Starting phenix.real_space_refine on Fri Aug 22 23:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk3_34843/08_2025/8hk3_34843.cif" } resolution = 3.2 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= 0.002 sd= 0.033 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 69 5.16 5 C 5585 2.51 5 N 1488 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1801 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2244 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 1 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 1.75, per 1000 atoms: 0.20 Number of scatterers: 8746 At special positions: 0 Unit cell: (105.04, 115.44, 131.04, 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 69 16.00 O 1604 8.00 N 1488 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " 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: 0.62 Conformation dependent library (CDL) restraints added in 454.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.111A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.976A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.661A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.020A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.855A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.597A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.552A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.876A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 51 removed outlier: 4.223A pdb=" N LEU C 38 " --> pdb=" O PHE C 34 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 4.043A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 3.772A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 removed outlier: 3.602A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 331 through 365 removed outlier: 5.709A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 372 through 403 removed outlier: 3.855A pdb=" N PHE C 376 " --> pdb=" O GLN C 372 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.552A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.623A pdb=" N LYS C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS C 420 " --> pdb=" O TRP C 416 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 439 through 454 removed outlier: 3.516A pdb=" N ARG C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.704A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.510A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.192A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.849A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.554A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.470A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.548A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.643A pdb=" N VAL H 5 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.107A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.587A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1194 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: 1.24 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.43: 2456 1.43 - 1.56: 4973 1.56 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 8935 Sorted by residual: bond pdb=" C LEU C 32 " pdb=" O LEU C 32 " ideal model delta sigma weight residual 1.236 1.183 0.054 1.26e-02 6.30e+03 1.82e+01 bond pdb=" C PHE C 345 " pdb=" O PHE C 345 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" C LEU C 38 " pdb=" O LEU C 38 " ideal model delta sigma weight residual 1.241 1.206 0.036 9.80e-03 1.04e+04 1.33e+01 bond pdb=" CA GLN C 372 " pdb=" C GLN C 372 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.30e-02 5.92e+03 5.32e+00 bond pdb=" C THR C 33 " pdb=" O THR C 33 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.16e-02 7.43e+03 4.76e+00 ... (remaining 8930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12061 2.45 - 4.90: 55 4.90 - 7.34: 4 7.34 - 9.79: 0 9.79 - 12.24: 1 Bond angle restraints: 12121 Sorted by residual: angle pdb=" N GLY C 91 " pdb=" CA GLY C 91 " pdb=" C GLY C 91 " ideal model delta sigma weight residual 112.83 119.62 -6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA LEU C 35 " pdb=" CB LEU C 35 " pdb=" CG LEU C 35 " ideal model delta sigma weight residual 116.30 128.54 -12.24 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " pdb=" CG GLN C 372 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N