Starting phenix.real_space_refine on Fri Dec 19 21:14:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.map" model { file = "/net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vai_8653/12_2025/5vai_8653.cif" } resolution = 4.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5777 2.51 5 N 1582 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9099 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2969 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 5, 'ASN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1905 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2586 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.27, per 1000 atoms: 0.25 Number of scatterers: 9099 At special positions: 0 Unit cell: (168, 101, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1684 8.00 N 1582 7.00 C 5777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.95 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 322.1 milliseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2210 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 43.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 123 through 127 Processing helix chain 'R' and resid 137 through 169 removed outlier: 4.122A pdb=" N LEU R 141 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER R 155 " --> pdb=" O GLY R 151 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 156 " --> pdb=" O TYR R 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 211 removed outlier: 3.614A pdb=" N MET R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 223 removed outlier: 4.286A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.544A pdb=" N LEU R 268 " --> pdb=" O ARG R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 292 removed outlier: 3.515A pdb=" N LEU R 278 " --> pdb=" O TRP R 274 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 304 through 338 removed outlier: 3.881A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.973A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 343 Processing helix chain 'R' and resid 345 through 355 removed outlier: 4.059A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 removed outlier: 3.521A pdb=" N LEU R 360 " --> pdb=" O LEU R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 369 Processing helix chain 'R' and resid 379 through 403 removed outlier: 3.911A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 8 through 34 removed outlier: 4.399A pdb=" N PHE P 12 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 16 " --> pdb=" O PHE P 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.778A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.814A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.682A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.653A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.748A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.023A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.691A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 2 through 25 removed outlier: 4.119A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 4.508A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.531A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.700A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.163A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.516A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.119A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.516A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.783A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.689A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.566A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2987 1.34 - 1.46: 2311 1.46 - 1.59: 3920 1.59 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 9293 Sorted by residual: bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.63e+00 bond pdb=" CG LEU R 142 " pdb=" CD1 LEU R 142 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 bond pdb=" CB TRP R 274 " pdb=" CG TRP R 274 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.03e+00 bond pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 3.02e+00 ... (remaining 9288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 12321 3.10 - 6.20: 255 6.20 - 9.29: 30 9.29 - 12.39: 4 12.39 - 15.49: 2 Bond angle restraints: 12612 Sorted by residual: angle pdb=" C LEU R 401 " pdb=" N TYR R 402 " pdb=" CA TYR R 402 " ideal