Starting phenix.real_space_refine on Wed Aug 5 13:18:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1r_63580/08_2026/9m1r_63580.cif" } resolution = 2.66 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= 0.090 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 65 5.16 5 C 6265 2.51 5 N 1695 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9870 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2566 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1857 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1737 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2297 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'AKG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 9870 At special positions: 0 Unit cell: (87.74, 124.64, 132.02, 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 65 16.00 O 1845 8.00 N 1695 7.00 C 6265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.24 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: 0.97 Conformation dependent library (CDL) restraints added in 377.0 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 36.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.958A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 16 through 40 removed outlier: 3.635A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.170A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.501A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.665A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.702A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.529A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 29 through 35 Processing helix chain 'R' and resid 35 through 61 Proline residue: R 49 - end of helix Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.747A pdb=" N SER R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.538A pdb=" N LEU R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.608A pdb=" N ARG R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.579A pdb=" N HIS R 145 " --> pdb=" O PHE R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.720A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.852A pdb=" N TRP R 197 " --> pdb=" O ASN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 225 Processing helix chain 'R' and resid 233 through 270 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix removed outlier: 3.798A pdb=" N ALA R 292 " --> pdb=" O ARG R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.521A pdb=" N VAL R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 313 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.517A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.753A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.864A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.862A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.470A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.785A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.755A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.814A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.742A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.530A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.084A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 174 through 175 502 hydrogen bonds defined for protein. 1380 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: 1.57 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1768 1.33 - 1.45: 2660 1.45 - 1.57: 5554 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10072 Sorted by residual: bond pdb=" C ILE R 136 " pdb=" N HIS R 137 " ideal model delta sigma weight residual 1.334 1.380 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" C1 AKG R 401 " pdb=" O2 AKG R 401 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C ILE R 29 " pdb=" N PRO R 30 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.36e-02 5.41e+03 1.12e+01 bond pdb=" C5 AKG R 401 " pdb=" O4 AKG R 401 " ideal model delta sigma weight residual 1.249 1.307 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C ASP A 223 " pdb=" O ASP A 223 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.13e-02 7.83e+03 8.01e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 13079 1.18 - 2.36: 453 2.36 - 3.53: 87 3.53 - 4.71: 28 4.71 - 5.89: 8 Bond angle restraints: 13655 Sorted by residual: angle pdb=" N GLY N 121 " pdb=" CA GLY N 121 " pdb=" C GLY N 121 " ideal model delta sigma weight residual 111.95 114.71 -2.76 9.50e-01 1.11e+00 8.45e+00 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 113.00 109.53 3.47 1.30e+00 5.92e-01 7.11e+00 angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 113.43 110.20 3.23 1.26e+00 6.30e-01 6.56e+00 angle pdb=" CA ASN S 77 " pdb=" C ASN S 77 " pdb=" O ASN S 77 " ideal model delta sigma weight residual 121.84 119.02 2.82 1.16e+00 7.43e-01 5.91e+00 angle pdb=" N GLY B 330 " pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 113.02 109.28 3.74 1.59e+00 3.96e-01 5.53e+00 ... (remaining 13650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5332 17.97 - 35.93: 487 35.93 - 53.90: 123 53.90 - 71.87: 23 71.87 - 89.83: 14 Dihedral angle restraints: 5979 sinusoidal: 2308 harmonic: 3671 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR N 32 " pdb=" C TYR N 32 " pdb=" N LYS N 33 " pdb=" CA LYS N 33 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1198 0.043 - 0.086: 257 0.086 - 0.128: 99 0.128 - 0.171: 4 0.171 - 0.214: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA GLN A 294 " pdb=" N GLN A 294 " pdb=" C GLN A 294 " pdb=" CB GLN A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASP A 223 " pdb=" N ASP A 223 " pdb=" C ASP A 223 " pdb=" CB ASP A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1556 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 101 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO N 102 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO N 102 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 102 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 46 " -0.158 9.50e-02 1.11e+02 7.10e-02 3.71e+00 pdb=" NE ARG B 46 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 46 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 46 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA N 40 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO N 41 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.018 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2066 2.78 - 3.31: 9276 3.31 - 3.84: 16836 3.84 - 4.37: 21012 4.37 - 4.90: 35754 Nonbonded interactions: 84944 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR R 40 " pdb=" O4 AKG R 401 " model vdw 2.247 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.271 3.040 nonbonded pdb=" O ASN N 31 " pdb=" O PRO N 102 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.305 3.040 ... (remaining 84939 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: 1.550 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 10073 Z= 0.204 Angle : 0.556 7.325 13657 Z= 0.308 Chirality : 0.041 0.214 1559 Planarity : 0.004 0.071 1733 Dihedral : 15.540 89.835 3606 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.37 % Allowed : 16.81 % Favored : 82.82 % 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: 1.18 (0.25), residues: 1244 helix: 1.93 (0.26), residues: 406 sheet: 0.24 (0.29), residues: 339 loop : 0.36 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 46 TYR 0.013 0.001 TYR S 103 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (10072) covalent geometry : angle 0.55263 / 0.31 (13655) SS BOND : bond 0.20415 / 10.74 ( 1) SS BOND : angle 5.44267 / 3.17 ( 2) hydrogen bonds : bond 0.17429 / 11.72 ( 502) hydrogen bonds : angle 7.34591 / 5.20 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 201 time to evaluate : 0.446 Fit side-chains REVERT: B 268 ASN cc_start: 0.8296 (m110) cc_final: 0.7957 (m110) REVERT: A 38 ARG cc_start: 0.8230 (tmt170) cc_final: 0.7845 (ttm-80) REVERT: S 65 LYS cc_start: 0.8276 (tptt) cc_final: 0.7979 (ttmt) REVERT: S 244 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7327 (tptp) REVERT: N 108 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7816 (m-80) outliers start: 4 outliers final: 4 residues processed: 204 average time/residue: 0.5577 time to fit residues: 122.0915 Evaluate side-chains 159 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN B 239 ASN S 82 GLN S 186 GLN N 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099597 restraints weight = 12053.170| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.17 r_work: 0.3055 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10073 Z= 0.208 Angle : 0.589 8.152 13657 Z= 0.317 Chirality : 0.045 0.202 1559 Planarity : 0.004 0.051 1733 Dihedral : 5.632 56.251 1387 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.71 % Allowed : 15.69 % Favored : 80.59 % 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: 1.28 (0.25), residues: 1244 helix: 2.22 (0.25), residues: 399 sheet: 0.15 (0.29), residues: 323 loop : 0.36 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.014 0.002 TYR S 190 PHE 0.014 0.002 PHE A 238 TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (10072) covalent geometry : angle 0.58854 / 0.32 (13655) SS BOND : bond 0.00541 / 0.28 ( 1) SS BOND : angle 0.21703 / 0.12 ( 2) hydrogen bonds : bond 0.04693 / 3.16 ( 502) hydrogen bonds : angle 5.19863 / 3.69 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.453 Fit side-chains REVERT: B 42 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7288 (tpt170) REVERT: B 325 MET cc_start: 0.8945 (mmt) cc_final: 0.8588 (mmm) REVERT: A 38 ARG cc_start: 0.8332 (tmt170) cc_final: 0.7186 (ttm-80) REVERT: A 209 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 356 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7778 (mmm160) REVERT: S 157 ILE cc_start: 0.8338 (mm) cc_final: 0.8054 (mp) REVERT: S 244 LYS cc_start: 0.7492 (ttpp) cc_final: 0.6548 (tptp) REVERT: G 20 LYS cc_start: 0.7627 (mtpp) cc_final: 0.7332 (mtmm) REVERT: N 108 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: R 62 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6996 (mtt) REVERT: R 146 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6885 (mtpt) outliers start: 40 outliers final: 16 residues processed: 189 average time/residue: 0.5008 time to fit residues: 101.8780 Evaluate side-chains 162 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 277 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN S 39 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100919 restraints weight = 12023.212| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.18 r_work: 0.3086 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10073 Z= 0.144 Angle : 0.522 6.929 13657 Z= 0.280 Chirality : 0.042 0.173 1559 Planarity : 0.004 0.045 1733 Dihedral : 5.317 56.399 1382 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.53 % Allowed : 17.27 % Favored : 79.20 % 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: 1.25 (0.24), residues: 1244 helix: 2.43 (0.25), residues: 394 sheet: -0.02 (0.28), residues: 328 loop : 0.27 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.018 0.001 TYR R 35 PHE 0.014 0.001 PHE A 212 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10072) covalent geometry : angle 0.52247 / 0.28 (13655) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.18040 / 0.10 ( 2) hydrogen bonds : bond 0.04113 / 2.76 ( 502) hydrogen bonds : angle 4.82462 / 3.42 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7651 (tpt170) cc_final: 0.7372 (tpt170) REVERT: B 44 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: B 134 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.7859 (ptp90) REVERT: B 267 ASP cc_start: 0.8923 (m-30) cc_final: 0.8531 (m-30) REVERT: B 325 MET cc_start: 0.8918 (mmt) cc_final: 0.8587 (mmm) REVERT: A 38 ARG cc_start: 0.8351 (tmt170) cc_final: 0.7177 (ttm-80) REVERT: A 209 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: S 157 ILE cc_start: 0.8335 (mm) cc_final: 0.8126 (mp) REVERT: S 159 CYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8137 (t) REVERT: S 244 LYS cc_start: 0.7511 (ttpp) cc_final: 0.6609 (tptp) REVERT: G 20 LYS cc_start: 0.7488 (mtpp) cc_final: 0.7207 (mtmm) REVERT: G 29 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7392 (tppt) REVERT: G 46 LYS cc_start: 0.8593 (ttmp) cc_final: 0.8156 (tppt) REVERT: N 91 THR cc_start: 0.8695 (t) cc_final: 0.8483 (m) REVERT: N 108 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: R 62 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6846 (mtt) REVERT: R 146 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6901 (mtpt) REVERT: R 311 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7808 (mm110) outliers start: 38 outliers final: 19 residues processed: 176 average time/residue: 0.5047 time to fit residues: 95.2656 Evaluate side-chains 172 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 264 ARG Chi-restraints excluded: chain R residue 277 GLU Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN S 39 