Starting phenix.real_space_refine on Wed Aug 5 19:04:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hr5_52355/08_2026/9hr5_52355.map" } resolution = 3.26 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 42 5.16 5 C 6851 2.51 5 N 1854 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 10987 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3051 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 365} Chain breaks: 1 Chain: "B" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2691 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3102 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 371} Chain: "D" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Time building chain proxies: 2.44, per 1000 atoms: 0.22 Number of scatterers: 10987 At special positions: 0 Unit cell: (119.79, 84.942, 129.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 44 15.00 O 2196 8.00 N 1854 7.00 C 6851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.57 Conformation dependent library (CDL) restraints added in 227.8 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2426 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 4 sheets defined 68.1% alpha, 1.8% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 18 through 38 removed outlier: 3.667A pdb=" N GLY A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.786A pdb=" N LYS A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 143 Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.013A pdb=" N ASP A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.118A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 181 Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.649A pdb=" N GLU A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 228 removed outlier: 3.538A pdb=" N CYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.665A pdb=" N GLN A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 290 through 311 removed outlier: 3.606A pdb=" N THR A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.569A pdb=" N LYS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 4.065A pdb=" N ALA A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.763A pdb=" N SER A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 4.096A pdb=" N LYS A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 38 removed outlier: 3.697A pdb=" N THR B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.565A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 127 through 144 removed outlier: 3.600A pdb=" N GLY B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.827A pdb=" N ASP B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.951A pdb=" N TYR B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.694A pdb=" N CYS B 179 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 Processing helix chain 'B' and resid 207 through 229 removed outlier: 3.564A pdb=" N ALA B 229 " --> pdb=" O MET B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.624A pdb=" N THR B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.706A pdb=" N GLN B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.566A pdb=" N ALA B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 341 removed outlier: 3.634A pdb=" N ARG B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.674A pdb=" N LYS B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 403 " --> pdb=" O ASN B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 39 removed outlier: 3.852A pdb=" N GLY C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 29 " --> pdb=" O TYR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.505A pdb=" N TRP C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 127 through 144 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.509A pdb=" N ILE C 155 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 168 removed outlier: 4.313A pdb=" N LYS C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 180 Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.628A pdb=" N ALA C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 201 " --> pdb=" O CYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 228 removed outlier: 4.173A pdb=" N ASN C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 252 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.839A pdb=" N GLN C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.653A pdb=" N ILE C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 311 Processing helix chain 'C' and resid 315 through 341 removed outlier: 3.560A pdb=" N ILE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 392 through 401 Processing helix chain 'D' and resid 266 through 272 removed outlier: 4.150A pdb=" N GLN D 270 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 