Starting phenix.real_space_refine on Wed Feb 4 14:28:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hr5_52355/02_2026/9hr5_52355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hr5_52355/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hr5_52355/02_2026/9hr5_52355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hr5_52355/02_2026/9hr5_52355.map" model { file = "/net/cci-nas-00/data/ceres_data/9hr5_52355/02_2026/9hr5_52355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hr5_52355/02_2026/9hr5_52355.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 44 5.49 5 S 42 5.16 5 C 6851 2.51 5 N 1854 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 2.35, per 1000 atoms: 0.21 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: 0.89 Conformation dependent library (CDL) restraints added in 373.4 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: 1.11 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: 1.38 Time building geometry restraints manager: 1.16 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=" 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=" N LEU D 281 " pdb=" CA LEU D 281 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 bond pdb=" N GLN A 280 " pdb=" CA GLN A 280 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.50e+00 ... (remaining 11316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 14890 1.48 - 2.95: 512 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=" C GLU A 290 " pdb=" CA GLU A 290 " pdb=" CB GLU A 290 " ideal model delta sigma weight residual 110.42 103.04 7.38 1.99e+00 2.53e-01 1.38e+01 angle pdb=" N LYS B 126 " pdb=" CA LYS B 126 " pdb=" C LYS B 126 " ideal model delta sigma weight residual 112.86 108.55 4.31 1.22e+00 6.72e-01 1.25e+01 angle pdb=" CA TRP A 389 " pdb=" C TRP A 389 " pdb=" O TRP A 389 " ideal model delta sigma weight residual 122.51 117.84 4.67 1.34e+00 5.57e-01 1.21e+01 angle pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" O ILE A 291 " ideal model delta sigma weight residual 120.78 116.45 4.33 1.25e+00 6.40e-01 1.20e+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: 1570 0.072 - 0.145: 144 0.145 - 0.217: 6 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: 4.610 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.230 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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= 0.198 Angle : 0.659 7.382 15529 Z= 0.384 Chirality : 0.043 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 covalent geometry : bond 0.00378 (11321) covalent geometry : angle 0.65891 (15529) hydrogen bonds : bond 0.14369 ( 605) hydrogen bonds : angle 6.02556 ( 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 : 0.263 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: 0.0901 time to fit residues: 23.3547 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 : 0.365 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.169797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116608 restraints weight = 16139.718| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.98 r_work: 0.3488 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11321 Z= 0.159 Angle : 0.589 7.418 15529 Z= 0.314 Chirality : 0.041 0.231 1723 Planarity : 0.005 0.045 1843 Dihedral : 16.961 87.559 1875 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 17.00 % Favored : 80.38 % 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: 0.24 (0.24), residues: 1246 helix: 0.96 (0.18), residues: 802 sheet: -2.38 (0.72), residues: 52 loop : -1.04 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 305 TYR 0.025 0.002 TYR B 244 PHE 0.013 0.001 PHE B 240 TRP 0.024 0.002 TRP B 330 HIS 0.008 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00353 (11321) covalent geometry : angle 0.58915 (15529) hydrogen bonds : bond 0.03827 ( 605) hydrogen bonds : angle 4.47596 ( 1760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7907 (m-30) cc_final: 0.7459 (t0) REVERT: A 341 HIS cc_start: 0.8368 (m90) cc_final: 0.8069 (m90) REVERT: A 355 PHE cc_start: 0.7544 (m-80) cc_final: 0.7103 (m-80) REVERT: A 390 HIS cc_start: 0.7660 (t-90) cc_final: 0.7163 (t-90) REVERT: B 100 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: B 123 ASN cc_start: 0.7832 (m-40) cc_final: 0.7495 (m110) REVERT: B 329 THR cc_start: 0.9104 (m) cc_final: 0.8801 (p) REVERT: B 380 ILE cc_start: 0.7848 (tt) cc_final: 0.7438 (mt) REVERT: C 107 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 332 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6882 (m-40) REVERT: C 341 HIS cc_start: 0.7376 (m90) cc_final: 0.7055 (m90) REVERT: D 272 TYR cc_start: 0.5954 (m-80) cc_final: 