ARG C 92 " pdb=" CA ARG C 92 " pdb=" C ARG C 92 " ideal model delta sigma weight residual 111.69 115.66 -3.97 1.23e+00 6.61e-01 1.04e+01 angle pdb=" C LEU C 38 " pdb=" N PRO C 39 " pdb=" CA PRO C 39 " ideal model delta sigma weight residual 118.97 115.99 2.98 1.04e+00 9.25e-01 8.22e+00 ... (remaining 12116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 5192 15.97 - 31.94: 67 31.94 - 47.92: 15 47.92 - 63.89: 2 63.89 - 79.86: 2 Dihedral angle restraints: 5278 sinusoidal: 1996 harmonic: 3282 Sorted by residual: dihedral pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " ideal model delta harmonic sigma weight residual 122.80 130.89 -8.09 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C GLN C 372 " pdb=" N GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual -122.60 -130.23 7.63 0 2.50e+00 1.60e-01 9.32e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1278 0.073 - 0.147: 107 0.147 - 0.220: 0 0.220 - 0.293: 2 0.293 - 0.367: 3 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA LEU C 38 " pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CB LEU C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA GLN C 372 " pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CB GLN C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU C 38 " pdb=" CB LEU C 38 " pdb=" CD1 LEU C 38 " pdb=" CD2 LEU C 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1387 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 90 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C TYR C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR C 90 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 31 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER C 31 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 31 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 345 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C PHE C 345 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE C 345 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 82 2.63 - 3.20: 8136 3.20 - 3.77: 12881 3.77 - 4.33: 18184 4.33 - 4.90: 30718 Nonbonded interactions: 70001 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.069 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OG1 THR C 58 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.197 3.040 ... (remaining 69996 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: 0.460 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.750 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.054 8936 Z= 0.150 Angle : 0.421 12.240 12123 Z= 0.233 Chirality : 0.042 0.367 1390 Planarity : 0.002 0.034 1528 Dihedral : 6.311 79.860 3155 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % 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 aren not related in a simple way. whole: -1.02 (0.24), residues: 1119 helix: 0.65 (0.26), residues: 397 sheet: -1.05 (0.28), residues: 287 loop : -1.56 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.003 0.000 TYR H 190 PHE 0.008 0.001 PHE C 34 TRP 0.003 0.000 TRP B 99 HIS 0.001 0.000 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8935) covalent geometry : angle 0.42085 (12121) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.84684 ( 2) hydrogen bonds : bond 0.19944 ( 427) hydrogen bonds : angle 6.49706 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7685 (mt) cc_final: 0.7460 (mp) REVERT: A 191 PHE cc_start: 0.8168 (t80) cc_final: 0.7968 (t80) REVERT: A 197 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7081 (mtpp) REVERT: B 61 MET cc_start: 0.6755 (ppp) cc_final: 0.6376 (ppp) REVERT: B 102 THR cc_start: 0.7984 (t) cc_final: 0.7770 (t) REVERT: B 170 ASP cc_start: 0.6201 (t70) cc_final: 0.5998 (t0) REVERT: B 246 ASP cc_start: 0.7459 (m-30) cc_final: 0.7216 (m-30) REVERT: B 277 SER cc_start: 0.8547 (t) cc_final: 0.8102 (m) REVERT: C 138 MET cc_start: 0.6859 (ttp) cc_final: 0.6429 (ttp) REVERT: C 141 SER cc_start: 0.7926 (t) cc_final: 0.7724 (p) REVERT: C 156 PRO cc_start: 0.7669 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: C 399 LEU cc_start: 0.7811 (mp) cc_final: 0.7580 (mt) REVERT: H 161 SER cc_start: 0.8318 (t) cc_final: 0.8116 (p) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.0748 time to fit residues: 28.7516 Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 110 ASN B 125 ASN B 220 GLN B 295 ASN C 63 HIS