282 removed outlier: 3.515A pdb=" N GLN D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 287 through 312 Processing helix chain 'D' and resid 315 through 341 removed outlier: 3.900A pdb=" N PHE D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.586A pdb=" N GLN D 359 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.671A pdb=" N SER D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.652A pdb=" N VAL D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.319A pdb=" N PHE B 106 " --> pdb=" O GLN B 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 62 through 65 574 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1808 1.32 - 1.44: 3154 1.44 - 1.57: 6213 1.57 - 1.69: 86 1.69 - 1.82: 60 Bond restraints: 11321 Sorted by residual: bond pdb=" N ILE A 283 " pdb=" CA ILE A 283 " ideal model delta sigma weight residual 1.463 1.507 -0.044 1.14e-02 7.69e+03 1.48e+01 bond pdb=" C3' DT G 22 " pdb=" C2' DT G 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 bond pdb=" C PRO A 287 " pdb=" O PRO A 287 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.39e+00 bond pdb=" N GLU D 282 " pdb=" CA GLU D 282 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.06e+00 bond pdb=" C3' DC H 22 " pdb=" C2' DC H 22 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.50e+00 ... (remaining 11316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 14774 1.48 - 2.95: 628 2.95 - 4.43: 99 4.43 - 5.91: 25 5.91 - 7.38: 3 Bond angle restraints: 15529 Sorted by residual: angle pdb=" N ILE A 283 " pdb=" CA ILE A 283 " pdb=" C ILE A 283 " ideal model delta sigma weight residual 110.23 104.63 5.60 1.04e+00 9.25e-01 2.90e+01 angle pdb=" N3 DT H 15 " pdb=" C4 DT H 15 " pdb=" O4 DT H 15 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O4' DC H 25 " pdb=" C4' DC H 25 " pdb=" C3' DC H 25 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" O4' DT G 22 " pdb=" C4' DT G 22 " pdb=" C3' DT G 22 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" O4' DG H 27 " pdb=" C4' DG H 27 " pdb=" C3' DG H 27 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 15524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5654 17.96 - 35.91: 716 35.91 - 53.87: 291 53.87 - 71.82: 67 71.82 - 89.77: 16 Dihedral angle restraints: 6744 sinusoidal: 3019 harmonic: 3725 Sorted by residual: dihedral pdb=" CA GLN D 279 " pdb=" C GLN D 279 " pdb=" N GLN D 280 " pdb=" CA GLN D 280 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASN C 213 " pdb=" C ASN C 213 " pdb=" N TYR C 214 " pdb=" CA TYR C 214 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C GLU A 290 " pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" CB GLU A 290 " ideal model delta harmonic sigma weight residual -122.60 -112.12 -10.48 0 2.50e+00 1.60e-01 1.76e+01 ... (remaining 6741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1540 0.072 - 0.145: 173 0.145 - 0.217: 7 0.217 - 0.290: 2 0.290 - 0.362: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CA ILE A 284 " pdb=" N ILE A 284 " pdb=" C ILE A 284 " pdb=" CB ILE A 284 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE A 283 " pdb=" N ILE A 283 " pdb=" C ILE A 283 " pdb=" CB ILE A 283 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1720 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 283 " 0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE A 283 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE A 283 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 284 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 330 " 0.020 2.00e-02 2.50e+03 1.51e-02 5.71e+00 pdb=" CG TRP B 330 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 330 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 330 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 330 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 330 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 330 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 330 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 330 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 330 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 346 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C GLU A 346 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU A 346 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 347 " 0.013 2.00e-02 2.50e+03 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 265 2.69 - 3.24: 11140 3.24 - 3.79: 18498 3.79 - 4.35: 24107 4.35 - 4.90: 38119 Nonbonded interactions: 92129 Sorted by model distance: nonbonded pdb=" OG SER C 156 " pdb=" OP2 DC H 22 " model vdw 2.132 3.040 nonbonded pdb=" O SER C 156 " pdb=" OG SER C 160 " model vdw 2.138 3.040 nonbonded pdb=" O GLU C 164 " pdb=" OG1 