP 0.023 0.002 TRP E 46 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9115) covalent geometry : angle 0.61135 / 0.31 (12352) SS BOND : bond 0.00741 / 0.38 ( 3) SS BOND : angle 3.06813 / 1.77 ( 6) hydrogen bonds : bond 0.03924 / 2.61 ( 445) hydrogen bonds : angle 4.79901 / 3.34 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6877 (m-30) cc_final: 0.6643 (m-30) REVERT: A 51 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7552 (pttm) REVERT: B 224 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7288 (mmt180) REVERT: B 239 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: E 33 MET cc_start: 0.6284 (mmm) cc_final: 0.6007 (mmp) REVERT: E 50 ILE cc_start: 0.6307 (tt) cc_final: 0.5784 (mt) REVERT: E 92 MET cc_start: 0.6275 (ptm) cc_final: 0.5706 (ttp) REVERT: E 220 GLU cc_start: 0.6316 (mp0) cc_final: 0.6112 (mp0) REVERT: G 20 MET cc_start: -0.2045 (OUTLIER) cc_final: -0.4379 (pp-130) REVERT: R 223 ARG cc_start: 0.5472 (tpt170) cc_final: 0.4709 (ttm-80) REVERT: R 339 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.5447 (mtt180) outliers start: 28 outliers final: 10 residues processed: 140 average time/residue: 0.3994 time to fit residues: 60.2482 Evaluate side-chains 132 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 339 ARG Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 375 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.222704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175078 restraints weight = 10290.124| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.38 r_work: 0.4017 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9118 Z= 0.151 Angle : 0.633 11.967 12358 Z= 0.321 Chirality : 0.044 0.194 1405 Planarity : 0.004 0.047 1547 Dihedral : 8.523 84.478 1440 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.45 % Allowed : 15.79 % Favored : 80.75 % 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: 1.15 (0.26), residues: 1107 helix: 2.33 (0.26), residues: 382 sheet: 0.62 (0.32), residues: 264 loop : -0.48 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 242 TYR 0.020 0.002 TYR R 198 PHE 0.014 0.002 PHE R 361 TRP 0.015 0.002 TRP E 46 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9115) covalent geometry : angle 0.63056 / 0.32 (12352) SS BOND : bond 0.00951 / 0.50 ( 3) SS BOND : angle 2.36093 / 1.35 ( 6) hydrogen bonds : bond 0.03920 / 2.62 ( 445) hydrogen bonds : angle 4.77493 / 3.31 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.6299 (m-30) cc_final: 0.6059 (m-30) REVERT: A 26 ASP cc_start: 0.7000 (m-30) cc_final: 0.6735 (m-30) REVERT: A 51 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7535 (pttm) REVERT: A 272 ASP cc_start: 0.6246 (m-30) cc_final: 0.6031 (m-30) REVERT: B 239 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 330 MET cc_start: 0.7575 (mmt) cc_final: 0.7326 (mmp) REVERT: E 50 ILE cc_start: 0.6389 (tt) cc_final: 0.5845 (mt) REVERT: E 92 MET cc_start: 0.6310 (ptm) cc_final: 0.5698 (ttp) REVERT: G 20 MET cc_start: -0.2033 (OUTLIER) cc_final: -0.4276 (pp-130) REVERT: G 46 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6809 (tm-30) REVERT: R 192 ASP cc_start: 0.8259 (t0) cc_final: 0.8046 (t0) REVERT: R 223 ARG cc_start: 0.5531 (tpt170) cc_final: 0.4785 (ttm-80) REVERT: R 377 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.5863 (mpp) outliers start: 33 outliers final: 17 residues processed: 150 average time/residue: 0.4207 time to fit residues: 67.9207 Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 375 CYS Chi-restraints excluded: chain R residue 377 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 306 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.216090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171425 restraints weight = 10343.266| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.51 r_work: 0.3938 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9118 Z= 0.230 Angle : 0.741 12.854 12358 Z= 0.379 Chirality : 0.048 0.260 1405 Planarity : 0.005 0.050 1547 Dihedral : 8.401 62.498 1440 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.50 % Allowed : 16.95 % Favored : 78.56 % 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: 0.53 (0.25), residues: 1107 helix: 1.67 (0.26), residues: 381 sheet: 0.28 (0.32), residues: 265 loop : -0.69 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 160 TYR 0.025 0.002 TYR B 269 PHE 0.021 0.003 PHE R 361 TRP 0.018 0.003 TRP E 46 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 9115) covalent geometry : angle 0.73947 / 0.38 (12352) SS BOND : bond 0.01044 / 0.54 ( 3) SS BOND : angle 2.49750 / 1.40 ( 6) hydrogen bonds : bond 0.04727 / 3.17 ( 445) hydrogen bonds : angle 5.13852 / 3.58 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6829 (ttmm) cc_final: 0.6603 (mttp) REVERT: A 35 LYS cc_start: 0.5212 (mtmt) cc_final: 0.4975 (mttp) REVERT: A 51 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7555 (pttm) REVERT: A 253 ILE cc_start: 0.7613 (mp) cc_final: 0.6921 (pp) REVERT: A 319 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7467 (mp) REVERT: B 239 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 273 ASN cc_start: 0.8435 (t0) cc_final: 0.8082 (m-40) REVERT: E 92 MET cc_start: 0.6213 (ptm) cc_final: 0.5504 (ttp) REVERT: G 20 MET cc_start: -0.2031 (OUTLIER) cc_final: -0.4230 (pp-130) REVERT: R 43 LEU cc_start: 0.7469 (tp) cc_final: 0.7207 (tt) REVERT: R 147 LYS cc_start: 0.7703 (mttm) cc_final: 0.7356 (mtmm) REVERT: R 223 ARG cc_start: 0.5877 (tpt170) cc_final: 0.5146 (ttm-80) outliers start: 43 outliers final: 19 residues processed: 154 average time/residue: 0.3704 time to fit residues: 61.5957 Evaluate side-chains 138 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN B 225 GLN B 244 ASN B 345 ASN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.219845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175811 restraints weight = 10240.712| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.50 r_work: 0.3996 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9118 Z= 0.150 Angle : 0.658 11.672 12358 Z= 0.334 Chirality : 0.044 0.214 1405 Planarity : 0.004 0.044 1547 Dihedral : 7.551 69.462 1440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.45 % Allowed : 18.93 % Favored : 77.62 % 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: 0.71 (0.25), residues: 1107 helix: 1.96 (0.26), residues: 386 sheet: 0.23 (0.32), residues: 263 loop : -0.63 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 313 TYR 0.023 0.002 TYR B 269 PHE 0.024 0.002 PHE E 31 TRP 0.015 0.002 TRP B 87 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9115) covalent geometry : angle 0.65566 / 0.33 (12352) SS BOND : bond 0.00850 / 0.44 ( 3) SS BOND : angle 2.70788 / 1.55 ( 6) hydrogen bonds : bond 0.03938 / 2.61 ( 445) hydrogen bonds : angle 4.84576 / 3.36 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7977 (pttm) cc_final: 0.7494 (pttm) REVERT: B 273 ASN cc_start: 0.8496 (t0) cc_final: 0.8090 (m-40) REVERT: E 50 ILE cc_start: 0.6537 (tt) cc_final: 0.5980 (mt) REVERT: E 92 MET cc_start: 0.6293 (ptm) cc_final: 0.5533 (ttp) REVERT: G 20 MET cc_start: -0.1923 (OUTLIER) cc_final: -0.3945 (pp-130) REVERT: R 43 LEU cc_start: 0.7417 (tp) cc_final: 0.7132 (tt) REVERT: R 147 LYS cc_start: 0.7630 (mttm) cc_final: 0.7355 (mtmm) REVERT: R 192 ASP cc_start: 0.8154 (t0) cc_final: 0.7758 (t0) REVERT: R 223 ARG cc_start: 0.5762 (tpt170) cc_final: 0.5097 (ttm-80) REVERT: R 335 MET cc_start: 0.4993 (tpp) cc_final: 0.4629 (ttm) outliers start: 33 outliers final: 16 residues processed: 155 average time/residue: 0.3562 time to fit residues: 60.0673 Evaluate side-chains 136 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 54 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 = 0.4539 r_free = 0.4539 target = 0.216511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169949 restraints weight = 10352.146| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.65 r_work: 0.3936 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9118 Z= 0.213 Angle : 0.732 13.522 12358 Z= 0.370 Chirality : 0.048 0.240 1405 Planarity : 0.005 0.050 1547 Dihedral : 7.591 71.554 1440 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.29 % Allowed : 18.93 % Favored : 76.78 % 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: 0.44 (0.25), residues: 1107 helix: 1.69 (0.26), residues: 378 sheet: -0.06 (0.31), residues: 280 loop : -0.62 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.018 0.002 TYR E 235 PHE 0.026 0.003 PHE