0.5744 (m-80) REVERT: D 280 GLN cc_start: 0.3855 (OUTLIER) cc_final: 0.3058 (tp40) REVERT: D 343 GLU cc_start: 0.7300 (mp0) cc_final: 0.7031 (mp0) REVERT: D 344 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7772 (pttm) REVERT: D 358 MET cc_start: 0.8326 (mmm) cc_final: 0.7981 (mmm) REVERT: D 360 PHE cc_start: 0.8540 (t80) cc_final: 0.8278 (t80) outliers start: 29 outliers final: 16 residues processed: 178 average time/residue: 0.0862 time to fit residues: 22.5835 Evaluate side-chains 163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 378 TYR Chi-restraints excluded: chain A residue 389 TRP Chi-restraints excluded: chain B residue 100 GLU 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: 2.9990 chunk 105 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4253 r_free = 0.4253 target = 0.170412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.116744 restraints weight = 16186.283| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.99 r_work: 0.3495 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11321 Z= 0.138 Angle : 0.555 9.375 15529 Z= 0.297 Chirality : 0.039 0.176 1723 Planarity : 0.005 0.049 1843 Dihedral : 16.636 64.864 1849 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.25 % Allowed : 17.54 % Favored : 79.20 % 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: 0.48 (0.24), residues: 1246 helix: 1.17 (0.18), residues: 802 sheet: -2.18 (0.73), residues: 51 loop : -1.04 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 305 TYR 0.015 0.001 TYR A 244 PHE 0.026 0.002 PHE D 373 TRP 0.021 0.001 TRP B 330 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00303 (11321) covalent geometry : angle 0.55546 (15529) hydrogen bonds : bond 0.03468 ( 605) hydrogen bonds : angle 4.25604 ( 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 193 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7921 (m-30) cc_final: 0.7474 (t0) REVERT: A 355 PHE cc_start: 0.7601 (m-80) cc_final: 0.7202 (m-80) REVERT: A 389 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.6510 (m-90) REVERT: A 390 HIS cc_start: 0.7670 (t-90) cc_final: 0.7132 (t-90) REVERT: B 244 TYR cc_start: 0.7937 (t80) cc_final: 0.7684 (t80) REVERT: B 329 THR cc_start: 0.9090 (m) cc_final: 0.8779 (p) REVERT: B 356 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 357 CYS cc_start: 0.7054 (p) cc_final: 0.6790 (p) REVERT: B 378 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: C 28 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: C 249 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: C 255 MET cc_start: 0.4222 (mmt) cc_final: 0.3825 (mmt) REVERT: D 272 TYR cc_start: 0.6074 (m-80) cc_final: 0.5776 (m-80) REVERT: D 344 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7809 (pttm) REVERT: D 354 TYR cc_start: 0.7537 (t80) cc_final: 0.7332 (t80) REVERT: D 358 MET cc_start: 0.8256 (mmm) cc_final: 0.7823 (mmm) REVERT: D 360 PHE cc_start: 0.8564 (t80) cc_final: 0.8282 (t80) outliers start: 36 outliers final: 18 residues processed: 185 average time/residue: 0.0874 time to fit residues: 23.5928 Evaluate side-chains 163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 ILE 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 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 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4284 r_free = 0.4284 target = 0.170082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118157 restraints weight = 16125.279| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.80 r_work: 0.3526 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1614 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= 0.138 Angle : 0.552 7.119 15529 Z= 0.294 Chirality : 0.039 0.164 1723 Planarity : 0.004 0.047 1843 Dihedral : 16.604 64.724 1845 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.35 % Allowed : 17.81 % Favored : 78.84 % 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: 0.68 (0.24), residues: 1246 helix: 1.34 (0.18), residues: 797 sheet: -2.23 (0.72), residues: 51 loop : -0.93 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 335 TYR 0.012 0.001 TYR A 244 PHE 0.023 0.002 PHE A 360 TRP 0.021 0.001 TRP D 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00308 (11321) covalent geometry : angle 0.55231 (15529) hydrogen bonds : bond 0.03302 ( 605) hydrogen bonds : angle 4.14794 ( 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 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7913 (m-30) cc_final: 0.7531 (t0) REVERT: A 300 MET cc_start: 0.8195 (mtt) cc_final: 0.7918 (mtt) REVERT: A 355 PHE cc_start: 0.7611 (m-80) cc_final: 0.7373 (m-80) REVERT: A 390 HIS cc_start: 0.7767 (t-90) cc_final: 