C 133 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111877 restraints weight = 12247.441| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.97 r_work: 0.3188 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8936 Z= 0.205 Angle : 0.600 8.858 12123 Z= 0.309 Chirality : 0.045 0.162 1390 Planarity : 0.005 0.044 1528 Dihedral : 4.311 57.780 1218 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.81 % Allowed : 8.52 % Favored : 89.67 % 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 aren not related in a simple way. whole: -0.17 (0.25), residues: 1119 helix: 1.56 (0.27), residues: 404 sheet: -0.52 (0.29), residues: 286 loop : -1.43 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 49 TYR 0.022 0.003 TYR H 102 PHE 0.032 0.002 PHE B 199 TRP 0.019 0.002 TRP B 339 HIS 0.008 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8935) covalent geometry : angle 0.60031 (12121) SS BOND : bond 0.00541 ( 1) SS BOND : angle 1.03880 ( 2) hydrogen bonds : bond 0.04421 ( 427) hydrogen bonds : angle 4.64219 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.215 Fit side-chains REVERT: A 10 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7434 (mttm) REVERT: A 14 GLU cc_start: 0.7748 (tp30) cc_final: 0.7444 (tp30) REVERT: A 197 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7925 (mtpt) REVERT: B 14 LEU cc_start: 0.7896 (mm) cc_final: 0.7678 (mt) REVERT: B 46 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7464 (mtp-110) REVERT: B 50 THR cc_start: 0.8427 (m) cc_final: 0.8146 (t) REVERT: B 61 MET cc_start: 0.8039 (ppp) cc_final: 0.7767 (ppp) REVERT: B 119 ASN cc_start: 0.7994 (m-40) cc_final: 0.7644 (m-40) REVERT: B 155 ASN cc_start: 0.7823 (t0) cc_final: 0.7340 (t0) REVERT: B 170 ASP cc_start: 0.7388 (t70) cc_final: 0.6894 (t0) REVERT: B 220 GLN cc_start: 0.8284 (mt0) cc_final: 0.7605 (mt0) REVERT: B 254 ASP cc_start: 0.7763 (t70) cc_final: 0.7539 (t0) REVERT: B 290 ASP cc_start: 0.7611 (m-30) cc_final: 0.7392 (m-30) REVERT: B 291 ASP cc_start: 0.7216 (m-30) cc_final: 0.6987 (m-30) REVERT: B 295 ASN cc_start: 0.8389 (m-40) cc_final: 0.8106 (m-40) REVERT: B 303 ASP cc_start: 0.7852 (m-30) cc_final: 0.7646 (m-30) REVERT: C 391 THR cc_start: 0.8366 (m) cc_final: 0.8159 (m) REVERT: C 399 LEU cc_start: 0.8059 (mp) cc_final: 0.7797 (mt) REVERT: C 409 LEU cc_start: 0.7215 (tp) cc_final: 0.7013 (tp) REVERT: C 434 LEU cc_start: 0.8149 (mt) cc_final: 0.7949 (mt) REVERT: H 94 TYR cc_start: 0.8213 (m-80) cc_final: 0.7883 (m-80) REVERT: H 119 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7281 (p) outliers start: 17 outliers final: 13 residues processed: 238 average time/residue: 0.0674 time to fit residues: 22.6291 Evaluate side-chains 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN B 156 GLN B 268 ASN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111391 restraints weight = 12129.241| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8936 Z= 0.132 Angle : 0.502 7.157 12123 Z= 0.258 Chirality : 0.041 0.150 1390 Planarity : 0.004 0.044 1528 Dihedral : 4.036 59.422 1218 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.70 % Allowed : 10.76 % Favored : 87.54 % 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 aren not related in a simple way. whole: 0.35 (0.25), residues: 1119 helix: 1.93 (0.27), residues: 404 sheet: -0.15 (0.29), residues: 286 loop : -1.13 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.015 0.001 TYR H 95 PHE 0.019 0.001 PHE B 199 TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8935) covalent geometry : angle 0.50200 (12121) SS BOND : bond 0.00313 ( 1) SS BOND : angle 0.47603 ( 2) hydrogen bonds : bond 0.03616 ( 427) hydrogen bonds : angle 4.30976 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.291 Fit side-chains REVERT: A 225 VAL cc_start: 0.8644 (p) cc_final: 0.8332 (m) REVERT: B 46 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7519 (mtp-110) REVERT: B 61 MET cc_start: 0.7879 (ppp) cc_final: 0.7564 (ppp) REVERT: B 119 ASN cc_start: 0.7953 (m-40) cc_final: 0.7536 (m-40) REVERT: B 137 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7938 (ttm170) REVERT: B 155 ASN cc_start: 0.7943 (t0) cc_final: 0.7516 (t0) REVERT: B 170 ASP cc_start: 0.7312 (t70) cc_final: 0.6926 (t0) REVERT: B 220 GLN cc_start: 0.8444 (mt0) cc_final: 0.8147 (mt0) REVERT: B 295 ASN