E 31 TRP 0.012 0.002 TRP E 46 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 9115) covalent geometry : angle 0.73089 / 0.37 (12352) SS BOND : bond 0.00993 / 0.51 ( 3) SS BOND : angle 1.67933 / 0.87 ( 6) hydrogen bonds : bond 0.04457 / 2.97 ( 445) hydrogen bonds : angle 5.07188 / 3.54 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7629 (pttm) REVERT: A 242 ARG cc_start: 0.7209 (mtp-110) cc_final: 0.6983 (mtp-110) REVERT: A 319 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7266 (mp) REVERT: B 239 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: E 92 MET cc_start: 0.6314 (ptm) cc_final: 0.5515 (ttp) REVERT: E 178 LEU cc_start: 0.5278 (tt) cc_final: 0.5076 (tm) REVERT: G 20 MET cc_start: -0.1867 (OUTLIER) cc_final: -0.3994 (pp-130) REVERT: R 147 LYS cc_start: 0.7689 (mttm) cc_final: 0.7469 (mtmm) REVERT: R 192 ASP cc_start: 0.8124 (t0) cc_final: 0.7691 (t0) REVERT: R 223 ARG cc_start: 0.5852 (tpt170) cc_final: 0.5195 (ttm-80) REVERT: R 335 MET cc_start: 0.5091 (tpp) cc_final: 0.4765 (ttm) outliers start: 41 outliers final: 22 residues processed: 150 average time/residue: 0.3578 time to fit residues: 58.5133 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 344 VAL Chi-restraints excluded: chain R residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** G 43 HIS ** 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 = 0.4578 r_free = 0.4578 target = 0.222042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.177125 restraints weight = 10304.018| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.61 r_work: 0.4012 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9118 Z= 0.131 Angle : 0.640 11.747 12358 Z= 0.323 Chirality : 0.044 0.199 1405 Planarity : 0.004 0.048 1547 Dihedral : 7.125 78.245 1440 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.03 % Allowed : 20.40 % Favored : 76.57 % 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: 0.72 (0.26), residues: 1107 helix: 2.01 (0.26), residues: 385 sheet: 0.11 (0.31), residues: 278 loop : -0.61 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.016 0.002 TYR B 269 PHE 0.021 0.002 PHE E 31 TRP 0.019 0.002 TRP R 387 HIS 0.019 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9115) covalent geometry : angle 0.63985 / 0.32 (12352) SS BOND : bond 0.00664 / 0.35 ( 3) SS BOND : angle 1.45053 / 0.80 ( 6) hydrogen bonds : bond 0.03719 / 2.44 ( 445) hydrogen bonds : angle 4.79902 / 3.33 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7563 (pttm) REVERT: A 182 THR cc_start: 0.6724 (p) cc_final: 0.6492 (t) REVERT: A 319 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7175 (mp) REVERT: B 239 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: E 92 MET cc_start: 0.6181 (ptm) cc_final: 0.5440 (ttp) REVERT: E 116 LEU cc_start: 0.4663 (mp) cc_final: 0.3976 (mt) REVERT: G 20 MET cc_start: -0.2041 (OUTLIER) cc_final: -0.3951 (pp-130) REVERT: R 147 LYS cc_start: 0.7612 (mttm) cc_final: 0.7398 (mtmm) REVERT: R 192 ASP cc_start: 0.8134 (t0) cc_final: 0.7768 (t0) REVERT: R 223 ARG cc_start: 0.5611 (tpt170) cc_final: 0.5036 (ttm-80) REVERT: R 335 MET cc_start: 0.5104 (tpp) cc_final: 0.4819 (ttm) outliers start: 29 outliers final: 17 residues processed: 145 average time/residue: 0.3562 time to fit residues: 56.1799 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 311 ASN ** G 43 HIS ** 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 = 0.4584 r_free = 0.4584 target = 0.222747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.178829 restraints weight = 10335.887| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.75 r_work: 0.4022 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9118 Z= 0.132 Angle : 0.647 11.490 12358 Z= 0.327 Chirality : 0.044 0.191 1405 Planarity : 0.004 0.048 1547 Dihedral : 7.051 82.511 1440 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.24 % Allowed : 20.71 % Favored : 76.05 % 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: 0.72 (0.26), residues: 1107 helix: 2.09 (0.26), residues: 385 sheet: 0.07 (0.31), residues: 275 loop : -0.65 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 313 TYR 0.017 0.002 TYR B 269 PHE 0.014 0.002 PHE B 297 TRP 0.016 0.002 TRP R 387 HIS 0.019 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9115) covalent