0.7268 (t-90) REVERT: B 100 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: B 329 THR cc_start: 0.9081 (m) cc_final: 0.8788 (p) REVERT: B 356 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7320 (mt-10) REVERT: C 28 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: C 249 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.7016 (mt0) REVERT: C 255 MET cc_start: 0.4428 (mmt) cc_final: 0.3967 (mmt) REVERT: D 272 TYR cc_start: 0.6154 (m-80) cc_final: 0.5856 (m-80) REVERT: D 280 GLN cc_start: 0.3196 (OUTLIER) cc_final: 0.2776 (tp40) REVERT: D 344 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7871 (pttm) REVERT: D 358 MET cc_start: 0.8430 (mmm) cc_final: 0.8077 (mmm) REVERT: D 360 PHE cc_start: 0.8640 (t80) cc_final: 0.8340 (t80) outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 0.0954 time to fit residues: 25.6108 Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 337 CYS 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 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS B 123 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.166836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114997 restraints weight = 16171.891| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.78 r_work: 0.3482 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11321 Z= 0.192 Angle : 0.588 7.002 15529 Z= 0.313 Chirality : 0.041 0.153 1723 Planarity : 0.005 0.047 1843 Dihedral : 16.769 67.037 1843 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.62 % Allowed : 18.17 % Favored : 78.21 % 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: 0.54 (0.24), residues: 1246 helix: 1.25 (0.18), residues: 800 sheet: -2.47 (0.70), residues: 51 loop : -1.01 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.016 0.002 TYR B 109 PHE 0.029 0.002 PHE C 373 TRP 0.020 0.002 TRP B 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00443 (11321) covalent geometry : angle 0.58769 (15529) hydrogen bonds : bond 0.03447 ( 605) hydrogen bonds : angle 4.16313 ( 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 182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7925 (m-30) cc_final: 0.7498 (t0) REVERT: A 173 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 300 MET cc_start: 0.8370 (mtt) cc_final: 0.8041 (mtt) REVERT: A 355 PHE cc_start: 0.7570 (m-80) cc_final: 0.7268 (m-80) REVERT: A 390 HIS cc_start: 0.7795 (t-90) cc_final: 0.7469 (t-90) REVERT: B 100 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: B 329 THR cc_start: 0.9113 (m) cc_final: 0.8810 (p) REVERT: B 334 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8593 (tp-100) REVERT: C 28 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7738 (mt0) REVERT: C 255 MET cc_start: 0.4445 (mmt) cc_final: 0.3521 (mmt) REVERT: C 341 HIS cc_start: 0.7387 (m90) cc_final: 0.7006 (m90) REVERT: C 351 LYS cc_start: 0.7115 (mttp) cc_final: 0.6639 (mttm) REVERT: D 272 TYR cc_start: 0.6252 (m-80) cc_final: 0.5900 (m-80) REVERT: D 280 GLN cc_start: 0.3376 (OUTLIER) cc_final: 0.3012 (tp40) REVERT: D 344 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7943 (pttm) REVERT: D 358 MET cc_start: 0.8494 (mmm) cc_final: 0.8290 (mmt) REVERT: D 360 PHE cc_start: 0.8660 (t80) cc_final: 0.8372 (t80) outliers start: 40 outliers final: 23 residues processed: 171 average time/residue: 0.0994 time to fit residues: 24.7561 Evaluate side-chains 165 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE 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 123 ASN 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 C residue 28 GLN 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 280 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain D residue 380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.166888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115163 restraints weight = 16183.173| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.78 r_work: 0.3511 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11321 Z= 0.173 Angle : 0.579 7.505 15529 Z= 0.306 Chirality : 0.040 0.152 1723 Planarity : 0.004 0.045 1843 Dihedral : 16.835 67.740 1841 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.44 % Allowed : 18.81 % Favored : 77.76 % 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: 1.31 (0.18), residues: 796 sheet: -3.03 (0.60), residues: 64 loop : -0.84 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.018 0.002 TYR A 244 PHE 0.016 0.002 PHE A 360 TRP 0.023 0.002 TRP D 330 HIS 0.006 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00395 (11321) covalent geometry : angle 0.57920 (15529) hydrogen bonds : bond 0.03364 ( 605) hydrogen bonds : angle 4.12062 ( 