Starting phenix.real_space_refine on Sun May 3 00:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n04_48774/05_2026/9n04_48774.map" } resolution = 2.3 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= 0.001 sd= 0.149 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 57 5.16 5 C 5945 2.51 5 N 1648 2.21 5 O 1754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9404 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1930 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3196 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9404 At special positions: 0 Unit cell: (80.75, 100.3, 173.4, 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 57 16.00 O 1754 8.00 N 1648 7.00 C 5945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 281.9 milliseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2210 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.505A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.699A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.639A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.541A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.594A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.840A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.577A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 27 through 49 removed outlier: 3.770A pdb=" N SER R 48 " --> pdb=" O HIS R 44 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.558A pdb=" N GLU R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS R 136 " --> pdb=" O LYS R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 171 through 203 Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 221 through 254 Processing helix chain 'R' and resid 263 through 273 Processing helix chain 'R' and resid 273 through 290 removed outlier: 3.702A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 336 removed outlier: 3.685A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.735A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 359 removed outlier: 3.852A pdb=" N PHE R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 360 through 364 removed outlier: 3.513A pdb=" N VAL R 363 " --> pdb=" O VAL R 360 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL R 364 " --> pdb=" O HIS R 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 360 through 364' Processing helix chain 'R' and resid 375 through 401 removed outlier: 4.412A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.992A pdb=" N ASN P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.574A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.589A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.739A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.815A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.603A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.515A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.554A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.843A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.810A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 57 through 58 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 80 removed outlier: 3.934A pdb=" N THR R 75 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS R 100 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA R 77 " --> pdb=" O LYS R 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS R 98 " --> pdb=" O ALA R 77 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1419 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: 1.44 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1526 1.29 - 1.42: 2617 1.42 - 1.55: 5362 1.55 - 1.69: 0 1.69 - 1.82: 79 Bond restraints: 9584 Sorted by residual: bond pdb=" C TYR R 239 " pdb=" O TYR R 239 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.26e-02 6.30e+03 3.68e+01 bond pdb=" CA SER P 2 " pdb=" CB SER P 2 " ideal model delta sigma weight residual 1.532 1.472 0.059 1.65e-02 3.67e+03 1.29e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.04e-02 9.25e+03 1.22e+01 bond pdb=" C VAL B 307 " pdb=" O VAL B 307 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" N SER A 366 " pdb=" CA SER A 366 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.04e+01 ... (remaining 9579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12650 2.00 - 4.00: 300 4.00 - 6.00: 27 6.00 - 8.00: 1 8.00 - 10.00: 2 Bond angle restraints: 12980 Sorted by residual: angle pdb=" C HIS B 311 " pdb=" CA HIS B 311 " pdb=" CB HIS B 311 " ideal model delta sigma weight residual 109.50 118.51 -9.01 1.69e+00 3.50e-01 2.84e+01 angle pdb=" C HIS P 1 " pdb=" CA HIS P 1 " pdb=" CB HIS P 1 " ideal model delta sigma weight residual 110.10 120.10 -10.00 1.90e+00 