model delta sigma weight residual 122.37 113.37 9.00 1.54e+00 4.22e-01 3.42e+01 angle pdb=" CA LEU R 166 " pdb=" CB LEU R 166 " pdb=" CG LEU R 166 " ideal model delta sigma weight residual 116.30 100.81 15.49 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N ASP R 68 " pdb=" CA ASP R 68 " pdb=" C ASP R 68 " ideal model delta sigma weight residual 113.28 106.56 6.72 1.57e+00 4.06e-01 1.83e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 109.34 100.67 8.67 2.08e+00 2.31e-01 1.74e+01 angle pdb=" N ALA A 366 " pdb=" CA ALA A 366 " pdb=" C ALA A 366 " ideal model delta sigma weight residual 111.69 106.63 5.06 1.23e+00 6.61e-01 1.69e+01 ... (remaining 12607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 5228 16.04 - 32.07: 224 32.07 - 48.11: 36 48.11 - 64.15: 6 64.15 - 80.18: 5 Dihedral angle restraints: 5499 sinusoidal: 2077 harmonic: 3422 Sorted by residual: dihedral pdb=" CA LEU R 167 " pdb=" C LEU R 167 " pdb=" N GLY R 168 " pdb=" CA GLY R 168 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA CYS R 296 " pdb=" C CYS R 296 " pdb=" N TRP R 297 " pdb=" CA TRP R 297 " ideal model delta harmonic sigma weight residual 180.00 159.74 20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 979 0.051 - 0.101: 353 0.101 - 0.152: 71 0.152 - 0.203: 9 0.203 - 0.253: 4 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA TRP R 297 " pdb=" N TRP R 297 " pdb=" C TRP R 297 " pdb=" CB TRP R 297 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PHE R 169 " pdb=" N PHE R 169 " pdb=" C PHE R 169 " pdb=" CB PHE R 169 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL A 367 " pdb=" N VAL A 367 " pdb=" C VAL A 367 " pdb=" CB VAL A 367 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1413 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 176 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ARG R 176 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG R 176 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN R 177 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 155 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C SER R 155 " -0.054 2.00e-02 2.50e+03 pdb=" O SER R 155 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 156 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 156 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C PHE R 156 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE R 156 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 195 2.62 - 3.19: 9343 3.19 - 3.76: 14482 3.76 - 4.33: 20190 4.33 - 4.90: 31115 Nonbonded interactions: 75325 Sorted by model distance: nonbonded pdb=" OG1 THR A 325 " pdb=" OH TYR A 339 " model vdw 2.049 3.040 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.074 3.040 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.100 3.040 nonbonded pdb=" OG1 THR R 175 " pdb=" OH TYR R 250 " model vdw 2.113 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH2 ARG A 336 " model vdw 2.121 3.120 ... (remaining 75320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.012 0.918 9299 Z= 0.602 Angle : 1.126 21.083 12624 Z= 0.632 Chirality : 0.054 0.253 1416 Planarity : 0.007 0.055 1612 Dihedral : 9.722 80.183 3271 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.40 % Favored : 95.26 % Rotamer: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.22), residues: 1160 helix: -0.71 (0.22), residues: 407 sheet: -1.16 (0.31), residues: 221 loop : -1.03 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 48 TYR 0.024 0.004 TYR N 32 PHE 0.034 0.004 PHE A 312 TRP 0.041 0.005 TRP R 120 HIS 0.021 0.004 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 9293) covalent geometry : angle 1.10919 (12612) SS BOND : bond 0.37475 ( 6) SS BOND : angle 6.39916 ( 12) hydrogen bonds : bond 0.15063 ( 473) hydrogen bonds : angle 10.59459 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 157 SER cc_start: 0.8754 (m) cc_final: 0.8529 (p) REVERT: R 176 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7290 (ttm-80) REVERT: R 229 VAL cc_start: 0.9257 (t) cc_final: 0.9050 (p) REVERT: R 272 ILE cc_start: 0.8281 (tt) cc_final: 0.7956 (mt) REVERT: R 325 ILE cc_start: 0.8536 (mt) cc_final: 0.8287 (mt) REVERT: R 340 MET cc_start: 0.7809 (tmt) cc_final: 0.7419 (tpt) REVERT: R 351 LYS cc_start: 0.8588 (tptt) cc_final: 0.8079 (tmtt) REVERT: R 387 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8679 (tm-30) REVERT: R 413 PHE cc_start: 