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 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7925 (m-30) cc_final: 0.7509 (t0) REVERT: A 173 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 300 MET cc_start: 0.8430 (mtt) cc_final: 0.8103 (mtt) REVERT: A 390 HIS cc_start: 0.7767 (t-90) cc_final: 0.7348 (t-90) REVERT: B 84 TRP cc_start: 0.8466 (m100) cc_final: 0.8256 (m100) REVERT: B 90 TRP cc_start: 0.8223 (m-10) cc_final: 0.7953 (m-10) REVERT: B 100 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: B 176 ARG cc_start: 0.7498 (tpt90) cc_final: 0.6837 (tpm170) REVERT: B 329 THR cc_start: 0.9095 (m) cc_final: 0.8780 (p) REVERT: B 348 ASP cc_start: 0.7790 (m-30) cc_final: 0.7560 (m-30) REVERT: C 28 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: C 341 HIS cc_start: 0.7276 (m90) cc_final: 0.6878 (m90) REVERT: C 351 LYS cc_start: 0.7153 (mttp) cc_final: 0.6632 (mttp) REVERT: D 272 TYR cc_start: 0.6378 (m-80) cc_final: 0.6012 (m-80) REVERT: D 279 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: D 280 GLN cc_start: 0.3174 (OUTLIER) cc_final: 0.2759 (tp40) REVERT: D 343 GLU cc_start: 0.7405 (mp0) cc_final: 0.7149 (mp0) REVERT: D 360 PHE cc_start: 0.8675 (t80) cc_final: 0.8385 (t80) outliers start: 38 outliers final: 22 residues processed: 177 average time/residue: 0.0988 time to fit residues: 25.6026 Evaluate side-chains 160 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE 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 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 28 GLN 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: 4.9990 chunk 106 optimal weight: 0.0050 chunk 57 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.7094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4271 r_free = 0.4271 target = 0.168778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117217 restraints weight = 16062.706| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.78 r_work: 0.3515 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11321 Z= 0.137 Angle : 0.566 8.301 15529 Z= 0.297 Chirality : 0.039 0.149 1723 Planarity : 0.004 0.054 1843 Dihedral : 16.895 67.417 1839 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.25 % Allowed : 19.80 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.25), residues: 1246 helix: 1.41 (0.18), residues: 797 sheet: -2.83 (0.62), residues: 63 loop : -0.81 (0.34), residues: 386 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 0.033 0.002 PHE C 373 TRP 0.023 0.001 TRP B 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00307 (11321) covalent geometry : angle 0.56590 (15529) hydrogen bonds : bond 0.03248 ( 605) hydrogen bonds : angle 4.05743 ( 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 183 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7919 (m-30) cc_final: 0.7495 (t0) REVERT: A 173 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 176 ARG cc_start: 0.7315 (mtm-85) cc_final: 0.6906 (mtm-85) REVERT: A 226 LEU cc_start: 0.8642 (tp) cc_final: 0.8320 (tp) REVERT: A 237 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7193 (ptm160) REVERT: A 300 MET cc_start: 0.8446 (mtt) cc_final: 0.8081 (mtt) REVERT: A 390 HIS cc_start: 0.7654 (t-90) cc_final: 0.7233 (t-90) REVERT: B 90 TRP cc_start: 0.8233 (m-10) cc_final: 0.7938 (m-10) REVERT: B 176 ARG cc_start: 0.7502 (tpt90) cc_final: 0.6819 (tpm170) REVERT: B 329 THR cc_start: 0.9107 (m) cc_final: 0.8832 (p) REVERT: B 348 ASP cc_start: 0.7777 (m-30) cc_final: 0.7544 (m-30) REVERT: C 28 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: C 351 LYS cc_start: 0.7085 (mttp) cc_final: 0.6401 (mttp) REVERT: D 272 TYR cc_start: 0.6382 (m-80) cc_final: 0.5975 (m-80) REVERT: D 279 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: D 280 GLN cc_start: 0.3161 (OUTLIER) cc_final: 0.2807 (tp40) REVERT: D 343 GLU cc_start: 0.7408 (mp0) cc_final: 0.7148 (mp0) REVERT: D 344 LYS cc_start: 0.8151 (pttm) cc_final: 0.7887 (pttp) REVERT: D 360 PHE cc_start: 0.8650 (t80) cc_final: 0.8382 (t80) outliers start: 36 outliers final: 26 residues processed: 175 average time/residue: 0.0963 time to fit residues: 24.6840 Evaluate side-chains 163 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 143 TRP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 377 CYS 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 367 MET Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 254 GLN 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 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 0.0370 chunk 109 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** 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 327 