Starting phenix.real_space_refine on Fri Jul 3 01:13:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hr5_52355/07_2026/9hr5_52355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hr5_52355/07_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_52355/07_2026/9hr5_52355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hr5_52355/07_2026/9hr5_52355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hr5_52355/07_2026/9hr5_52355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hr5_52355/07_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-dev-6108/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: 2.66, per 1000 atoms: 0.24 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: 0.86 Conformation dependent library (CDL) restraints added in 354.4 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: 1.23 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: 1.71 Time building geometry restraints manager: 1.08 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: 14776 1.48 - 2.95: 626 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- 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= 0.463 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 0.68958 / 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 : 0.603 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: 0.1086 time to fit residues: 28.5234 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 : 0.436 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.169774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116652 restraints weight = 16136.535| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.99 r_work: 0.3487 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0914 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= 0.163 Angle : 0.621 9.816 15529 Z= 0.335 Chirality : 0.043 0.256 1723 Planarity : 0.005 0.051 1843 Dihedral : 17.102 69.824 1875 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.80 % Allowed : 17.09 % Favored : 80.11 % 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: 0.90 (0.18), residues: 803 sheet: -2.40 (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 0.014 0.002 PHE B 240 TRP 0.024 0.002 TRP B 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (11321) covalent geometry : angle 0.62092 / 0.33 (15529) hydrogen bonds : bond 0.04305 / 2.85 ( 605) hydrogen bonds : angle 4.64221 / 3.21 ( 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 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7877 (m-30) cc_final: 0.7471 (t0) REVERT: A 341 HIS cc_start: 0.8369 (m90) cc_final: 0.8077 (m90) REVERT: A 355 PHE cc_start: 0.7594 (m-80) cc_final: 0.6710 (m-80) REVERT: A 390 HIS cc_start: 0.7672 (t-90) cc_final: 0.7155 (t-90) REVERT: B 100 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: B 123 ASN cc_start: 0.7888 (m-40) cc_final: 0.7580 (m110) REVERT: B 329 THR cc_start: 0.9114 (m) cc_final: 0.8801 (p) REVERT: B 380 ILE cc_start: 0.7850 (tt) cc_final: 0.7445 (mt) REVERT: C 107 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 332 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6891 (m-40) REVERT: D 272 TYR cc_start: 0.5832 (m-80) cc_final: 0.5601 (m-80) REVERT: D 280 GLN cc_start: 0.4320 (OUTLIER) cc_final: 0.3810 (tp40) REVERT: D 343 GLU cc_start: 0.7279 (mp0) cc_final: 0.7051 (mp0) REVERT: D 344 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7735 (pttm) REVERT: D 358 MET cc_start: 0.8310 (mmm) cc_final: 0.8004 (mmm) outliers start: 31 outliers final: 18 residues processed: 180 average time/residue: 0.0872 time to fit residues: 22.6189 Evaluate side-chains 168 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 98 optimal weight: 0.1980 chunk 124 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.170401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117053 restraints weight = 16189.204| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.99 r_work: 0.3497 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11321 Z= 0.139 Angle : 0.580 10.202 15529 Z= 0.312 Chirality : 0.041 0.197 1723 Planarity : 0.005 0.052 1843 Dihedral : 17.003 89.370 1854 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 18.26 % Favored : 78.66 % 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: 0.34 (0.24), residues: 1246 helix: 1.06 (0.18), residues: 802 sheet: -2.26 (0.73), residues: 51 loop : -1.08 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.017 0.001 TYR A 244 PHE 0.024 0.002 PHE A 360 TRP 0.025 0.001 TRP D 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (11321) covalent geometry : angle 0.57984 / 0.31 (15529) hydrogen bonds : bond 0.03857 / 2.54 ( 605) hydrogen bonds : angle 4.41801 / 3.06 ( 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 188 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7896 (m-30) cc_final: 0.7469 (t0) REVERT: A 341 HIS cc_start: 0.8358 (m90) cc_final: 0.8042 (m90) REVERT: A 347 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8489 (mm-40) REVERT: A 355 PHE cc_start: 0.7637 (m-80) cc_final: 0.7268 (m-80) REVERT: A 390 HIS cc_start: 0.7659 (t-90) cc_final: 0.7132 (t-90) REVERT: B 100 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: B 244 TYR cc_start: 0.7922 (t80) cc_final: 0.7692 (t80) REVERT: B 329 THR cc_start: 0.9102 (m) cc_final: 0.8793 (p) REVERT: B 380 ILE cc_start: 0.7824 (tt) cc_final: 0.7420 (mt) REVERT: D 272 TYR cc_start: 0.5872 (m-80) cc_final: 0.5610 (m-80) REVERT: D 280 GLN cc_start: 0.3694 (OUTLIER) cc_final: 0.2948 (tp40) REVERT: D 344 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7796 (pttm) REVERT: D 354 TYR cc_start: 0.7518 (t80) cc_final: 0.7280 (t80) REVERT: D 358 MET cc_start: 0.8301 (mmm) cc_final: 0.7856 (mmm) outliers start: 34 outliers final: 20 residues processed: 177 average time/residue: 0.0846 time to fit residues: 22.1710 Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain B residue 248 VAL 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 105 ILE 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: 10.0000 chunk 82 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 38 optimal weight: 0.4980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.170221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117089 restraints weight = 16185.052| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.97 r_work: 0.3498 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11321 Z= 0.138 Angle : 0.567 9.477 15529 Z= 0.305 Chirality : 0.041 0.171 1723 Planarity : 0.005 0.056 1843 Dihedral : 17.013 89.002 1851 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.35 % Allowed : 18.54 % 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: 0.49 (0.24), residues: 1246 helix: 1.18 (0.18), residues: 802 sheet: -2.19 (0.73), residues: 51 loop : -1.04 (0.33), residues: 393 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 0.023 0.002 PHE A 360 TRP 0.022 0.001 TRP D 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (11321) covalent geometry : angle 0.56732 / 0.31 (15529) hydrogen bonds : bond 0.03610 / 2.36 ( 605) hydrogen bonds : angle 4.31040 / 2.99 ( 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 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7921 (m-30) cc_final: 0.7479 (t0) REVERT: A 341 HIS cc_start: 0.8336 (m90) cc_final: 0.7994 (m90) REVERT: A 347 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8445 (mm-40) REVERT: A 355 PHE cc_start: 0.7614 (m-80) cc_final: 0.7289 (m-80) REVERT: A 390 HIS cc_start: 0.7693 (t-90) cc_final: 0.7156 (t-90) REVERT: B 329 THR cc_start: 0.9082 (m) cc_final: 0.8761 (p) REVERT: B 378 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: C 17 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 28 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: D 272 TYR cc_start: 0.6003 (m-80) cc_final: 0.5724 (m-80) REVERT: D 280 GLN cc_start: 0.3416 (OUTLIER) cc_final: 0.2752 (tp40) REVERT: D 344 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7842 (pttm) REVERT: D 358 MET cc_start: 0.8304 (mmm) cc_final: 0.7979 (mmt) outliers start: 37 outliers final: 25 residues processed: 174 average time/residue: 0.0984 time to fit residues: 25.2535 Evaluate side-chains 169 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 211 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 0.0050 chunk 38 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.115586 restraints weight = 16200.648| |-----------------------------------------------------------------------------| 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: 0.7637 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11321 Z= 0.152 Angle : 0.567 7.822 15529 Z= 0.305 Chirality : 0.041 0.153 1723 Planarity : 0.005 0.057 1843 Dihedral : 17.020 88.917 1848 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.53 % Allowed : 19.08 % Favored : 77.40 % 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: 0.58 (0.24), residues: 1246 helix: 1.27 (0.18), residues: 797 sheet: -2.27 (0.73), residues: 51 loop : -1.00 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 335 TYR 0.018 0.001 TYR A 244 PHE 0.027 0.002 PHE D 373 TRP 0.027 0.001 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11321) covalent geometry : angle 0.56712 / 0.31 (15529) hydrogen bonds : bond 0.03583 / 2.35 ( 605) hydrogen bonds : angle 4.25683 / 2.96 ( 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 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7901 (m-30) cc_final: 0.7457 (t0) REVERT: A 347 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8451 (mm-40) REVERT: A 355 