cc_start: 0.8525 (m-40) cc_final: 0.8269 (m-40) REVERT: B 303 ASP cc_start: 0.7847 (m-30) cc_final: 0.7644 (m-30) REVERT: C 340 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7470 (ttp-170) REVERT: C 391 THR cc_start: 0.8446 (m) cc_final: 0.8217 (m) REVERT: C 399 LEU cc_start: 0.8149 (mp) cc_final: 0.7921 (mt) REVERT: C 414 MET cc_start: 0.7917 (mtp) cc_final: 0.7429 (mpp) REVERT: G 27 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8038 (mtt-85) REVERT: H 93 MET cc_start: 0.8236 (ttp) cc_final: 0.8008 (ttt) REVERT: H 119 VAL cc_start: 0.7886 (t) cc_final: 0.7464 (p) outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 0.0720 time to fit residues: 20.5957 Evaluate side-chains 212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112360 restraints weight = 12249.868| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.02 r_work: 0.3198 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8936 Z= 0.093 Angle : 0.453 6.784 12123 Z= 0.235 Chirality : 0.039 0.149 1390 Planarity : 0.003 0.044 1528 Dihedral : 3.874 59.481 1218 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.49 % Allowed : 13.21 % Favored : 85.30 % 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 aren not related in a simple way. whole: 0.66 (0.25), residues: 1119 helix: 2.11 (0.26), residues: 408 sheet: -0.00 (0.29), residues: 292 loop : -0.89 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.009 0.001 TYR H 95 PHE 0.017 0.001 PHE B 199 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8935) covalent geometry : angle 0.45312 (12121) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.39065 ( 2) hydrogen bonds : bond 0.03058 ( 427) hydrogen bonds : angle 4.04951 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8611 (p) cc_final: 0.8314 (m) REVERT: B 61 MET cc_start: 0.7773 (ppp) cc_final: 0.7476 (ppp) REVERT: B 78 LYS cc_start: 0.8364 (mttm) cc_final: 0.8129 (mttp) REVERT: B 119 ASN cc_start: 0.7903 (m-40) cc_final: 0.7486 (m-40) REVERT: B 155 ASN cc_start: 0.7943 (t0) cc_final: 0.7478 (t0) REVERT: B 170 ASP cc_start: 0.7220 (t70) cc_final: 0.6835 (t0) REVERT: B 220 GLN cc_start: 0.8406 (mt0) cc_final: 0.8073 (mt0) REVERT: B 234 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 303 ASP cc_start: 0.7834 (m-30) cc_final: 0.7583 (m-30) REVERT: C 340 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7399 (ttp-170) REVERT: C 387 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7617 (mt) REVERT: C 391 THR cc_start: 0.8394 (m) cc_final: 0.8157 (m) REVERT: C 414 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7411 (mpp) REVERT: G 27 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8178 (mtt-85) REVERT: H 119 VAL cc_start: 0.7809 (t) cc_final: 0.7360 (p) outliers start: 14 outliers final: 8 residues processed: 216 average time/residue: 0.0813 time to fit residues: 23.7594 Evaluate side-chains 213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 100 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108898 restraints weight = 12228.827| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.94 r_work: 0.3221 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8936 Z= 0.157 Angle : 0.501 7.213 12123 Z= 0.262 Chirality : 0.041 0.147 1390 Planarity : 0.004 0.049 1528 Dihedral : 4.176 59.385 1218 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.02 % Allowed : 13.10 % Favored : 84.88 % 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 aren not related in a simple way. whole: 0.74 (0.25), residues: 1119 helix: 2.14 (0.26), residues: 406 sheet: 0.04 (0.30), residues: 286 loop : -0.79 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.018 0.002 TYR H 95 PHE 0.022 0.002 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8935) covalent geometry : angle 0.50125 (12121) SS BOND : bond 0.00388 ( 1) SS BOND : angle 0.43489 ( 2) hydrogen bonds : bond 0.03697 ( 427) hydrogen bonds : angle 4.18339 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: A 225 VAL cc_start: 0.8711 (p) cc_final: 0.8362 (m) REVERT: A 351 CYS cc_start: 0.8017 (m) cc_final: 0.7773 (m) REVERT: B 50 THR cc_start: 0.8532 (m) cc_final: 0.8239 (t) REVERT: B 155 ASN cc_start: 0.8080 (t0) cc_final: 0.7741 (t0) REVERT: B 170 ASP cc_start: 0.7499 (t70) cc_final: 0.7145 (t0) REVERT: B 234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 303 ASP