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.170834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118828 restraints weight = 16173.698| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.81 r_work: 0.3539 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2368 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= 0.122 Angle : 0.562 8.760 15529 Z= 0.292 Chirality : 0.039 0.256 1723 Planarity : 0.004 0.049 1843 Dihedral : 16.845 66.481 1839 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.98 % Allowed : 20.07 % Favored : 76.94 % 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: 0.81 (0.25), residues: 1246 helix: 1.47 (0.18), residues: 801 sheet: -2.67 (0.63), residues: 63 loop : -0.82 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.030 0.001 TYR D 354 PHE 0.022 0.001 PHE A 355 TRP 0.054 0.002 TRP B 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00267 (11321) covalent geometry : angle 0.56231 (15529) hydrogen bonds : bond 0.03182 ( 605) hydrogen bonds : angle 4.02055 ( 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 178 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.447 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: 0.7480 (t0) REVERT: A 173 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8241 (tt) REVERT: A 176 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6893 (mtm-85) REVERT: A 237 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7076 (ttt-90) REVERT: A 300 MET cc_start: 0.8444 (mtt) cc_final: 0.8089 (mtt) REVERT: A 390 HIS cc_start: 0.7625 (t-90) cc_final: 0.7195 (t-90) REVERT: B 90 TRP cc_start: 0.8245 (m-10) cc_final: 0.7936 (m-10) REVERT: B 100 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: B 329 THR cc_start: 0.9118 (m) cc_final: 0.8841 (p) REVERT: B 348 ASP cc_start: 0.7771 (m-30) cc_final: 0.7539 (m-30) REVERT: C 351 LYS cc_start: 0.7080 (mttp) cc_final: 0.6426 (mttp) REVERT: D 272 TYR cc_start: 0.6426 (m-80) cc_final: 0.6018 (m-80) REVERT: D 279 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: D 330 TRP cc_start: 0.7398 (t60) cc_final: 0.6884 (t60) REVERT: D 343 GLU cc_start: 0.7425 (mp0) cc_final: 0.7209 (mp0) REVERT: D 360 PHE cc_start: 0.8685 (t80) cc_final: 0.8441 (t80) outliers start: 33 outliers final: 21 residues processed: 170 average time/residue: 0.0999 time to fit residues: 24.7879 Evaluate side-chains 153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 277 PHE 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 337 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 254 GLN Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 175 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.170690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.119056 restraints weight = 15947.317| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.77 r_work: 0.3541 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11321 Z= 0.128 Angle : 0.568 8.140 15529 Z= 0.295 Chirality : 0.039 0.224 1723 Planarity : 0.004 0.048 1843 Dihedral : 16.806 66.255 1839 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.98 % Allowed : 19.98 % 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: 0.88 (0.25), residues: 1246 helix: 1.53 (0.18), residues: 805 sheet: -2.53 (0.64), residues: 63 loop : -0.87 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 176 TYR 0.018 0.002 TYR A 244 PHE 0.030 0.001 PHE C 373 TRP 0.053 0.002 TRP B 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00283 (11321) covalent geometry : angle 0.56809 (15529) hydrogen bonds : bond 0.03159 ( 605) hydrogen bonds : angle 4.00079 ( 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 167 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7927 (m-30) cc_final: 0.7470 (t0) REVERT: A 173 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 176 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6889 (mtm-85) REVERT: A 226 LEU cc_start: 0.8591 (tp) cc_final: 0.8333 (tp) REVERT: A 237 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7104 (ttt-90) REVERT: A 300 MET cc_start: 0.8452 (mtt) cc_final: 0.8109 (mtt) REVERT: A 390 HIS cc_start: 0.7616 (t-90) cc_final: 0.7189 (t-90) REVERT: B 90 TRP cc_start: 0.8252 (m-10) cc_final: 0.7953 (m-10) REVERT: B 100 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: B 329 THR cc_start: 0.9120 (m) cc_final: 0.8820 (p) REVERT: B 348 ASP cc_start: 0.7776 (m-30) cc_final: 0.7555 (m-30) REVERT: C 28 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: C 303 PHE cc_start: 0.8553 (t80) cc_final: 0.8247 (t80) REVERT: C 334 GLN cc_start: 0.8645 (tt0) cc_final: 0.7999 (pp30) REVERT: C 351 LYS cc_start: 0.7094 (mttp) cc_final: 0.6655 (mttp) REVERT: D 