THR C 168 " model vdw 2.180 3.040 nonbonded pdb=" OE2 GLU B 107 " pdb=" OG1 THR B 184 " model vdw 2.182 3.040 nonbonded pdb=" O GLU A 290 " pdb=" N LEU A 292 " model vdw 2.197 3.120 ... (remaining 92124 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 48 or resid 80 through 111 or resid 118 through \ 153 or resid 156 through 184 or resid 190 through 403)) selection = (chain 'B' and (resid 26 through 250 or resid 257 through 403)) selection = (chain 'C' and (resid 26 through 48 or resid 80 through 111 or resid 118 through \ 153 or resid 156 through 184 or resid 190 through 250 or resid 257 through 403) \ ) } 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.300 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.044 11321 Z= 0.290 Angle : 0.690 7.382 15529 Z= 0.464 Chirality : 0.045 0.362 1723 Planarity : 0.005 0.038 1843 Dihedral : 19.052 89.775 4318 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.85 % Favored : 95.75 % Rotamer: Outliers : 2.53 % Allowed : 17.18 % Favored : 80.29 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1246 helix: 0.70 (0.19), residues: 767 sheet: -2.28 (0.73), residues: 51 loop : -0.63 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.013 0.002 TYR B 241 PHE 0.031 0.002 PHE C 360 TRP 0.040 0.002 TRP B 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.29 (11321) covalent geometry : angle 0.69043 / 0.46 (15529) hydrogen bonds : bond 0.14369 / 9.76 ( 605) hydrogen bonds : angle 6.02556 / 4.24 ( 1760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7640 (mm) cc_final: 0.7423 (mt) REVERT: A 170 ASP cc_start: 0.8010 (m-30) cc_final: 0.7659 (t70) REVERT: A 355 PHE cc_start: 0.7699 (m-80) cc_final: 0.7026 (m-80) REVERT: A 378 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 390 HIS cc_start: 0.7420 (t-90) cc_final: 0.7129 (t-90) REVERT: B 100 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: C 362 ILE cc_start: 0.8242 (tp) cc_final: 0.8025 (tp) REVERT: D 262 GLN cc_start: 0.5569 (pm20) cc_final: 0.5200 (mp10) REVERT: D 271 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5210 (tp30) REVERT: D 307 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6196 (t0) outliers start: 28 outliers final: 17 residues processed: 181 average time/residue: 0.0854 time to fit residues: 22.6233 Evaluate side-chains 160 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 307 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN C 132 GLN C 332 ASN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.169712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116643 restraints weight = 16134.679| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.97 r_work: 0.3487 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11321 Z= 0.162 Angle : 0.620 9.670 15529 Z= 0.334 Chirality : 0.043 0.235 1723 Planarity : 0.005 0.050 1843 Dihedral : 17.080 70.320 1875 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 2.80 % Allowed : 17.27 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.24), residues: 1246 helix: 0.89 (0.18), residues: 803 sheet: -2.41 (0.72), residues: 52 loop : -1.08 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 305 TYR 0.024 0.002 TYR B 244 PHE 0.015 0.001 PHE B 240 TRP 0.023 0.002 TRP B 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (11321) covalent geometry : angle 0.61983 / 0.33 (15529) hydrogen bonds : bond 0.04505 / 2.99 ( 605) hydrogen bonds : angle 4.67719 / 3.24 ( 1760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7878 (m-30) cc_final: 0.7470 (t0) REVERT: A 341 HIS cc_start: 0.8361 (m90) cc_final: 0.8055 (m90) REVERT: A 355 PHE cc_start: 0.7608 (m-80) cc_final: 0.6688 (m-80) REVERT: A 390 HIS cc_start: 0.7661 (t-90) cc_final: 0.7159 (t-90) REVERT: B 100 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: B 123 ASN cc_start: 0.7834 (m-40) cc_final: 0.7515 (m110) REVERT: B 329 THR cc_start: 0.9112 (m) cc_final: 0.8800 (p) REVERT: B 380 ILE cc_start: 0.7841 (tt) cc_final: 0.7434 (mt) REVERT: C 332 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.6918 (m-40) REVERT: D 272 TYR cc_start: 0.5810 (m-80) cc_final: 0.5553 (m-80) REVERT: D 280 GLN cc_start: 0.4401 (OUTLIER) cc_final: 0.3706 (tp40) REVERT: D 344 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (pttm) REVERT: D 358 MET cc_start: 0.8336 (mmm) cc_final: 0.8046 (mmm) outliers start: 31 outliers final: 18 residues processed: 177 average time/residue: 0.0854 time to fit residues: 22.0294 Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN B 89 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115333 restraints weight = 16258.894| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.98 r_work: 0.3471 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11321 