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099586 restraints weight = 11755.269| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.25 r_work: 0.3066 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10073 Z= 0.104 Angle : 0.486 6.883 13657 Z= 0.258 Chirality : 0.040 0.149 1559 Planarity : 0.004 0.040 1733 Dihedral : 5.056 56.979 1380 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.09 % Allowed : 17.73 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1244 helix: 2.58 (0.25), residues: 394 sheet: 0.11 (0.28), residues: 321 loop : 0.19 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.014 0.001 TYR S 190 PHE 0.012 0.001 PHE A 212 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10072) covalent geometry : angle 0.48647 / 0.26 (13655) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.35879 / 0.19 ( 2) hydrogen bonds : bond 0.03511 / 2.35 ( 502) hydrogen bonds : angle 4.52589 / 3.19 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.375 Fit side-chains REVERT: B 25 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7074 (t) REVERT: B 42 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7062 (tpt170) REVERT: B 175 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7272 (mm110) REVERT: B 258 ASP cc_start: 0.8304 (t0) cc_final: 0.8060 (t70) REVERT: B 267 ASP cc_start: 0.8899 (m-30) cc_final: 0.8524 (m-30) REVERT: B 325 MET cc_start: 0.8843 (mmt) cc_final: 0.8488 (mmm) REVERT: A 38 ARG cc_start: 0.8298 (tmt170) cc_final: 0.7075 (ttm-80) REVERT: A 209 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 280 ARG cc_start: 0.8361 (tmt170) cc_final: 0.8127 (tmt170) REVERT: S 159 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8103 (t) REVERT: S 244 LYS cc_start: 0.7532 (ttpp) cc_final: 0.6607 (tptp) REVERT: G 20 LYS cc_start: 0.7371 (mtpp) cc_final: 0.7112 (mtmm) REVERT: G 29 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7178 (tppt) REVERT: G 46 LYS cc_start: 0.8568 (ttmp) cc_final: 0.8103 (tppt) REVERT: G 58 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8023 (mt-10) REVERT: N 3 GLN cc_start: 0.7764 (tt0) cc_final: 0.7413 (mm-40) REVERT: N 52 SER cc_start: 0.8693 (m) cc_final: 0.8264 (p) REVERT: N 108 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: R 33 MET cc_start: 0.8105 (ptm) cc_final: 0.7786 (ptt) REVERT: R 62 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6689 (mtt) REVERT: R 146 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6808 (mtpt) REVERT: R 264 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6302 (ttt90) outliers start: 44 outliers final: 20 residues processed: 187 average time/residue: 0.4722 time to fit residues: 94.8021 Evaluate side-chains 182 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 264 ARG Chi-restraints excluded: chain R residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN S 39 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100998 restraints weight = 12122.290| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10073 Z= 0.152 Angle : 0.522 7.889 13657 Z= 0.275 Chirality : 0.042 0.175 1559 Planarity : 0.004 0.041 1733 Dihedral : 5.215 56.089 1380 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.09 % Allowed : 18.57 % Favored : 77.34 % 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: 1.30 (0.24), residues: 1244 helix: 2.62 (0.26), residues: 394 sheet: 0.03 (0.28), residues: 326 loop : 0.14 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.015 0.001 TYR R 35 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10072) covalent geometry : angle 0.52248 / 0.28 (13655) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.15034 / 0.08 ( 2) hydrogen bonds : bond 0.03886 / 2.62 ( 502) hydrogen bonds : angle 4.60256 / 3.27 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.343 Fit side-chains REVERT: B 25 CYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7136 (t) REVERT: B 42 ARG cc_start: 0.7608 (tpt170) cc_final: 0.7229 (tpt170) REVERT: B 134 ARG cc_start: 0.8162 (ptt-90) cc_final: 0.7908 (ptp90) REVERT: B 258 ASP cc_start: 0.8497 (t0) cc_final: 0.8171 (t70) REVERT: B 267 ASP cc_start: 0.8923 (m-30) cc_final: 0.8568 (m-30) REVERT: B 325 MET cc_start: 0.8968 (mmt) cc_final: 0.8667 (mmm) REVERT: A 38 ARG cc_start: 0.8351 (tmt170) cc_final: 0.7183 (ttm-80) REVERT: A 209 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: S 3 GLN cc_start: 