2.77e-01 2.77e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 112.43 107.64 4.79 9.20e-01 1.18e+00 2.71e+01 angle pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 113.80 118.75 -4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" N TYR A 253 " pdb=" CA TYR A 253 " pdb=" C TYR A 253 " ideal model delta sigma weight residual 113.38 107.55 5.83 1.23e+00 6.61e-01 2.25e+01 ... (remaining 12975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5194 17.41 - 34.82: 388 34.82 - 52.23: 74 52.23 - 69.63: 18 69.63 - 87.04: 8 Dihedral angle restraints: 5682 sinusoidal: 2262 harmonic: 3420 Sorted by residual: dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -151.82 65.82 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -155.76 -24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual 180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1113 0.047 - 0.094: 219 0.094 - 0.141: 73 0.141 - 0.188: 17 0.188 - 0.235: 3 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA GLU B 215 " pdb=" N GLU B 215 " pdb=" C GLU B 215 " pdb=" CB GLU B 215 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE R 206 " pdb=" N ILE R 206 " pdb=" C ILE R 206 " pdb=" CB ILE R 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA VAL A 367 " pdb=" N VAL A 367 " pdb=" C VAL A 367 " pdb=" CB VAL A 367 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1422 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 215 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C GLU B 215 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU B 215 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY B 216 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " 0.287 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG B 314 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 220 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C ALA R 220 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 220 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL R 221 " -0.016 2.00e-02 2.50e+03 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 80 2.63 - 3.20: 8025 3.20 - 3.76: 14668 3.76 - 4.33: 21267 4.33 - 4.90: 34343 Nonbonded interactions: 78383 Sorted by model distance: nonbonded pdb=" O HOH R 515 " pdb=" O HOH R 519 " model vdw 2.061 3.040 nonbonded pdb=" O HOH R 512 " pdb=" O HOH R 520 " model vdw 2.173 3.040 nonbonded pdb=" O GLY N 8 " pdb=" OG1 THR N 122 " model vdw 2.293 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.307 3.120 nonbonded pdb=" O GLY A 355 " pdb=" NH2 ARG A 389 " model vdw 2.341 3.120 ... (remaining 78378 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=0.00 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: 1.970 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.040 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 9591 Z= 0.350 Angle : 0.652 10.004 12992 Z= 0.437 Chirality : 0.045 0.235 1425 Planarity : 0.005 0.129 1662 Dihedral : 12.982 87.042 3454 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.38 % Favored : 98.54 % Rotamer: Outliers : 0.20 % Allowed : 0.99 % Favored : 98.81 % Cbeta Deviations : 0.09 % 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: 1163 helix: 1.95 (0.23), residues: 470 sheet: 1.16 (0.32), residues: 240 loop : -0.11 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.009 0.001 TYR N 115 PHE 0.018 0.001 PHE R 384 TRP 0.013 0.001 TRP A 234 HIS 0.011 0.001 HIS P 1 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9584) covalent geometry : angle 0.65110 (12980) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.48326 ( 12) hydrogen bonds : bond 0.20623 ( 496) hydrogen bonds : angle 6.28791 ( 1419) Misc. bond : bond 0.18512 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.371 Fit side-chains REVERT: R 134 VAL cc_start: 0.7617 (m) cc_final: 0.7349 (p) REVERT: R 136 LYS cc_start: 0.6973 (mtmt) cc_final: 0.6646 (tttm) REVERT: R 344 LYS cc_start: 0.6846 (mttp) cc_final: 0.6575 (mmtt) outliers start: 2 outliers final: 1 residues processed: 167 average time/residue: 0.7181 time to fit residues: 126.6660 Evaluate side-chains 135 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 230 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 268 ASN G 18 GLN G 59 ASN R 174 ASN R 298 ASN P 17 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145819 restraints weight = 8445.582| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.68 r_work: 0.3457 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9591 Z= 0.115 Angle : 0.497 8.330 12992 Z= 0.273 Chirality : 0.040 0.153 1425 Planarity : 0.003 0.045 1662 Dihedral : 4.379 50.150 1286 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.49 % Allowed : 6.84 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1163 helix: 2.70 (0.23), residues: 476 sheet: 1.15 (0.32), residues: 234 loop : -0.19 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.033 0.001 TYR R 145 PHE 0.017 0.001 PHE R 384 TRP 0.017 0.001 TRP B 297 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9584) covalent geometry : angle 0.49639 (12980) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.92969 ( 12) hydrogen bonds : bond 0.05607 ( 496) hydrogen bonds : angle 4.52154 ( 1419) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.335 Fit side-chains REVERT: A 209 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.6642 (tp30) REVERT: R 64 LYS cc_start: 0.5185 (mmtm) cc_final: 0.4692 (mttt) REVERT: R 136 LYS cc_start: 0.7310 (mtmt) cc_final: 0.6752 (tttp) REVERT: R 137 MET cc_start: 0.7872 (tmm) cc_final: 0.7477 (tmm) REVERT: R 260 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6174 (mt-10) REVERT: R 324 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7381 (mpp-170) REVERT: R 344 LYS cc_start: 0.6860 (mttp) cc_final: 0.6188 (mmtt) outliers start: 15 outliers final: 5 residues processed: 153 average time/residue: 0.7483 time to fit residues: 120.7889 Evaluate side-chains 142 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN G 59 ASN R 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.191445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137645 restraints weight = 8287.402| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.77 r_work: 0.3340 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9591 Z= 0.176 Angle : 0.598 10.183 12992 Z= 0.325 Chirality : 0.044 0.185 1425 Planarity : 0.004 0.048 1662 Dihedral : 4.577 20.610 1284 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 8.92 % Favored : 89.10 % 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: 1.69 (0.24), residues: 1163 helix: 2.54 (0.23), residues: 477 sheet: 0.88 (0.32), residues: 238 loop : -0.30 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.032 0.002 TYR R 145 PHE 0.020 0.002 PHE R 384 TRP 0.016 0.002 TRP A 234 HIS 0.013 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9584) covalent geometry : angle 0.59691 (12980) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.19264 ( 12) hydrogen bonds : bond 0.06344 ( 496) hydrogen bonds : angle 4.67935 ( 1419) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.362 Fit side-chains REVERT: A 21 GLU cc_start: 0.7512 (pt0) cc_final: 0.6871 (mm-30) REVERT: A 32 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7444 (mttm) REVERT: B 38 ASP cc_start: 0.7786 (m-30) cc_final: 0.7313 (t70) REVERT: B 217 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7993 (pmm) REVERT: N 3 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7291 (mm110) REVERT: R 64 LYS cc_start: 0.5097 (mmtm) cc_final: 0.4569 (mttt) REVERT: R 136 LYS cc_start: 0.7438 (mtmt) cc_final: 0.6674 (tppp) REVERT: R 260 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6348 (mt-10) REVERT: R 276 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6764 (mmm) REVERT: R 344 LYS cc_start: 0.6905 (mttp) cc_final: 0.6172 (mmtt) REVERT: P 17 GLN cc_start: 0.7727 (mm110) cc_final: 0.7497 (mm-40) outliers start: 20 outliers final: 7 residues processed: 151 average time/residue: 0.7131 time to fit residues: 113.8745 Evaluate side-chains 150 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 292 ASN B 75 GLN B 268 ASN B 340 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139962 restraints weight = 8383.825| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.70 r_work: 0.3395 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9591 Z= 0.125 Angle : 0.510 10.983 12992 Z= 0.277 Chirality : 0.041 0.153 1425 Planarity : 0.003 0.050 1662 Dihedral : 4.307 20.264 1284 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.78 % Allowed : 10.31 % Favored : 87.91 % 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: 1.76 (0.24), residues: 1163 helix: 2.69 (0.23), residues: 476 sheet: 0.84 (0.32), residues: 244 loop : -0.34 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.027 0.002 TYR R 145 PHE 0.016 0.002 PHE R 384 TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9584) covalent geometry : angle 0.50937 (12980) SS BOND : bond 0.00313 ( 6) SS BOND : angle 0.90688 ( 12) hydrogen bonds : bond 0.05296 ( 496) hydrogen bonds : angle 4.38128 ( 1419) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.363 Fit side-chains REVERT: B 38 ASP cc_start: 0.7728 (m-30) cc_final: 0.7291 (t70) REVERT: B 46 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7196 (mmp-170) REVERT: N 3 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7313 (mm110) REVERT: N 120 GLN cc_start: 0.7659 (mp10) cc_final: 0.7215 (pp30) REVERT: R 64 LYS cc_start: 0.5030 (mmtm) cc_final: 0.4504 (mttt) REVERT: R 136 LYS cc_start: 0.7467 (mtmt) cc_final: 0.6746 (tppp) REVERT: R 137 MET cc_start: 0.7936 (tmm) cc_final: 0.7620 (tmm) REVERT: R 276 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6755 (mmm) REVERT: R 290 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6187 (mt-10) REVERT: R 344 LYS cc_start: 0.6967 (mttp) cc_final: 0.6233 (mmtt) REVERT: P 17 GLN cc_start: 0.7693 (mm110) cc_final: 0.7451 (mm-40) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.7019 time to fit residues: 107.7599 Evaluate side-chains 146 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN B 340 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.190666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136191 restraints weight = 8358.974| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.80 r_work: 0.3344 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9591 Z= 0.176 Angle : 0.587 11.423 12992 Z= 0.318 Chirality : 0.044 0.170 1425 Planarity : 0.004 0.049 1662 Dihedral : 4.586 20.731 1284 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 10.60 % Favored : 86.92 % 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: 1.61 (0.24), residues: 1163 helix: 2.52 (0.23), residues: 476 sheet: 0.78 (0.32), residues: 243 loop : -0.39 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.026 0.002 TYR R 145 PHE 0.019 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9584) covalent geometry : angle 0.58600 (12980) SS BOND : bond 0.00467 ( 6) SS BOND : angle 1.08353 ( 12) hydrogen bonds : bond 0.05998 ( 496) hydrogen bonds : angle 4.54346 ( 1419) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.312 Fit side-chains REVERT: A 32 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7396 (mttm) REVERT: B 38 ASP cc_start: 0.7756 (m-30) cc_final: 0.7303 (t70) REVERT: B 134 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6804 (ppt170) REVERT: N 3 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7277 (mm110) REVERT: R 64 LYS cc_start: 0.5041 (mmtm) cc_final: 0.4482 (mttt) REVERT: R 136 LYS cc_start: 0.7475 (mtmt) cc_final: 0.6646 (tppp) REVERT: R 137 MET cc_start: 0.7798 (tmm) cc_final: 0.7452 (tmm) REVERT: R 276 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6777 (mmm) REVERT: R 290 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6330 (mt-10) REVERT: R 344 LYS cc_start: 0.6995 (mttp) cc_final: 0.6282 (mmtt) REVERT: P 17 GLN cc_start: 0.7660 (mm110) cc_final: 0.7411 (mm-40) outliers start: 25 outliers final: 11 residues processed: 147 average time/residue: 0.7033 time to fit residues: 109.2395 Evaluate side-chains 146 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN B 340 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.197997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144978 restraints weight = 8378.378| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.92 r_work: 0.3565 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9591 Z= 0.117 Angle : 0.503 11.233 12992 Z= 0.272 Chirality : 0.040 0.155 1425 Planarity : 0.003 0.051 1662 Dihedral : 4.275 20.634 1284 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.59 % Allowed : 11.50 % Favored : 86.92 % 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: 1.70 (0.24), residues: 1163 helix: 2.72 (0.23), residues: 476 sheet: 0.74 (0.31), residues: 244 loop : -0.43 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.023 0.001 TYR R 145 PHE 0.015 0.001 PHE R 384 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9584) covalent geometry : angle 0.50273 (12980) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.82639 ( 12) hydrogen bonds : bond 0.05068 ( 496) hydrogen bonds : angle 4.25844 ( 1419) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.374 Fit side-chains REVERT: B 33 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6921 (mt) REVERT: B 38 ASP cc_start: 0.7799 (m-30) cc_final: 0.7338 (t70) REVERT: N 3 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7215 (mm110) REVERT: N 120 GLN cc_start: 0.7676 (mp10) cc_final: 0.7164 (pp30) REVERT: R 64 LYS cc_start: 0.4852 (mmtm) cc_final: 0.4315 (mttt) REVERT: R 136 LYS cc_start: 0.7438 (mtmt) cc_final: 0.6643 (tppp) REVERT: R 157 LEU cc_start: 0.7583 (mt) cc_final: 0.7204 (mm) REVERT: R 276 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6807 (mmm) REVERT: R 290 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6285 (mt-10) REVERT: R 344 LYS cc_start: 0.6879 (mttp) cc_final: 0.6139 (mmtt) REVERT: P 17 GLN cc_start: 0.7700 (mm110) cc_final: 0.7455 (mm-40) outliers