Z= 0.166 Angle : 0.601 10.578 15529 Z= 0.322 Chirality : 0.042 0.193 1723 Planarity : 0.005 0.052 1843 Dihedral : 17.021 88.915 1854 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.35 % Allowed : 18.08 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1246 helix: 1.02 (0.18), residues: 802 sheet: -2.35 (0.72), residues: 51 loop : -1.14 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.017 0.002 TYR A 244 PHE 0.024 0.002 PHE A 360 TRP 0.024 0.001 TRP D 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (11321) covalent geometry : angle 0.60053 / 0.32 (15529) hydrogen bonds : bond 0.03979 / 2.62 ( 605) hydrogen bonds : angle 4.48625 / 3.11 ( 1760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7912 (m-30) cc_final: 0.7478 (t0) REVERT: A 341 HIS cc_start: 0.8328 (m90) cc_final: 0.8006 (m90) REVERT: A 347 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (mm-40) REVERT: A 355 PHE cc_start: 0.7655 (m-80) cc_final: 0.7256 (m-80) REVERT: A 390 HIS cc_start: 0.7671 (t-90) cc_final: 0.7163 (t-90) REVERT: B 100 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: B 244 TYR cc_start: 0.7907 (t80) cc_final: 0.7612 (t80) REVERT: B 329 THR cc_start: 0.9113 (m) cc_final: 0.8798 (p) REVERT: B 380 ILE cc_start: 0.7859 (tt) cc_final: 0.7454 (mt) REVERT: C 17 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 28 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: D 272 TYR cc_start: 0.5854 (m-80) cc_final: 0.5546 (m-80) REVERT: D 280 GLN cc_start: 0.3861 (OUTLIER) cc_final: 0.3103 (tp40) REVERT: D 344 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7802 (pttm) REVERT: D 354 TYR cc_start: 0.7536 (t80) cc_final: 0.7301 (t80) REVERT: D 358 MET cc_start: 0.8299 (mmm) cc_final: 0.7882 (mmm) outliers start: 37 outliers final: 24 residues processed: 176 average time/residue: 0.0847 time to fit residues: 21.9176 Evaluate side-chains 168 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.169127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115629 restraints weight = 16180.409| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.97 r_work: 0.3479 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11321 Z= 0.144 Angle : 0.575 9.393 15529 Z= 0.308 Chirality : 0.041 0.217 1723 Planarity : 0.005 0.054 1843 Dihedral : 17.058 88.742 1852 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.25 % Allowed : 18.63 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1246 helix: 1.13 (0.18), residues: 803 sheet: -2.42 (0.71), residues: 52 loop : -1.09 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.017 0.001 TYR A 244 PHE 0.027 0.002 PHE A 360 TRP 0.025 0.001 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (11321) covalent geometry : angle 0.57517 / 0.31 (15529) hydrogen bonds : bond 0.03673 / 2.41 ( 605) hydrogen bonds : angle 4.34204 / 3.01 ( 1760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7885 (m-30) cc_final: 0.7460 (t0) REVERT: A 347 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8438 (mm-40) REVERT: A 355 PHE cc_start: 0.7586 (m-80) cc_final: 0.7239 (m-80) REVERT: A 390 HIS cc_start: 0.7691 (t-90) cc_final: 0.7157 (t-90) REVERT: B 329 THR cc_start: 0.9083 (m) cc_final: 0.8760 (p) REVERT: B 378 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: C 17 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 28 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: C 215 LEU cc_start: 0.8010 (mt) cc_final: 0.7730 (mp) REVERT: D 272 TYR cc_start: 0.6004 (m-80) cc_final: 0.5702 (m-80) REVERT: D 344 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7815 (pttm) REVERT: D 358 MET cc_start: 0.8307 (mmm) cc_final: 0.7990 (mmm) outliers start: 36 outliers final: 25 residues processed: 182 average time/residue: 0.0763 time to fit residues: 20.2829 Evaluate side-chains 170 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.167961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.114652 restraints weight = 16195.005| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.96 r_work: 0.3465 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11321 Z= 0.160 Angle : 0.584 10.197 15529 Z= 0.312 Chirality : 0.042 0.165 1723 Planarity : 0.005 0.066 1843 Dihedral : 17.046 89.141 1848 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.80 % Allowed : 18.54 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1246 helix: 1.21 (0.18), residues: 804 sheet: -2.39 (0.72), residues: 51 loop : -1.08 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.018 0.002 TYR A 244 PHE 0.030 0.002 PHE D 373 TRP 0.021 0.001 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11321) covalent geometry : angle 0.58384 / 0.31 (15529) hydrogen bonds : bond 0.03615 / 