PHE cc_start: 0.7558 (m-80) cc_final: 0.7304 (m-80) REVERT: A 390 HIS cc_start: 0.7759 (t-90) cc_final: 0.7177 (t-90) REVERT: B 100 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: B 329 THR cc_start: 0.9066 (m) cc_final: 0.8758 (p) REVERT: B 378 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7432 (m-10) REVERT: C 17 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7786 (mm-30) REVERT: C 28 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: C 159 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7623 (mp) REVERT: D 272 TYR cc_start: 0.6110 (m-80) cc_final: 0.5727 (m-80) REVERT: D 358 MET cc_start: 0.8299 (mmm) cc_final: 0.7966 (mmt) outliers start: 39 outliers final: 24 residues processed: 182 average time/residue: 0.0962 time to fit residues: 25.8653 Evaluate side-chains 172 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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 111 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 282 GLU 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: 6.9990 chunk 47 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.167990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.114775 restraints weight = 16223.942| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.95 r_work: 0.3467 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11321 Z= 0.163 Angle : 0.579 8.008 15529 Z= 0.311 Chirality : 0.042 0.182 1723 Planarity : 0.005 0.055 1843 Dihedral : 17.070 88.561 1846 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.62 % Allowed : 19.08 % Favored : 77.31 % 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: 0.53 (0.24), residues: 1246 helix: 1.25 (0.18), residues: 798 sheet: -2.44 (0.72), residues: 52 loop : -1.05 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 335 TYR 0.018 0.002 TYR A 244 PHE 0.021 0.002 PHE A 360 TRP 0.036 0.002 TRP D 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (11321) covalent geometry : angle 0.57868 / 0.31 (15529) hydrogen bonds : bond 0.03563 / 2.34 ( 605) hydrogen bonds : angle 4.23081 / 2.94 ( 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 188 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7912 (m-30) cc_final: 0.7444 (t0) REVERT: A 173 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 341 HIS cc_start: 0.8311 (m90) cc_final: 0.8038 (m90) REVERT: A 347 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: A 355 PHE cc_start: 0.7593 (m-80) cc_final: 0.7232 (m-80) REVERT: A 390 HIS cc_start: 0.7757 (t-90) cc_final: 0.7227 (t-90) REVERT: B 100 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: B 329 THR cc_start: 0.9091 (m) cc_final: 0.8771 (p) REVERT: B 334 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8765 (tp-100) REVERT: C 17 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7784 (mm-30) REVERT: C 28 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: C 351 LYS cc_start: 0.6951 (mttp) cc_final: 0.6534 (mttm) REVERT: D 275 ASP cc_start: 0.6741 (t0) cc_final: 0.5553 (m-30) REVERT: D 279 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: D 280 GLN cc_start: 0.3191 (OUTLIER) cc_final: 0.2754 (tp40) REVERT: D 358 MET cc_start: 0.8336 (mmm) cc_final: 0.8040 (mmm) outliers start: 40 outliers final: 26 residues processed: 180 average time/residue: 0.0981 time to fit residues: 26.1043 Evaluate side-chains 174 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.168873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116893 restraints weight = 16105.648| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.79 r_work: 0.3511 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11321 Z= 0.147 Angle : 0.582 7.953 15529 Z= 0.309 Chirality : 0.041 0.181 1723 Planarity : 0.005 0.073 1843 Dihedral : 17.124 87.562 1846 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.80 % Allowed : 19.17 % Favored : 77.03 % 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: 1.28 (0.18), residues: 804 sheet: -2.39 (0.70), residues: 51 loop : -1.20 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.019 0.002 TYR A 244 PHE 0.031 0.002 PHE D 373 TRP 0.047 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11321) covalent geometry : angle 0.58209 / 0.31 (15529) hydrogen bonds : bond 0.03476 / 2.27 ( 605) hydrogen bonds : angle 4.20256 / 2.92 ( 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: 42 poor density : 143 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7922 (m-30) cc_final: 0.7517 (t0) REVERT: A 173 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8318 (tt) REVERT: A 341 HIS cc_start: 0.8332 (m90) cc_final: 0.8066 (m90) REVERT: A 347 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: A 355 PHE cc_start: 0.7560 (m-80) cc_final: 0.7256 (m-80) REVERT: A 390 HIS cc_start: 0.7865 (t-90) cc_final: 0.7331 (t-90) REVERT: B 100 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: B 329 THR cc_start: 0.9114 (m) cc_final: 0.8799 (p) REVERT: C 17 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 28 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: C 351 LYS cc_start: 0.7079 (mttp) cc_final: 0.6695 (mttm) REVERT: D 279 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: D 280 GLN cc_start: 0.3213 (OUTLIER) cc_final: 0.2737 (tp40) REVERT: D 358 MET cc_start: 0.8344 (mmm) cc_final: 0.8030 (mmm) REVERT: D 360 PHE cc_start: 0.8629 (t80) cc_final: 0.8373 (t80) outliers start: 42 outliers final: 29 residues processed: 177 average time/residue: 0.0916 time to fit residues: 24.0618 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 : 0.327 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 0.0070 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 0.0770 chunk 109 optimal weight: 6.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 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 = 0.4289 r_free = 0.4289 target = 0.170310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.118800 restraints weight = 16161.171| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.79 r_work: 0.3534 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11321 Z= 0.125 Angle : 0.573 8.110 15529 Z= 0.303 Chirality : 0.040 0.170 1723 Planarity : 0.005 0.052 1843 Dihedral : 17.123 86.074 1846 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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: 0.58 (0.24), residues: 1246 helix: 1.34 (0.18), residues: 805 sheet: -2.85 (0.62), residues: 64 loop : -1.04 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 335 TYR 0.019 0.002 TYR A 244 PHE 0.027 0.002 PHE D 373 TRP 0.051 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11321) covalent geometry : angle 0.57252 / 0.30 (15529) hydrogen bonds : bond 0.03354 / 2.20 ( 605) hydrogen bonds : angle 4.15567 / 2.89 ( 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 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7910 (m-30) cc_final: 0.7492 (t0) REVERT: A 173 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 341 HIS cc_start: 0.8298 (m90) cc_final: 0.8034 (m90) REVERT: A 347 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: A 390 HIS cc_start: 0.7834 (t-90) cc_final: 0.7300 (t-90) REVERT: B 100 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: B 329 THR cc_start: 0.9090 (m) cc_final: 0.8768 (p) REVERT: B 334 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8763 (tp-100) REVERT: B 352 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5783 (mt) REVERT: B 356 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7325 (mt-10) REVERT: C 351 LYS cc_start: 0.7122 (mttp) cc_final: 0.6747 (mttm) REVERT: D 279 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: D 280 GLN cc_start: 0.3034 (OUTLIER) cc_final: 0.2649 (tp40) REVERT: D 358 MET cc_start: 0.8355 (mmm) cc_final: 0.8028 (mmt) REVERT: D 360 PHE cc_start: 0.8629 (t80) cc_final: 0.8379 (t80) outliers start: 39 outliers final: 25 residues processed: 184 average time/residue: 0.0868 time to fit residues: 23.7684 Evaluate side-chains 174 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 291 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 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 226 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 47 optimal weight: 0.0670 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.171259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.119737 restraints weight = 15899.953| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.76 r_work: 0.3548 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11321 Z= 0.124 Angle : 0.582 8.026 15529 Z= 0.306 Chirality : 0.040 0.165 1723 Planarity : 0.005 0.055 1843 Dihedral : 17.096 86.002 1846 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.25 % Allowed : 20.25 % Favored : 76.49 % 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: 0.64 (0.24), residues: 1246 helix: 1.39 (0.18), residues: 804 sheet: -2.73 (0.62), residues: 63 loop : -1.03 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 176 TYR 0.018 0.001 TYR D 354 PHE 0.027 0.002 PHE D 373 TRP 0.062 0.002 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11321) covalent geometry : angle 0.58191 / 0.31 (15529) hydrogen bonds : bond 0.03367 / 2.22 ( 605) hydrogen bonds : angle 4.13257 / 2.87 ( 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 187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7907 (m-30) cc_final: 0.7505 (t0) REVERT: A 173 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 341 HIS cc_start: 0.8285 (m90) cc_final: 0.8008 (m90) REVERT: A 347 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8372 (mm-40) REVERT: A 390 HIS cc_start: 0.7792 (t-90) cc_final: 0.7296 (t-90) REVERT: B 90 TRP cc_start: 0.8170 (m-10) cc_final: 0.7946 (m-10) REVERT: B 100 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: B 176 ARG cc_start: 0.7684 (mmm160) cc_final: 0.6706 (tpm170) REVERT: B 329 THR cc_start: 0.9097 (m) cc_final: 0.8788 (p) REVERT: B 352 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5756 (mt) REVERT: B 356 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7331 (mt-10) REVERT: C 351 LYS cc_start: 0.7111 (mttp) cc_final: 0.6476 (mttp) REVERT: D 279 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: D 358 MET cc_start: 0.8345 (mmm) cc_final: 0.8017 (mmt) REVERT: D 360 PHE cc_start: 0.8639 (t80) cc_final: 0.8390 (t80) outliers start: 36 outliers final: 24 residues processed: 178 average time/residue: 0.0877 time to fit residues: 23.0213 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 : 0.323 ------------------------------------------------------------------------------- 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 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 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 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 226 LEU 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 111 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.170344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118604 restraints weight = 16233.229| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.78 r_work: 0.3534 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11321 Z= 0.148 Angle : 0.609 8.902 15529 Z= 0.320 Chirality : 0.041 0.162 1723 Planarity : 0.005 0.047 1843 Dihedral : 17.147 87.117 1844 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.71 % Allowed : 20.80 % Favored : 76.49 % 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: 0.59 (0.24), residues: 1246 helix: 1.34 (0.18), residues: 804 sheet: -2.78 (0.62), residues: 63 loop : -1.03 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 176 TYR 0.019 0.002 TYR D 354 PHE 0.027 0.002 PHE D 373 TRP 0.078 0.003 TRP B 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (11321) covalent geometry : angle 0.60857 / 0.32 (15529) hydrogen bonds : bond 0.03431 / 2.27 ( 605) hydrogen bonds : angle 4.17129 / 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 175 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.415 Fit side-chains 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: 0.7525 (t0) REVERT: A 173 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 226 LEU cc_start: 0.8632 (tp) cc_final: 0.8373 (tp) REVERT: A 347 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: A 390 HIS cc_start: 0.7811 (t-90) cc_final: 0.7307 (t-90) REVERT: B 90 TRP cc_start: 0.8182 (m-10) cc_final: 0.7883 (m-10) REVERT: B 100 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: B 108 LEU cc_start: 0.8353 (tp) cc_final: 0.8105 (tp) REVERT: B 329 THR cc_start: 0.9124 (m) cc_final: 0.8820 (p) REVERT: B 352 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5757 (mt) REVERT: B 356 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 351 LYS cc_start: 0.7102 (mttp) cc_final: 0.6464 (mttp) REVERT: D 279 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: D 358 MET cc_start: 0.8370 (mmm) cc_final: 0.8047 (mmt) REVERT: D 360 PHE cc_start: 0.8651 (t80) cc_final: 0.8399 (t80) outliers start: 30 outliers final: 22 residues processed: 165 average time/residue: 0.0937 time to fit residues: 22.8653 Evaluate side-chains 165 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.7980 chunk 120 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4292 r_free = 0.4292 target = 0.170521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118884 restraints weight = 16105.560| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.77 r_work: 0.3538 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11321 Z= 0.141 Angle : 0.605 8.156 15529 Z= 0.319 Chirality : 0.041 0.170 1723 Planarity : 0.005 0.054 1843 Dihedral : 17.184 87.887 1844 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.35 % Allowed : 21.34 % 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: 0.57 (0.24), residues: 1246 helix: 1.32 (0.18), residues: 805 sheet: -2.79 (0.61), residues: 63 loop : -1.04 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 176 TYR 0.019 0.002 TYR D 354 PHE 0.026 0.002 PHE D 373 TRP 0.071 0.002 TRP B 330 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11321) covalent geometry : angle 0.60531 / 0.32 (15529) hydrogen bonds : bond 0.03461 / 2.30 ( 605) hydrogen bonds : angle 4.19522 / 2.92 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.70 seconds wall clock time: 49 minutes 13.80 seconds (2953.80 seconds total)