275 ASP cc_start: 0.6827 (t0) cc_final: 0.5750 (m-30) REVERT: D 279 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: D 343 GLU cc_start: 0.7426 (mp0) cc_final: 0.7189 (mp0) REVERT: D 358 MET cc_start: 0.7864 (mmt) cc_final: 0.7295 (mmp) REVERT: D 360 PHE cc_start: 0.8663 (t80) cc_final: 0.8453 (t80) outliers start: 33 outliers final: 24 residues processed: 161 average time/residue: 0.0889 time to fit residues: 21.2203 Evaluate side-chains 154 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 173 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 377 CYS 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 292 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.170854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118830 restraints weight = 16277.366| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.81 r_work: 0.3538 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11321 Z= 0.132 Angle : 0.585 9.005 15529 Z= 0.305 Chirality : 0.040 0.223 1723 Planarity : 0.005 0.053 1843 Dihedral : 16.762 66.375 1839 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.71 % Allowed : 20.34 % Favored : 76.94 % 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: 0.85 (0.25), residues: 1246 helix: 1.53 (0.18), residues: 804 sheet: -2.47 (0.64), residues: 63 loop : -0.93 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 176 TYR 0.017 0.001 TYR A 244 PHE 0.027 0.001 PHE A 355 TRP 0.050 0.002 TRP B 330 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00293 (11321) covalent geometry : angle 0.58469 (15529) hydrogen bonds : bond 0.03216 ( 605) hydrogen bonds : angle 4.04870 ( 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 158 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7929 (m-30) cc_final: 0.7466 (t0) REVERT: A 173 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 176 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: A 226 LEU cc_start: 0.8575 (tp) cc_final: 0.8294 (tp) REVERT: A 237 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7113 (ttt-90) REVERT: A 300 MET cc_start: 0.8454 (mtt) cc_final: 0.8108 (mtt) REVERT: A 343 GLU cc_start: 0.7072 (pp20) cc_final: 0.6778 (pp20) REVERT: A 390 HIS cc_start: 0.7618 (t-90) cc_final: 0.7200 (t-90) REVERT: B 90 TRP cc_start: 0.8249 (m-10) cc_final: 0.7951 (m-10) REVERT: B 100 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: B 329 THR cc_start: 0.9117 (m) cc_final: 0.8824 (p) REVERT: C 28 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 303 PHE cc_start: 0.8577 (t80) cc_final: 0.8264 (t80) REVERT: C 351 LYS cc_start: 0.7045 (mttp) cc_final: 0.6614 (mttp) REVERT: D 275 ASP cc_start: 0.6803 (t0) cc_final: 0.5816 (m-30) REVERT: D 279 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: D 331 LYS cc_start: 0.8787 (tttm) cc_final: 0.8497 (tmtt) REVERT: D 343 GLU cc_start: 0.7368 (mp0) cc_final: 0.7147 (mp0) REVERT: D 358 MET cc_start: 0.7867 (mmt) cc_final: 0.7536 (mmp) REVERT: D 360 PHE cc_start: 0.8624 (t80) cc_final: 0.8417 (t80) outliers start: 30 outliers final: 23 residues processed: 152 average time/residue: 0.1067 time to fit residues: 23.6125 Evaluate side-chains 153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 237 ARG Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 377 CYS 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 292 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 396 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 0.0030 chunk 115 optimal weight: 0.9980 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** B 123 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.170883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119358 restraints weight = 16140.286| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.78 r_work: 0.3547 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11321 Z= 0.131 Angle : 0.586 9.264 15529 Z= 0.306 Chirality : 0.039 0.197 1723 Planarity : 0.005 0.053 1843 Dihedral : 16.733 65.810 1839 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 20.71 % Favored : 76.85 % 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: 0.89 (0.25), residues: 1246 helix: 1.55 (0.18), residues: 805 sheet: -2.48 (0.64), residues: 64 loop : -0.87 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 176 TYR 0.017 0.001 TYR A 244 PHE 0.022 0.001 PHE A 355 TRP 0.077 0.002 TRP B 330 HIS 0.011 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00292 (11321) covalent geometry : angle 0.58630 (15529) hydrogen bonds : bond 0.03220 ( 605) hydrogen bonds : angle 4.04224 ( 1760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.42 seconds wall clock time: 48 minutes 5.89 seconds (2885.89 seconds total)