cc_start: 0.7861 (m-30) cc_final: 0.7623 (m-30) REVERT: C 340 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7489 (ttp-170) REVERT: C 391 THR cc_start: 0.8527 (m) cc_final: 0.8294 (m) REVERT: C 414 MET cc_start: 0.7948 (mtp) cc_final: 0.7474 (mpp) REVERT: C 443 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7906 (mtm-85) REVERT: G 27 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8055 (mtt-85) REVERT: H 67 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7876 (ttm170) REVERT: H 119 VAL cc_start: 0.7877 (t) cc_final: 0.7461 (p) REVERT: H 166 LEU cc_start: 0.8503 (tp) cc_final: 0.8290 (tt) outliers start: 19 outliers final: 13 residues processed: 214 average time/residue: 0.0819 time to fit residues: 23.1300 Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110399 restraints weight = 12277.262| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.95 r_work: 0.3235 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8936 Z= 0.134 Angle : 0.496 7.144 12123 Z= 0.255 Chirality : 0.041 0.150 1390 Planarity : 0.004 0.045 1528 Dihedral : 4.123 58.363 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.49 % Allowed : 13.74 % Favored : 84.77 % 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 aren not related in a simple way. whole: 0.78 (0.25), residues: 1119 helix: 2.15 (0.26), residues: 407 sheet: 0.04 (0.30), residues: 290 loop : -0.74 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.011 0.001 TYR A 320 PHE 0.020 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8935) covalent geometry : angle 0.49584 (12121) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.39020 ( 2) hydrogen bonds : bond 0.03485 ( 427) hydrogen bonds : angle 4.11031 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8685 (p) cc_final: 0.8343 (m) REVERT: A 240 MET cc_start: 0.4873 (mmm) cc_final: 0.4582 (mmm) REVERT: B 46 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7537 (mtp-110) REVERT: B 155 ASN cc_start: 0.8095 (t0) cc_final: 0.7750 (t0) REVERT: B 170 ASP cc_start: 0.7458 (t70) cc_final: 0.7084 (t0) REVERT: B 234 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: B 290 ASP cc_start: 0.7711 (m-30) cc_final: 0.7462 (m-30) REVERT: B 303 ASP cc_start: 0.7867 (m-30) cc_final: 0.7593 (m-30) REVERT: C 340 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7446 (ttp-170) REVERT: C 391 THR cc_start: 0.8519 (m) cc_final: 0.8292 (m) REVERT: C 414 MET cc_start: 0.7911 (mtp) cc_final: 0.7433 (mpp) REVERT: C 443 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: G 27 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8056 (mtt-85) REVERT: H 119 VAL cc_start: 0.7925 (t) cc_final: 0.7501 (p) REVERT: H 166 LEU cc_start: 0.8512 (tp) cc_final: 0.8303 (tt) outliers start: 14 outliers final: 11 residues processed: 207 average time/residue: 0.0908 time to fit residues: 24.9090 Evaluate side-chains 209 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 10 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111329 restraints weight = 12404.519| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.95 r_work: 0.3261 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8936 Z= 0.094 Angle : 0.468 6.594 12123 Z= 0.242 Chirality : 0.040 0.132 1390 Planarity : 0.004 0.047 1528 Dihedral : 3.943 58.966 1218 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.60 % Allowed : 14.27 % Favored : 84.13 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1119 helix: 2.16 (0.26), residues: 414 sheet: 0.11 (0.30), residues: 292 loop : -0.63 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.009 0.001 TYR H 190 PHE 0.022 0.001 PHE H 68 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8935) covalent geometry : angle 0.46796 (12121) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.30474 ( 2) hydrogen bonds : bond 0.03049 ( 427) hydrogen bonds : angle 3.95373 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8672 (p) cc_final: 0.8331 (m) REVERT: A 341 ASP cc_start: 0.7715 (t70) cc_final: 0.7202 (t0) REVERT: B 119 ASN cc_start: 0.7963 (m-40) cc_final: 0.7578 (m-40) REVERT: B 136 SER cc_start: 0.8431 (t) cc_final: 0.8204 (p) REVERT: B 155 ASN cc_start: 0.8049 (t0) cc_final: 0.7696 (t0) REVERT: B 170 ASP cc_start: 0.7420 (t70) cc_final: 0.7053 (t0) REVERT: B 230 ASN cc_start: 0.8304 (m110) cc_final: 0.7911 (m110) REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: B 246 ASP cc_start: 0.7961 (m-30) cc_final: 0.7560 (m-30) REVERT: B 290 ASP cc_start: 0.7749 (m-30) cc_final: 0.7520 (m-30) REVERT: C 340 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7361 (ttp-170) REVERT: C 391 THR cc_start: 0.8475 (m) cc_final: 0.8247 (m) REVERT: C 414 MET cc_start: 0.7908 (mtp) cc_final: 0.7443 (mpp) REVERT: G 27 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8195 (mtt-85) REVERT: H 90 ASP cc_start: 0.7791 (m-30) cc_final: 0.7533 (m-30) REVERT: H 166 LEU cc_start: 0.8524 (tp) cc_final: 0.8318 (tt) outliers start: 15 outliers final: 10 residues processed: 217 average time/residue: 0.0950 time to fit residues: 27.3368 Evaluate side-chains 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 107 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111002 restraints weight = 12276.199| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.92 r_work: 0.3248 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8936 Z= 0.115 Angle : 0.482 7.193 12123 Z= 0.250 Chirality : 0.040 0.156 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.003 59.479 1218 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.92 % Allowed : 14.06 % Favored : 84.03 % 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 aren not related in a simple way. whole: 0.97 (0.26), residues: 1119 helix: 2.32 (0.26), residues: 408 sheet: 0.08 (0.29), residues: 295 loop : -0.60 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.010 0.001 TYR H 190 PHE 0.034 0.001 PHE H 68 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8935) covalent geometry : angle 0.48205 (12121) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.28328 ( 2) hydrogen bonds : bond 0.03239 ( 427) hydrogen bonds : angle 3.98035 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8453 (mtmm) REVERT: A 198 MET cc_start: 0.8329 (mtp) cc_final: 0.8032 (ttm) REVERT: A 225 VAL cc_start: 0.8700 (p) cc_final: 0.8372 (m) REVERT: A 240 MET cc_start: 0.4734 (mmm) cc_final: 0.4487 (mmm) REVERT: A 341 ASP cc_start: 0.7699 (t70) cc_final: 0.7169 (t0) REVERT: B 50 THR cc_start: 0.8450 (m) cc_final: 0.8150 (t) REVERT: B 136 SER cc_start: 0.8427 (t) cc_final: 0.8186 (p) REVERT: B 155 ASN cc_start: 0.8093 (t0) cc_final: 0.7745 (t0) REVERT: B 170 ASP cc_start: 0.7497 (t70) cc_final: 0.7056 (t0) REVERT: B 234 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: B 290 ASP cc_start: 0.7741 (m-30) cc_final: 0.7500 (m-30) REVERT: C 340 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7373 (ttp-170) REVERT: C 391 THR cc_start: 0.8462 (m) cc_final: 0.8229 (m) REVERT: C 414 MET cc_start: 0.7894 (mtp) cc_final: 0.7422 (mpp) REVERT: G 27 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8217 (mtt-85) REVERT: H 29 PHE cc_start: 0.8464 (t80) cc_final: 0.8246 (t80) REVERT: H 90 ASP cc_start: 0.7859 (m-30) cc_final: 0.7563 (m-30) outliers start: 18 outliers final: 13 residues processed: 214 average time/residue: 0.0891 time to fit residues: 24.9340 Evaluate side-chains 218 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110250 restraints weight = 12290.388| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3237 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8936 Z= 0.114 Angle : 0.483 7.420 12123 Z= 0.251 Chirality : 0.041 0.140 1390 Planarity : 0.004 0.046 1528 Dihedral : 3.995 59.020 1218 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.49 % Allowed : 14.48 % Favored : 84.03 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1119 helix: 2.35 (0.26), residues: 408 sheet: 0.07 (0.29), residues: 296 loop : -0.58 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.010 0.001 TYR H 190 PHE 0.031 0.001 PHE H 68 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8935) covalent geometry : angle 0.48318 (12121) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.30384 ( 2) hydrogen bonds : bond 0.03212 ( 427) hydrogen bonds : angle 3.96690 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8457 (mtmm) REVERT: A 198 MET cc_start: 0.8336 (mtp) cc_final: 0.8055 (ttm) REVERT: A 240 MET cc_start: 0.4711 (mmm) cc_final: 0.4464 (mmm) REVERT: A 245 GLU cc_start: 0.7278 (tp30) cc_final: 0.6524 (tp30) REVERT: A 341 ASP cc_start: 0.7708 (t70) cc_final: 0.7178 (t0) REVERT: B 50 THR cc_start: 0.8441 (m) cc_final: 0.8122 (t) REVERT: B 155 ASN