0.8063 (tt0) cc_final: 0.7782 (tt0) REVERT: S 159 CYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8170 (t) REVERT: S 244 LYS cc_start: 0.7631 (ttpp) cc_final: 0.6699 (tptp) REVERT: G 20 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7207 (mtmm) REVERT: G 29 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7308 (tppt) REVERT: G 46 LYS cc_start: 0.8605 (ttmp) cc_final: 0.8184 (tppt) REVERT: G 58 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8086 (mt-10) REVERT: R 33 MET cc_start: 0.8202 (ptm) cc_final: 0.7862 (ptt) REVERT: R 62 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6928 (mtt) REVERT: R 146 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6951 (mtpt) REVERT: R 264 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6410 (ttt90) REVERT: R 311 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7837 (mm110) outliers start: 44 outliers final: 23 residues processed: 184 average time/residue: 0.4364 time to fit residues: 86.5562 Evaluate side-chains 180 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 264 ARG Chi-restraints excluded: chain R residue 307 ASP Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 237 ASN S 39 GLN S 82 GLN R 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098726 restraints weight = 11784.770| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.29 r_work: 0.3043 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10073 Z= 0.112 Angle : 0.491 5.941 13657 Z= 0.259 Chirality : 0.041 0.155 1559 Planarity : 0.004 0.038 1733 Dihedral : 4.734 48.614 1378 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.53 % Allowed : 19.68 % Favored : 76.79 % 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: 1.33 (0.24), residues: 1244 helix: 2.67 (0.26), residues: 397 sheet: 0.09 (0.28), residues: 319 loop : 0.10 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.021 0.001 TYR R 35 PHE 0.013 0.001 PHE R 170 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10072) covalent geometry : angle 0.49145 / 0.26 (13655) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.26742 / 0.14 ( 2) hydrogen bonds : bond 0.03525 / 2.36 ( 502) hydrogen bonds : angle 4.46164 / 3.17 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.334 Fit side-chains REVERT: B 25 CYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6968 (t) REVERT: B 42 ARG cc_start: 0.7491 (tpt170) cc_final: 0.7107 (tpt170) REVERT: B 134 ARG cc_start: 0.8140 (ptt-90) cc_final: 0.7911 (ptp90) REVERT: B 170 ASP cc_start: 0.8413 (t70) cc_final: 0.7896 (t70) REVERT: B 175 GLN cc_start: 0.7910 (mm110) cc_final: 0.7406 (mm110) REVERT: B 258 ASP cc_start: 0.8381 (t0) cc_final: 0.8063 (t70) REVERT: B 267 ASP cc_start: 0.8909 (m-30) cc_final: 0.8550 (m-30) REVERT: B 325 MET cc_start: 0.8881 (mmt) cc_final: 0.8574 (mmm) REVERT: A 38 ARG cc_start: 0.8303 (tmt170) cc_final: 0.7109 (ttm-80) REVERT: A 209 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: A 309 GLU cc_start: 0.8236 (mp0) cc_final: 0.8028 (mp0) REVERT: S 3 GLN cc_start: 0.8004 (tt0) cc_final: 0.7734 (tt0) REVERT: S 159 CYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8125 (t) REVERT: S 244 LYS cc_start: 0.7476 (ttpp) cc_final: 0.6561 (tptp) REVERT: G 20 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7045 (mtmm) REVERT: G 29 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7062 (tppt) REVERT: G 46 LYS cc_start: 0.8567 (ttmp) cc_final: 0.8129 (tppt) REVERT: G 58 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7848 (mp0) REVERT: N 52 SER cc_start: 0.8646 (m) cc_final: 0.8209 (p) REVERT: R 33 MET cc_start: 0.8184 (ptm) cc_final: 0.7877 (ptt) REVERT: R 62 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6706 (mtt) REVERT: R 146 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6777 (mtpt) REVERT: R 166 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8284 (mm) REVERT: R 264 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6275 (ttt90) REVERT: R 311 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7841 (mm110) outliers start: 38 outliers final: 22 residues processed: 185 average time/residue: 0.5057 time to fit residues: 100.2967 Evaluate side-chains 183 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 264 ARG Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN S 39 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097793 restraints