start: 16 outliers final: 7 residues processed: 149 average time/residue: 0.7170 time to fit residues: 113.0046 Evaluate side-chains 145 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN B 340 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.200213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147712 restraints weight = 8444.534| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.92 r_work: 0.3598 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9591 Z= 0.099 Angle : 0.472 11.481 12992 Z= 0.253 Chirality : 0.039 0.151 1425 Planarity : 0.003 0.051 1662 Dihedral : 3.969 20.219 1284 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.78 % Allowed : 11.69 % Favored : 86.52 % 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: 1.89 (0.24), residues: 1163 helix: 2.92 (0.23), residues: 476 sheet: 0.91 (0.32), residues: 222 loop : -0.36 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.022 0.001 TYR R 145 PHE 0.014 0.001 PHE R 384 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 9584) covalent geometry : angle 0.47190 (12980) SS BOND : bond 0.00233 ( 6) SS BOND : angle 0.72060 ( 12) hydrogen bonds : bond 0.04415 ( 496) hydrogen bonds : angle 4.02329 ( 1419) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.374 Fit side-chains REVERT: A 32 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7243 (mttm) REVERT: B 38 ASP cc_start: 0.7730 (m-30) cc_final: 0.7297 (t70) REVERT: B 134 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6724 (ppt170) REVERT: B 217 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8032 (pmt) REVERT: N 120 GLN cc_start: 0.7583 (mp10) cc_final: 0.7073 (pp30) REVERT: R 64 LYS cc_start: 0.4889 (mmtm) cc_final: 0.4391 (mttt) REVERT: R 136 LYS cc_start: 0.7352 (mtmt) cc_final: 0.6591 (tppp) REVERT: R 137 MET cc_start: 0.7732 (tmm) cc_final: 0.7467 (tmm) REVERT: R 157 LEU cc_start: 0.7414 (mt) cc_final: 0.7047 (mm) REVERT: R 344 LYS cc_start: 0.6922 (mttp) cc_final: 0.6166 (mmtt) REVERT: P 17 GLN cc_start: 0.7675 (mm110) cc_final: 0.7427 (mm-40) outliers start: 18 outliers final: 5 residues processed: 149 average time/residue: 0.7144 time to fit residues: 112.6564 Evaluate side-chains 145 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 324 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 99 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.194616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141589 restraints weight = 8263.078| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.90 r_work: 0.3526 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9591 Z= 0.204 Angle : 0.633 12.311 12992 Z= 0.341 Chirality : 0.045 0.205 1425 Planarity : 0.004 0.048 1662 Dihedral : 4.642 20.797 1284 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 12.09 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1163 helix: 2.56 (0.23), residues: 476 sheet: 0.74 (0.32), residues: 232 loop : -0.46 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.025 0.003 TYR R 145 PHE 0.021 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS R 250 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9584) covalent geometry : angle 0.63271 (12980) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.14322 ( 12) hydrogen bonds : bond 0.06182 ( 496) hydrogen bonds : angle 4.52771 ( 1419) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.389 Fit side-chains REVERT: A 32 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7479 (mttm) REVERT: B 38 ASP cc_start: 0.7841 (m-30) cc_final: 0.7379 (t70) REVERT: B 134 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6809 (ppt170) REVERT: N 3 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7259 (mm110) REVERT: R 136 LYS cc_start: 0.7420 (mtmt) cc_final: 0.6482 (tppp) REVERT: R 157 LEU cc_start: 0.7542 (mt) cc_final: 0.7174 (mm) REVERT: R 218 ASP cc_start: 0.6366 (m-30) cc_final: 0.4870 (t70) REVERT: R 276 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6821 (mmm) REVERT: R 344 LYS cc_start: 0.6901 (mttp) cc_final: 0.6145 (mmtt) REVERT: P 17 GLN cc_start: 0.7691 (mm110) cc_final: 0.7453 (mm-40) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 0.7170 time to fit residues: 109.9083 Evaluate side-chains 147 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN G 59 ASN R 174 ASN R 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.197698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145290 restraints weight = 8321.465| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.93 r_work: 0.3567 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9591 Z= 0.117 Angle : 0.517 12.024 12992 Z= 0.278 Chirality : 0.040 0.154 1425 Planarity : 0.003 0.051 1662 Dihedral : 4.255 20.981 1284 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.83 % 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: 1.70 (0.24), residues: 1163 helix: 2.74 (0.23), residues: 476 sheet: 0.72 (0.32), residues: 233 loop : -0.42 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.023 0.001 TYR R 145 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9584) covalent geometry : angle 0.51714 (12980) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.80472 ( 12) hydrogen bonds : bond 0.04923 ( 496) hydrogen bonds : angle 4.24035 ( 1419) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.414 Fit side-chains REVERT: A 32 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7323 (mttm) REVERT: B 38 ASP cc_start: 0.7797 (m-30) cc_final: 0.7341 (t70) REVERT: B 134 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6719 (ppt170) REVERT: R 136 LYS cc_start: 0.7327 (mtmt) cc_final: 0.6536 (tppp) REVERT: R 157 LEU cc_start: 0.7397 (mt) cc_final: 0.7053 (mm) REVERT: R 218 ASP cc_start: 0.6350 (m-30) cc_final: 0.4824 (t70) REVERT: R 344 LYS cc_start: 0.7042 (mttp) cc_final: 0.6270 (mmtt) REVERT: R 412 ARG cc_start: 0.5733 (mmm160) cc_final: 0.5149 (mtm180) REVERT: P 17 GLN cc_start: 0.7698 (mm110) cc_final: 0.7443 (mm-40) outliers start: 15 outliers final: 9 residues processed: 141 average time/residue: 0.7422 time to fit residues: 110.5831 Evaluate side-chains 142 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 92 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN G 18 GLN R 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.197771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145210 restraints weight = 8347.200| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.93 r_work: 0.3567 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9591 Z= 0.118 Angle : 0.522 12.113 12992 Z= 0.278 Chirality : 0.040 0.154 1425 Planarity : 0.004 0.052 1662 Dihedral : 4.212 20.626 1284 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.29 % Allowed : 12.98 % Favored : 85.73 % 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: 1.76 (0.24), residues: 1163 helix: 2.82 (0.23), residues: 477 sheet: 0.73 (0.32), residues: 233 loop : -0.40 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE R 384 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9584) covalent geometry : angle 0.52168 (12980) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.79441 ( 12) hydrogen bonds : bond 0.04889 ( 496) hydrogen bonds : angle 4.22119 ( 1419) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.323 Fit side-chains REVERT: A 32 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7324 (mttm) REVERT: B 38 ASP cc_start: 0.7803 (m-30) cc_final: 0.7352 (t70) REVERT: B 134 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6790 (ppt170) REVERT: R 136 LYS cc_start: 0.7352 (mtmt) cc_final: 0.6543 (tppp) REVERT: R 157 LEU cc_start: 0.7399 (mt) cc_final: 0.7045 (mm) REVERT: R 218 ASP cc_start: 0.6371 (m-30) cc_final: 0.4847 (t70) REVERT: R 344 LYS cc_start: 0.7046 (mttp) cc_final: 0.6285 (mmtt) REVERT: R 412 ARG cc_start: 0.5772 (mmm160) cc_final: 0.5182 (mtm180) REVERT: P 17 GLN cc_start: 0.7703 (mm110) cc_final: 0.7451 (mm-40) outliers start: 13 outliers final: 8 residues processed: 142 average time/residue: 0.7203 time to fit residues: 108.2457 Evaluate side-chains 142 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 362 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.0060 chunk 19 optimal weight: 10.0000 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 268 ASN G 18 GLN R 174 ASN R 404 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.197901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139468 restraints weight = 8283.133| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.65 r_work: 0.3585 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 9591 Z= 0.162 Angle : 0.844 59.196 12992 Z= 0.496 Chirality : 0.040 0.274 1425 Planarity : 0.004 0.052 1662 Dihedral : 4.297 32.763 1284 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.29 % Allowed : 12.88 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.77 (0.24), residues: 1163 helix: 2.83 (0.23), residues: 477 sheet: 0.74 (0.32), residues: 233 loop : -0.41 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE R 384 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9584) covalent geometry : angle 0.84415 (12980) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.78026 ( 12) hydrogen bonds : bond 0.04865 ( 496) hydrogen bonds : angle 4.22148 ( 1419) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5205.72 seconds wall clock time: 89 minutes 0.95 seconds (5340.95 seconds total)