2.37 ( 605) hydrogen bonds : angle 4.29486 / 2.99 ( 1760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7907 (m-30) cc_final: 0.7450 (t0) REVERT: A 237 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6757 (ptm160) REVERT: A 341 HIS cc_start: 0.8317 (m90) cc_final: 0.8069 (m90) REVERT: A 355 PHE cc_start: 0.7573 (m-80) cc_final: 0.7262 (m-80) REVERT: A 390 HIS cc_start: 0.7771 (t-90) cc_final: 0.7215 (t-90) REVERT: B 100 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: B 329 THR cc_start: 0.9076 (m) cc_final: 0.8760 (p) REVERT: C 17 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7789 (mm-30) REVERT: C 28 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: C 215 LEU cc_start: 0.8050 (mt) cc_final: 0.7776 (mp) REVERT: D 272 TYR cc_start: 0.6070 (m-80) cc_final: 0.5678 (m-80) REVERT: D 280 GLN cc_start: 0.3376 (OUTLIER) cc_final: 0.2880 (tp40) REVERT: D 344 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: D 358 MET cc_start: 0.8307 (mmm) cc_final: 0.7983 (mmt) outliers start: 42 outliers final: 30 residues processed: 180 average time/residue: 0.0899 time to fit residues: 23.7218 Evaluate side-chains 172 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.167854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114562 restraints weight = 16202.934| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.95 r_work: 0.3464 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11321 Z= 0.156 Angle : 0.583 8.152 15529 Z= 0.311 Chirality : 0.041 0.179 1723 Planarity : 0.005 0.052 1843 Dihedral : 17.083 88.333 1848 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.98 % Allowed : 18.81 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1246 helix: 1.25 (0.18), residues: 798 sheet: -2.49 (0.71), residues: 52 loop : -1.02 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 335 TYR 0.018 0.002 TYR A 244 PHE 0.022 0.002 PHE A 360 TRP 0.022 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11321) covalent geometry : angle 0.58318 / 0.31 (15529) hydrogen bonds : bond 0.03571 / 2.35 ( 605) hydrogen bonds : angle 4.25352 / 2.96 ( 1760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7892 (m-30) cc_final: 0.7415 (t0) REVERT: A 173 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 237 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6846 (ptm160) REVERT: A 300 MET cc_start: 0.7972 (mtt) cc_final: 0.7752 (mtt) REVERT: A 341 HIS cc_start: 0.8302 (m90) cc_final: 0.8023 (m90) REVERT: A 347 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8424 (mm-40) REVERT: A 355 PHE cc_start: 0.7579 (m-80) cc_final: 0.7329 (m-80) REVERT: A 390 HIS cc_start: 0.7761 (t-90) cc_final: 0.7191 (t-90) REVERT: B 100 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: B 329 THR cc_start: 0.9102 (m) cc_final: 0.8785 (p) REVERT: B 334 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8763 (tp-100) REVERT: C 17 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7798 (mm-30) REVERT: C 28 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: C 300 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7951 (mtm) REVERT: D 272 TYR cc_start: 0.6144 (m-80) cc_final: 0.5785 (m-80) REVERT: D 279 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: D 280 GLN cc_start: 0.3358 (OUTLIER) cc_final: 0.2840 (tp40) REVERT: D 344 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7926 (pttm) REVERT: D 358 MET cc_start: 0.8337 (mmm) cc_final: 0.8047 (mmm) outliers start: 44 outliers final: 26 residues processed: 182 average time/residue: 0.0766 time to fit residues: 20.9493 Evaluate side-chains 177 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114873 restraints weight = 16123.577| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.81 r_work: 0.3477 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11321 Z= 0.177 Angle : 0.595 8.205 15529 Z= 0.317 Chirality : 0.042 0.219 1723 Planarity : 0.005 0.053 1843 Dihedral : 17.160 88.151 1846 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.16 % Allowed : 19.17 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1246 helix: 1.24 (0.18), residues: 795 sheet: -2.45 (0.71), residues: 51 loop : -1.04 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.017 0.002 TYR A 244 PHE 0.033 0.002 PHE D 373 TRP 0.021 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (11321) covalent geometry : angle 0.59496 / 0.32 (15529) hydrogen bonds : bond 0.03598 / 2.35 ( 605) hydrogen bonds : angle 4.27060 / 2.98 ( 1760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7925 (m-30) cc_final: 0.7502 (t0) REVERT: A 173 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 237 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7149 (ptm160) REVERT: A 300 MET