cc_start: 0.8118 (t0) cc_final: 0.7759 (t0) REVERT: B 230 ASN cc_start: 0.8294 (m110) cc_final: 0.8086 (m-40) REVERT: B 234 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 290 ASP cc_start: 0.7762 (m-30) cc_final: 0.7546 (m-30) REVERT: B 304 ARG cc_start: 0.8255 (ttp80) cc_final: 0.8038 (ttt-90) REVERT: C 340 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7379 (ttp-170) REVERT: C 391 THR cc_start: 0.8460 (m) cc_final: 0.8230 (m) REVERT: C 414 MET cc_start: 0.7929 (mtp) cc_final: 0.7447 (mpp) REVERT: H 29 PHE cc_start: 0.8429 (t80) cc_final: 0.8221 (t80) REVERT: H 52 SER cc_start: 0.8427 (t) cc_final: 0.8075 (p) REVERT: H 90 ASP cc_start: 0.7827 (m-30) cc_final: 0.7454 (m-30) outliers start: 14 outliers final: 11 residues processed: 209 average time/residue: 0.0855 time to fit residues: 23.6949 Evaluate side-chains 214 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109691 restraints weight = 12260.366| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.99 r_work: 0.3242 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8936 Z= 0.109 Angle : 0.479 7.350 12123 Z= 0.248 Chirality : 0.040 0.154 1390 Planarity : 0.004 0.047 1528 Dihedral : 3.987 59.490 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.17 % Allowed : 14.70 % Favored : 84.13 % 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 aren not related in a simple way. whole: 1.02 (0.26), residues: 1119 helix: 2.39 (0.26), residues: 409 sheet: 0.16 (0.30), residues: 289 loop : -0.63 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.009 0.001 TYR H 190 PHE 0.040 0.001 PHE H 68 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8935) covalent geometry : angle 0.47897 (12121) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.28757 ( 2) hydrogen bonds : bond 0.03175 ( 427) hydrogen bonds : angle 3.95325 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8469 (mtmm) REVERT: A 198 MET cc_start: 0.8355 (mtp) cc_final: 0.8070 (ttm) REVERT: A 240 MET cc_start: 0.4718 (mmm) cc_final: 0.4476 (mmm) REVERT: A 245 GLU cc_start: 0.7279 (tp30) cc_final: 0.6514 (tp30) REVERT: A 341 ASP cc_start: 0.7715 (t70) cc_final: 0.7189 (t0) REVERT: B 50 THR cc_start: 0.8441 (m) cc_final: 0.8124 (t) REVERT: B 137 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7756 (ptm160) REVERT: B 155 ASN cc_start: 0.8117 (t0) cc_final: 0.7722 (t0) REVERT: B 170 ASP cc_start: 0.7435 (t70) cc_final: 0.7028 (t0) REVERT: B 230 ASN cc_start: 0.8300 (m110) cc_final: 0.8080 (m-40) REVERT: B 234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: B 290 ASP cc_start: 0.7781 (m-30) cc_final: 0.7561 (m-30) REVERT: B 304 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8016 (ttt-90) REVERT: C 340 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7395 (ttp-170) REVERT: C 391 THR cc_start: 0.8424 (m) cc_final: 0.8187 (m) REVERT: C 414 MET cc_start: 0.7928 (mtp) cc_final: 0.7445 (mpp) REVERT: H 52 SER cc_start: 0.8443 (t) cc_final: 0.8100 (p) REVERT: H 90 ASP cc_start: 0.7828 (m-30) cc_final: 0.7420 (m-30) REVERT: H 192 MET cc_start: 0.7703 (ptm) cc_final: 0.7241 (ptm) outliers start: 11 outliers final: 9 residues processed: 215 average time/residue: 0.0880 time to fit residues: 24.9988 Evaluate side-chains 214 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110528 restraints weight = 12207.070| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.98 r_work: 0.3246 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8936 Z= 0.103 Angle : 0.478 7.611 12123 Z= 0.247 Chirality : 0.040 0.153 1390 Planarity : 0.004 0.046 1528 Dihedral : 3.954 59.531 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 15.02 % Favored : 83.71 % 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 aren not related in a simple way. whole: 1.05 (0.26), residues: 1119 helix: 2.38 (0.26), residues: 408 sheet: 0.14 (0.29), residues: 300 loop : -0.56 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.009 0.001 TYR H 190 PHE 0.039 0.001 PHE H 68 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8935) covalent geometry : angle 0.47816 (12121) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.24307 ( 2) hydrogen bonds : bond 0.03102 ( 427) hydrogen bonds : angle 3.96411 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.65 seconds wall clock time: 33 minutes 29.94 seconds (2009.94 seconds total)