weight = 11885.776| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.30 r_work: 0.3034 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10073 Z= 0.124 Angle : 0.506 7.591 13657 Z= 0.263 Chirality : 0.041 0.161 1559 Planarity : 0.004 0.038 1733 Dihedral : 4.657 45.672 1378 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.53 % Allowed : 19.87 % Favored : 76.60 % 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: 1.38 (0.24), residues: 1244 helix: 2.77 (0.25), residues: 389 sheet: 0.09 (0.28), residues: 321 loop : 0.13 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.020 0.001 TYR R 35 PHE 0.013 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10072) covalent geometry : angle 0.50601 / 0.26 (13655) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.24594 / 0.13 ( 2) hydrogen bonds : bond 0.03594 / 2.41 ( 502) hydrogen bonds : angle 4.47078 / 3.18 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.320 Fit side-chains REVERT: B 25 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7014 (t) REVERT: B 46 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: B 134 ARG cc_start: 0.8181 (ptt-90) cc_final: 0.7936 (ptp90) REVERT: B 170 ASP cc_start: 0.8442 (t70) cc_final: 0.7914 (t70) REVERT: B 175 GLN cc_start: 0.7951 (mm110) cc_final: 0.7434 (mm110) REVERT: B 258 ASP cc_start: 0.8418 (t0) cc_final: 0.8097 (t70) REVERT: B 267 ASP cc_start: 0.8912 (m-30) cc_final: 0.8564 (m-30) REVERT: B 325 MET cc_start: 0.8925 (mmt) cc_final: 0.8625 (mmm) REVERT: A 38 ARG cc_start: 0.8334 (tmt170) cc_final: 0.7133 (ttm-80) REVERT: A 209 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: A 309 GLU cc_start: 0.8253 (mp0) cc_final: 0.8042 (mp0) REVERT: S 3 GLN cc_start: 0.8042 (tt0) cc_final: 0.7708 (tt0) REVERT: S 159 CYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8144 (t) REVERT: S 202 ARG cc_start: 0.6885 (ptt-90) cc_final: 0.6675 (ptt-90) REVERT: S 244 LYS cc_start: 0.7561 (ttpp) cc_final: 0.6643 (tptp) REVERT: G 20 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7076 (mtmm) REVERT: G 29 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7090 (tppt) REVERT: G 46 LYS cc_start: 0.8580 (ttmp) cc_final: 0.8146 (tppt) REVERT: G 58 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7843 (mp0) REVERT: N 52 SER cc_start: 0.8708 (m) cc_final: 0.8211 (p) REVERT: N 53 GLN cc_start: 0.8083 (mp10) cc_final: 0.7725 (mp10) REVERT: N 76 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8314 (ptpp) REVERT: R 33 MET cc_start: 0.8234 (ptm) cc_final: 0.7874 (ptt) REVERT: R 62 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6786 (mtt) REVERT: R 146 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6834 (mtpt) REVERT: R 166 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8342 (mm) REVERT: R 277 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: R 311 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7825 (mm110) outliers start: 38 outliers final: 23 residues processed: 179 average time/residue: 0.5148 time to fit residues: 98.8668 Evaluate side-chains 185 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 277 GLU Chi-restraints excluded: chain R residue 311 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 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 = 0.3719 r_free = 0.3719 target = 0.144222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101629 restraints weight = 11958.100| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.16 r_work: 0.3090 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10073 Z= 0.143 Angle : 0.521 6.880 13657 Z= 0.272 Chirality : 0.042 0.236 1559 Planarity : 0.004 0.045 1733 Dihedral : 4.719 50.648 1378 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.71 % Allowed : 19.50 % Favored : 76.79 % 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: 1.32 (0.24), residues: 1244 helix: 2.64 (0.25), residues: 397 sheet: 0.04 (0.28), residues: 326 loop : 0.13 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 264 TYR 0.019 0.001 TYR R 35 PHE 0.013 0.001 PHE A 212 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10072) covalent geometry : angle 0.52096 / 0.27 (13655) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.25813 / 0.14 ( 2) hydrogen bonds : bond 0.03716 / 2.50 ( 502) hydrogen bonds : angle 4.53576 / 3.23 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.321 