cc_start: 0.8209 (mtt) cc_final: 0.7934 (mtt) REVERT: A 347 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8453 (mm-40) REVERT: A 355 PHE cc_start: 0.7608 (m-80) cc_final: 0.7288 (m-80) REVERT: A 390 HIS cc_start: 0.7878 (t-90) cc_final: 0.7380 (t-90) REVERT: B 84 TRP cc_start: 0.8468 (m100) cc_final: 0.8246 (m100) REVERT: B 90 TRP cc_start: 0.8179 (m-10) cc_final: 0.7901 (m-10) REVERT: B 100 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7190 (pm20) REVERT: B 329 THR cc_start: 0.9123 (m) cc_final: 0.8808 (p) REVERT: C 28 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: C 300 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7914 (mtm) REVERT: C 332 ASN cc_start: 0.7491 (m-40) cc_final: 0.7284 (m-40) REVERT: D 272 TYR cc_start: 0.6158 (m-80) cc_final: 0.5780 (m-80) REVERT: D 280 GLN cc_start: 0.3179 (OUTLIER) cc_final: 0.2616 (tp40) REVERT: D 344 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7938 (pttm) REVERT: D 358 MET cc_start: 0.8382 (mmm) cc_final: 0.8060 (mmm) REVERT: D 360 PHE cc_start: 0.8624 (t80) cc_final: 0.8342 (t80) outliers start: 46 outliers final: 28 residues processed: 174 average time/residue: 0.0806 time to fit residues: 20.6160 Evaluate side-chains 168 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.168202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116556 restraints weight = 16180.397| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.78 r_work: 0.3504 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11321 Z= 0.142 Angle : 0.596 8.279 15529 Z= 0.312 Chirality : 0.041 0.204 1723 Planarity : 0.005 0.049 1843 Dihedral : 17.184 87.360 1846 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.53 % Allowed : 20.25 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1246 helix: 1.27 (0.18), residues: 796 sheet: -2.91 (0.62), residues: 64 loop : -0.94 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 335 TYR 0.017 0.002 TYR A 244 PHE 0.015 0.002 PHE A 360 TRP 0.049 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11321) covalent geometry : angle 0.59567 / 0.31 (15529) hydrogen bonds : bond 0.03472 / 2.28 ( 605) hydrogen bonds : angle 4.22083 / 2.94 ( 1760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7917 (m-30) cc_final: 0.7502 (t0) REVERT: A 173 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 237 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7267 (ptm160) REVERT: A 300 MET cc_start: 0.8277 (mtt) cc_final: 0.7971 (mtt) REVERT: A 347 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: A 355 PHE cc_start: 0.7567 (m-80) cc_final: 0.7248 (m-80) REVERT: A 390 HIS cc_start: 0.7860 (t-90) cc_final: 0.7348 (t-90) REVERT: B 90 TRP cc_start: 0.8177 (m-10) cc_final: 0.7923 (m-10) REVERT: B 100 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: B 329 THR cc_start: 0.9104 (m) cc_final: 0.8783 (p) REVERT: B 334 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8762 (tp-100) REVERT: B 348 ASP cc_start: 0.7717 (m-30) cc_final: 0.7492 (m-30) REVERT: C 300 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: C 351 LYS cc_start: 0.7065 (mttp) cc_final: 0.6645 (mttm) REVERT: D 279 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: D 280 GLN cc_start: 0.3191 (OUTLIER) cc_final: 0.2786 (tp40) REVERT: D 335 ARG cc_start: 0.7574 (tpt90) cc_final: 0.7354 (tpt90) REVERT: D 344 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (pttm) REVERT: D 358 MET cc_start: 0.8395 (mmm) cc_final: 0.8079 (mtt) REVERT: D 360 PHE cc_start: 0.8646 (t80) cc_final: 0.8361 (t80) outliers start: 39 outliers final: 27 residues processed: 176 average time/residue: 0.0750 time to fit residues: 19.6724 Evaluate side-chains 173 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 67 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.169963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118518 restraints weight = 15942.191| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.76 r_work: 0.3533 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11321 Z= 0.125 Angle : 0.575 8.169 15529 Z= 0.303 Chirality : 0.041 0.193 1723 Planarity : 0.005 0.048 1843 Dihedral : 17.124 86.040 1846 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.53 % Allowed : 20.16 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1246 helix: 1.41 (0.18), residues: 792 sheet: -2.75 (0.64), residues: 63 loop : -0.87 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 176 TYR 0.019 0.002 TYR A 244 PHE 0.017 0.001 PHE D 373 TRP 0.053 0.002 TRP D 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11321) covalent geometry : angle 0.57526 / 0.30 (15529) hydrogen bonds : bond 0.03344 / 2.20 ( 605) hydrogen bonds : angle 4.14708 / 2.89 ( 