geometry : angle 0.64673 / 0.33 (12352) SS BOND : bond 0.00656 / 0.34 ( 3) SS BOND : angle 1.40769 / 0.76 ( 6) hydrogen bonds : bond 0.03660 / 2.40 ( 445) hydrogen bonds : angle 4.76573 / 3.31 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7545 (pttm) REVERT: A 182 THR cc_start: 0.6761 (p) cc_final: 0.6509 (t) REVERT: A 319 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7301 (mp) REVERT: B 239 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: E 92 MET cc_start: 0.6315 (ptm) cc_final: 0.5415 (ttp) REVERT: E 116 LEU cc_start: 0.4829 (mp) cc_final: 0.4014 (mt) REVERT: G 20 MET cc_start: -0.2096 (OUTLIER) cc_final: -0.3906 (pp-130) REVERT: R 147 LYS cc_start: 0.7628 (mttm) cc_final: 0.7384 (mtmm) REVERT: R 192 ASP cc_start: 0.8120 (t0) cc_final: 0.7734 (t0) REVERT: R 223 ARG cc_start: 0.5742 (tpt170) cc_final: 0.5053 (ttm-80) REVERT: R 335 MET cc_start: 0.5048 (tpp) cc_final: 0.4756 (ttm) outliers start: 31 outliers final: 18 residues processed: 148 average time/residue: 0.3368 time to fit residues: 54.6850 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 180 GLN B 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.219775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.174194 restraints weight = 10311.361| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.63 r_work: 0.3971 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9118 Z= 0.178 Angle : 0.701 12.405 12358 Z= 0.356 Chirality : 0.046 0.226 1405 Planarity : 0.005 0.051 1547 Dihedral : 7.319 85.948 1440 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.24 % Allowed : 20.71 % Favored : 76.05 % 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: 0.47 (0.25), residues: 1107 helix: 1.87 (0.26), residues: 378 sheet: -0.05 (0.31), residues: 280 loop : -0.75 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.019 0.002 TYR E 235 PHE 0.015 0.002 PHE B 156 TRP 0.017 0.002 TRP A 258 HIS 0.019 0.002 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9115) covalent geometry : angle 0.69992 / 0.36 (12352) SS BOND : bond 0.00841 / 0.44 ( 3) SS BOND : angle 1.74161 / 0.94 ( 6) hydrogen bonds : bond 0.04157 / 2.74 ( 445) hydrogen bonds : angle 4.96023 / 3.46 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7457 (pttm) REVERT: A 319 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 239 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: E 46 TRP cc_start: 0.5050 (t60) cc_final: 0.4603 (t60) REVERT: E 92 MET cc_start: 0.6211 (ptm) cc_final: 0.5351 (ttp) REVERT: E 116 LEU cc_start: 0.4572 (mp) cc_final: 0.3878 (mt) REVERT: E 178 LEU cc_start: 0.5155 (tt) cc_final: 0.4892 (tm) REVERT: G 20 MET cc_start: -0.2119 (OUTLIER) cc_final: -0.3978 (pp-130) REVERT: R 192 ASP cc_start: 0.8137 (t0) cc_final: 0.7776 (t0) REVERT: R 223 ARG cc_start: 0.5767 (tpt170) cc_final: 0.5102 (ttm-80) REVERT: R 335 MET cc_start: 0.5151 (tpp) cc_final: 0.4756 (ttm) outliers start: 31 outliers final: 18 residues processed: 139 average time/residue: 0.3442 time to fit residues: 52.2518 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.224489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.180302 restraints weight = 10237.044| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.58 r_work: 0.4035 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9118 Z= 0.126 Angle : 0.648 11.283 12358 Z= 0.326 Chirality : 0.043 0.190 1405 Planarity : 0.004 0.050 1547 Dihedral : 7.010 86.314 1440 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.82 % Allowed : 21.34 % Favored : 75.84 % 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: 0.66 (0.26), residues: 1107 helix: 2.09 (0.26), residues: 385 sheet: -0.01 (0.31), residues: 285 loop : -0.71 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.015 0.001 TYR R 198 PHE 0.012 0.001 PHE B 156 TRP 0.017 0.002 TRP B 87 HIS 0.021 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9115) covalent geometry : angle 0.64772 / 0.33 (12352) SS BOND : bond 0.00624 / 0.33 ( 3) SS BOND : angle 1.30650 / 0.71 ( 6) hydrogen bonds : bond 0.03542 / 2.32 ( 445) hydrogen bonds : angle 4.74770 / 3.30 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.48 seconds wall clock time: 51 minutes 30.50 seconds (3090.50 seconds total)