Fit side-chains REVERT: B 25 CYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7173 (t) REVERT: B 175 GLN cc_start: 0.8031 (mm110) cc_final: 0.7682 (mm-40) REVERT: B 258 ASP cc_start: 0.8510 (t0) cc_final: 0.8162 (t70) REVERT: B 267 ASP cc_start: 0.8914 (m-30) cc_final: 0.8574 (m-30) REVERT: B 325 MET cc_start: 0.8944 (mmt) cc_final: 0.8650 (mmm) REVERT: A 38 ARG cc_start: 0.8374 (tmt170) cc_final: 0.7205 (ttm-80) REVERT: A 209 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: A 365 CYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7543 (t) REVERT: S 3 GLN cc_start: 0.8091 (tt0) cc_final: 0.7760 (tt0) REVERT: S 159 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8201 (t) REVERT: S 244 LYS cc_start: 0.7653 (ttpp) cc_final: 0.6729 (tptp) REVERT: G 20 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7172 (mtmm) REVERT: G 29 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7244 (tppt) REVERT: G 46 LYS cc_start: 0.8569 (ttmp) cc_final: 0.8195 (tppt) REVERT: G 58 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: N 53 GLN cc_start: 0.8159 (mp10) cc_final: 0.7785 (mp10) REVERT: N 76 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8382 (ptpp) REVERT: R 62 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6859 (mtt) REVERT: R 146 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6994 (mtpt) REVERT: R 166 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (mm) REVERT: R 277 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7471 (tm-30) outliers start: 40 outliers final: 24 residues processed: 179 average time/residue: 0.4933 time to fit residues: 94.5790 Evaluate side-chains 182 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 277 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100751 restraints weight = 11780.354| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3081 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10073 Z= 0.097 Angle : 0.489 8.386 13657 Z= 0.252 Chirality : 0.040 0.142 1559 Planarity : 0.004 0.040 1733 Dihedral : 4.472 54.055 1378 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.60 % Allowed : 20.80 % Favored : 76.60 % 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: 1.46 (0.24), residues: 1244 helix: 2.82 (0.26), residues: 392 sheet: 0.18 (0.28), residues: 319 loop : 0.14 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.016 0.001 TYR N 95 PHE 0.012 0.001 PHE A 212 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (10072) covalent geometry : angle 0.48874 / 0.25 (13655) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.33977 / 0.19 ( 2) hydrogen bonds : bond 0.03274 / 2.19 ( 502) hydrogen bonds : angle 4.36248 / 3.10 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.389 Fit side-chains REVERT: B 25 CYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6992 (t) REVERT: B 170 ASP cc_start: 0.8348 (t70) cc_final: 0.7869 (t70) REVERT: B 175 GLN cc_start: 0.7855 (mm110) cc_final: 0.7291 (mm110) REVERT: B 258 ASP cc_start: 0.8317 (t0) cc_final: 0.8045 (t70) REVERT: B 267 ASP cc_start: 0.8900 (m-30) cc_final: 0.8569 (m-30) REVERT: B 325 MET cc_start: 0.8888 (mmt) cc_final: 0.8542 (mmm) REVERT: A 38 ARG cc_start: 0.8300 (tmt170) cc_final: 0.7093 (ttm-80) REVERT: A 209 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: A 309 GLU cc_start: 0.8256 (mp0) cc_final: 0.8047 (mp0) REVERT: S 159 CYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8148 (t) REVERT: S 244 LYS cc_start: 0.7494 (ttpp) cc_final: 0.6597 (tptp) REVERT: G 20 LYS cc_start: 0.7295 (mtpp) cc_final: 0.7049 (mtmm) REVERT: G 29 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7062 (tppt) REVERT: G 46 LYS cc_start: 0.8535 (ttmp) cc_final: 0.8135 (tppt) REVERT: G 58 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7804 (mp0) REVERT: N 52 SER cc_start: 0.8650 (m) cc_final: 0.8164 (p) REVERT: N 53 GLN cc_start: 0.8045 (mp10) cc_final: 0.7721 (mp10) REVERT: N 76 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8301 (ptpp) REVERT: R 33 MET cc_start: 0.8207 (ptm) cc_final: 0.7948 (ptt) REVERT: R 62 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6513 (mtt) REVERT: R 166 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8291 (mm) REVERT: R 277 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7363 (tm-30) outliers start: 28 outliers final: 19 residues processed: 175 