1760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7924 (m-30) cc_final: 0.7496 (t0) REVERT: A 173 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 226 LEU cc_start: 0.8627 (tp) cc_final: 0.8364 (tp) REVERT: A 300 MET cc_start: 0.8269 (mtt) cc_final: 0.7956 (mtt) REVERT: A 347 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8385 (mm-40) REVERT: A 355 PHE cc_start: 0.7541 (m-80) cc_final: 0.7279 (m-80) REVERT: A 390 HIS cc_start: 0.7837 (t-90) cc_final: 0.7310 (t-90) REVERT: B 90 TRP cc_start: 0.8214 (m-10) cc_final: 0.7970 (m-10) REVERT: B 100 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: B 329 THR cc_start: 0.9119 (m) cc_final: 0.8797 (p) REVERT: B 357 CYS cc_start: 0.7179 (p) cc_final: 0.6827 (p) REVERT: C 300 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7967 (mtm) REVERT: C 351 LYS cc_start: 0.7120 (mttp) cc_final: 0.6684 (mttm) REVERT: D 272 TYR cc_start: 0.6146 (m-80) cc_final: 0.5819 (m-80) REVERT: D 279 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: D 280 GLN cc_start: 0.3081 (OUTLIER) cc_final: 0.2724 (tp40) REVERT: D 358 MET cc_start: 0.8388 (mmm) cc_final: 0.8071 (mtt) REVERT: D 360 PHE cc_start: 0.8648 (t80) cc_final: 0.8371 (t80) outliers start: 39 outliers final: 23 residues processed: 178 average time/residue: 0.0831 time to fit residues: 22.0717 Evaluate side-chains 169 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.170704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118260 restraints weight = 16293.334| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.84 r_work: 0.3530 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11321 Z= 0.132 Angle : 0.612 8.393 15529 Z= 0.319 Chirality : 0.041 0.240 1723 Planarity : 0.005 0.051 1843 Dihedral : 17.123 86.844 1844 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.89 % Allowed : 21.25 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1246 helix: 1.43 (0.18), residues: 792 sheet: -2.63 (0.64), residues: 63 loop : -0.85 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 176 TYR 0.019 0.002 TYR D 354 PHE 0.011 0.001 PHE A 360 TRP 0.079 0.002 TRP B 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11321) covalent geometry : angle 0.61175 / 0.32 (15529) hydrogen bonds : bond 0.03340 / 2.21 ( 605) hydrogen bonds : angle 4.17264 / 2.90 ( 1760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7916 (m-30) cc_final: 0.7502 (t0) REVERT: A 173 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 237 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7103 (ttt-90) REVERT: A 300 MET cc_start: 0.8272 (mtt) cc_final: 0.7965 (mtt) REVERT: A 347 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8369 (mm-40) REVERT: A 390 HIS cc_start: 0.7844 (t-90) cc_final: 0.7336 (t-90) REVERT: B 90 TRP cc_start: 0.8221 (m-10) cc_final: 0.7874 (m-10) REVERT: B 100 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: B 329 THR cc_start: 0.9137 (m) cc_final: 0.8828 (p) REVERT: B 348 ASP cc_start: 0.7773 (m-30) cc_final: 0.7522 (m-30) REVERT: B 357 CYS cc_start: 0.7095 (p) cc_final: 0.6754 (p) REVERT: C 300 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: C 351 LYS cc_start: 0.7101 (mttp) cc_final: 0.6387 (mttp) REVERT: D 272 TYR cc_start: 0.6081 (m-80) cc_final: 0.5759 (m-80) REVERT: D 279 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: D 358 MET cc_start: 0.8383 (mmm) cc_final: 0.8072 (mtt) REVERT: D 360 PHE cc_start: 0.8642 (t80) cc_final: 0.8368 (t80) outliers start: 32 outliers final: 24 residues processed: 166 average time/residue: 0.0846 time to fit residues: 20.7266 Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.0170 chunk 120 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.172054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120700 restraints weight = 16038.567| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.78 r_work: 0.3562 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11321 Z= 0.123 Angle : 0.607 9.002 15529 Z= 0.314 Chirality : 0.041 0.243 1723 Planarity : 0.005 0.056 1843 Dihedral : 17.116 87.437 1844 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.89 % Allowed : 20.98 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1246 helix: 1.44 (0.18), residues: 797 sheet: -2.51 (0.65), residues: 63 loop : -0.88 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 176 TYR 0.020 0.002 TYR D 354 PHE 0.019 0.001 PHE D 373 TRP 0.071 0.003 TRP B 330 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11321) covalent geometry : angle 0.60698 / 0.31 (15529) hydrogen bonds : bond 0.03291 / 2.16 ( 605) hydrogen bonds : angle 4.11540 / 2.86 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.87 seconds wall clock time: 43 minutes 56.56 seconds (2636.56 seconds total)