average time/residue: 0.4953 time to fit residues: 93.0766 Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 168 MET Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN S 39 GLN S 82 GLN R 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.145256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102776 restraints weight = 11946.716| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10073 Z= 0.124 Angle : 0.518 8.976 13657 Z= 0.266 Chirality : 0.041 0.156 1559 Planarity : 0.004 0.037 1733 Dihedral : 4.575 56.328 1378 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.88 % Allowed : 20.71 % Favored : 76.42 % 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: 1.42 (0.24), residues: 1244 helix: 2.82 (0.26), residues: 392 sheet: 0.07 (0.28), residues: 326 loop : 0.15 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.017 0.001 TYR N 95 PHE 0.014 0.001 PHE R 170 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10072) covalent geometry : angle 0.51797 / 0.27 (13655) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.29958 / 0.17 ( 2) hydrogen bonds : bond 0.03499 / 2.35 ( 502) hydrogen bonds : angle 4.43700 / 3.16 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.312 Fit side-chains REVERT: B 25 CYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7188 (t) REVERT: B 46 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7950 (mtp85) REVERT: B 170 ASP cc_start: 0.8450 (t70) cc_final: 0.7998 (t70) REVERT: B 175 GLN cc_start: 0.7961 (mm110) cc_final: 0.7398 (mm110) REVERT: B 258 ASP cc_start: 0.8444 (t0) cc_final: 0.8149 (t70) REVERT: B 267 ASP cc_start: 0.8910 (m-30) cc_final: 0.8563 (m-30) REVERT: B 325 MET cc_start: 0.8967 (mmt) cc_final: 0.8690 (mmm) REVERT: A 38 ARG cc_start: 0.8369 (tmt170) cc_final: 0.7208 (ttm-80) REVERT: A 209 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: S 3 GLN cc_start: 0.8074 (tt0) cc_final: 0.7676 (tt0) REVERT: S 18 ARG cc_start: 0.7317 (tpp-160) cc_final: 0.7096 (tpp-160) REVERT: S 159 CYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8209 (t) REVERT: S 244 LYS cc_start: 0.7663 (ttpp) cc_final: 0.6742 (tptp) REVERT: G 20 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7237 (mtmm) REVERT: G 29 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7262 (tppt) REVERT: G 46 LYS cc_start: 0.8557 (ttmp) cc_final: 0.8192 (tppt) REVERT: G 58 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7952 (mp0) REVERT: N 52 SER cc_start: 0.8728 (m) cc_final: 0.8291 (p) REVERT: N 53 GLN cc_start: 0.8132 (mp10) cc_final: 0.7779 (mp10) REVERT: N 76 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8412 (ptpp) REVERT: R 33 MET cc_start: 0.8299 (ptm) cc_final: 0.8031 (ptt) REVERT: R 62 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6724 (mtt) REVERT: R 166 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8371 (mm) REVERT: R 263 ILE cc_start: 0.8976 (mm) cc_final: 0.8746 (mt) REVERT: R 277 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7399 (tm-30) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.5079 time to fit residues: 92.4064 Evaluate side-chains 177 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 88 optimal weight: 0.0370 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN S 39 GLN S 82 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102330 restraints weight = 11816.669| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.25 r_work: 0.3092 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10073 Z= 0.101 Angle : 0.507 9.061 13657 Z= 0.258 Chirality : 0.041 0.141 1559 Planarity : 0.004 0.038 1733 Dihedral : 4.470 59.740 1378 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.69 % Allowed : 21.36 % Favored : 75.95 % 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: 1.47 (0.24), residues: 1244 helix: 2.84 (0.26), residues: 392 sheet: 0.17 (0.28), residues: 319 loop : 0.15 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 202 TYR 0.018 0.001 TYR R 40 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (10072) covalent geometry : angle 0.50710 / 0.26 (13655) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.32455 / 0.18 ( 2) hydrogen bonds : bond 0.03286 / 2.20 ( 502) hydrogen bonds : angle 4.35936 / 3.10 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3691.62 seconds wall clock time: 63 minutes 35.90 seconds (3815.90 seconds total)