0.8138 (t80) cc_final: 0.7909 (t80) REVERT: P 15 ASP cc_start: 0.8876 (t0) cc_final: 0.8602 (t0) REVERT: A 11 ASP cc_start: 0.8495 (t0) cc_final: 0.8012 (t0) REVERT: A 28 LYS cc_start: 0.7186 (mmpt) cc_final: 0.6584 (ptpp) REVERT: A 44 LEU cc_start: 0.8878 (tp) cc_final: 0.8342 (tp) REVERT: A 222 PHE cc_start: 0.7438 (t80) cc_final: 0.7215 (t80) REVERT: A 229 ASP cc_start: 0.8079 (p0) cc_final: 0.7570 (p0) REVERT: A 255 MET cc_start: 0.6727 (ptt) cc_final: 0.6397 (ptm) REVERT: A 283 ARG cc_start: 0.8608 (mtt180) cc_final: 0.7981 (ptp-170) REVERT: A 285 ILE cc_start: 0.9116 (mm) cc_final: 0.8906 (tp) REVERT: A 309 GLU cc_start: 0.9112 (pt0) cc_final: 0.8607 (tp30) REVERT: A 318 TYR cc_start: 0.6146 (t80) cc_final: 0.5829 (t80) REVERT: A 344 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8687 (mm-30) REVERT: A 360 TYR cc_start: 0.8502 (m-10) cc_final: 0.8001 (m-10) REVERT: A 386 MET cc_start: 0.9090 (tmt) cc_final: 0.8635 (tmm) REVERT: B 12 GLU cc_start: 0.8520 (tt0) cc_final: 0.8302 (tm-30) REVERT: B 49 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7168 (mmt-90) REVERT: B 120 ILE cc_start: 0.8720 (mt) cc_final: 0.8422 (mm) REVERT: B 148 CYS cc_start: 0.8588 (t) cc_final: 0.8010 (t) REVERT: B 160 SER cc_start: 0.8678 (p) cc_final: 0.8254 (t) REVERT: B 210 LEU cc_start: 0.9040 (tp) cc_final: 0.8793 (tp) REVERT: B 228 ASP cc_start: 0.7546 (m-30) cc_final: 0.7334 (m-30) REVERT: B 235 PHE cc_start: 0.7800 (t80) cc_final: 0.7373 (t80) REVERT: B 264 TYR cc_start: 0.6493 (m-10) cc_final: 0.6167 (m-80) REVERT: B 273 ILE cc_start: 0.9099 (mp) cc_final: 0.8808 (mp) REVERT: N 45 LEU cc_start: 0.8001 (mp) cc_final: 0.7593 (mt) REVERT: N 47 TRP cc_start: 0.8346 (t60) cc_final: 0.7129 (t60) REVERT: N 51 ILE cc_start: 0.8450 (tt) cc_final: 0.8248 (tp) REVERT: N 81 LEU cc_start: 0.9292 (tp) cc_final: 0.8910 (tp) REVERT: N 86 LEU cc_start: 0.8453 (mp) cc_final: 0.8172 (mt) outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.1123 time to fit residues: 75.6530 Evaluate side-chains 340 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN R 240 ASN R 302 ASN R 363 HIS A 227 GLN A 267 GLN A 271 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.134908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.116846 restraints weight = 27444.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120616 restraints weight = 15604.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123207 restraints weight = 10063.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.125023 restraints weight = 7048.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.126190 restraints weight = 5254.876| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9299 Z= 0.193 Angle : 0.819 12.347 12624 Z= 0.434 Chirality : 0.048 0.209 1416 Planarity : 0.006 0.061 1612 Dihedral : 5.733 28.249 1277 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.72 % Rotamer: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.23), residues: 1160 helix: -0.05 (0.23), residues: 426 sheet: -0.74 (0.34), residues: 207 loop : -0.55 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 20 TYR 0.026 0.003 TYR R 289 PHE 0.025 0.003 PHE R 381 TRP 0.022 0.003 TRP P 31 HIS 0.011 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9293) covalent geometry : angle 0.81706 (12612) SS BOND : bond 0.02411 ( 6) SS BOND : angle 2.19973 ( 12) hydrogen bonds : bond 0.05822 ( 473) hydrogen bonds : angle 7.17286 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 433 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 123 LEU cc_start: 0.7087 (tt) cc_final: 0.6883 (mm) REVERT: R 176 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7267 (ttm-80) REVERT: R 180 HIS cc_start: 0.8152 (m-70) cc_final: 0.7883 (m-70) REVERT: R 229 VAL cc_start: 0.9184 (t) cc_final: 0.8943 (p) REVERT: R 272 ILE cc_start: 0.8161 (tt) cc_final: 0.7913 (mt) REVERT: R 351 LYS cc_start: 0.8552 (tptt) cc_final: 0.7927 (tmtt) REVERT: A 28 LYS cc_start: 0.6936 (mmpt) cc_final: 0.6673 (ptpp) REVERT: A 32 LYS cc_start: 0.9172 (mttt) cc_final: 0.8951 (mttp) REVERT: A 209 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6834 (tm-30) REVERT: A 229 ASP cc_start: 0.8123 (p0) cc_final: 0.7651 (p0) REVERT: A 237 CYS cc_start: 0.8691 (m) cc_final: 0.8208 (m) REVERT: A 273 PHE cc_start: 0.9157 (t80) cc_final: 0.8648 (t80) REVERT: A 279 ASN cc_start: 0.8765 (t0) cc_final: 0.8450 (t0) REVERT: A 283 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8051 (ptp-170) REVERT: A 287 VAL cc_start: 0.8950 (t) cc_final: 0.8723 (t) REVERT: A 289 LEU cc_start: 0.8861 (tp) cc_final: 0.8196 (tp) REVERT: A 360 TYR cc_start: 0.8712 (m-10) cc_final: 0.8334 (m-10) REVERT: A 371 ASN cc_start: 0.8340 (p0) cc_final: 0.8081 (p0) REVERT: A 383 ILE cc_start: 0.9169 (tt) cc_final: 0.8721 (tp) REVERT: A 386 MET cc_start: 0.8150 (ttt) cc_final: 0.7942 (tmm) REVERT: A 388 LEU cc_start: 0.9242 (mm) cc_final: 0.8899 (mm) REVERT: B 6 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 13 GLN cc_start: 0.8695 (tt0) cc_final: 0.8236 (pt0) REVERT: B 49 ARG cc_start: 0.7639 (mmt-90) cc_final: 0.7410 (mmt-90) REVERT: B 52 ARG cc_start: 0.7373 (ptp-170) cc_final: 0.7045 (ptp-170) REVERT: B 62 HIS cc_start: 0.8179 (t-170) cc_final: 0.7963 (t-170) REVERT: B 63 TRP cc_start: 0.8610 (m100) cc_final: 0.8295 (m100) REVERT: B 66 ASP cc_start: 0.8155 (p0) cc_final: 0.7949 (p0) REVERT: B 89 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8933 (mmmm) REVERT: B 120 ILE cc_start: 0.8667 (mt) cc_final: 0.8395 (mm) REVERT: B 153 ASP cc_start: 0.8213 (p0) cc_final: 0.7233 (p0) REVERT: B 210 LEU cc_start: 0.8922 (tp) cc_final: 0.8398 (tp) REVERT: B 220 GLN cc_start: 0.7916 (mp10) cc_final: 0.7284 (mp10) REVERT: B 235 PHE cc_start: 0.8075 (t80) cc_final: 0.7619 (t80) REVERT: B 246 ASP cc_start: 0.8263 (m-30) cc_final: 0.7950 (m-30) REVERT: B 251 ARG cc_start: 0.7039 (mtt180) cc_final: 0.5656 (mtt180) REVERT: B 264 TYR cc_start: 0.6759 (m-10) cc_final: 0.6296 (m-80) REVERT: B 273 ILE cc_start: 0.9137 (mp) cc_final: 0.8709 (mp) REVERT: B 278 PHE cc_start: 0.7365 (m-80) cc_final: 0.7131 (m-80) REVERT: B 283 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.8156 (tpt170) REVERT: B 308 LEU cc_start: 0.7068 (mt) cc_final: 0.6823 (mt) REVERT: B 325 MET cc_start: 0.8318 (tpp) cc_final: 0.7804 (tmm) REVERT: B 337 LYS cc_start: 0.8610 (tppt) cc_final: 0.8167 (tppt) REVERT: N 34 MET cc_start: 0.9171 (ttm) cc_final: 0.8851 (ttp) REVERT: N 47 TRP cc_start: 0.8221 (t60) cc_final: 0.6885 (t60) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.1044 time to fit residues: 60.5575 Evaluate side-chains 345 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN R 177 ASN R 212 HIS R 213 GLN R 240 ASN A 271 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.117784 restraints weight = 27465.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121617 restraints weight = 15741.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.124225 restraints weight = 10137.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.125976 restraints weight = 7077.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.127321 restraints weight = 5306.260| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9299 Z= 0.167 Angle : 0.719 8.946 12624 Z= 0.385 Chirality : 0.045 0.176 1416 Planarity : 0.005 0.064 1612 Dihedral : 5.522 25.811 1277 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1160 helix: -0.15 (0.23), residues: 435 sheet: -0.68 (0.34), residues: 214 loop : -0.56 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 40 TYR 0.045 0.002 TYR R 269 PHE 0.036 0.003 PHE R 184 TRP 0.025 0.003 TRP B 169 HIS 0.009 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9293) covalent geometry : angle 0.71777 (12612) SS BOND : bond 0.01114 ( 6) SS BOND : angle 1.37173 ( 12) hydrogen bonds : bond 0.05156 ( 473) hydrogen bonds : angle 6.64003 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 229 VAL cc_start: 0.9195 (t) cc_final: 0.8953 (p) REVERT: R 272 ILE cc_start: 0.8240 (tt) cc_final: 0.7985 (mt) REVERT: R 351 LYS cc_start: 0.8572 (tptt) cc_final: 0.7939 (tmtt) REVERT: R 397 MET cc_start: 0.7569 (mmp) cc_final: 0.7359 (mtp) REVERT: A 28 LYS cc_start: 0.6900 (mmpt) cc_final: 0.6495 (ptpp) REVERT: A 32 LYS cc_start: 0.9143 (mttt) cc_final: 0.8929 (mttp) REVERT: A 45 LEU cc_start: 0.9270 (tp) cc_final: 0.9058 (tp) REVERT: A 229 ASP cc_start: 0.8102 (p0) cc_final: 0.7665 (p0) REVERT: A 241 VAL cc_start: 0.9148 (t) cc_final: 0.8780 (p) REVERT: A 271 ASN cc_start: 0.8488 (m110) cc_final: 0.8154 (m-40) REVERT: A 279 ASN cc_start: 0.8819 (t0) cc_final: 0.8500 (t0) REVERT: A 283 ARG cc_start: 0.8309 (mtt180) cc_final: 0.8048 (mtt-85) REVERT: A 291 LEU cc_start: 0.9348 (mt) cc_final: 0.9026 (mt) REVERT: A 383 ILE cc_start: 0.9135 (tt) cc_final: 0.8783 (tp) REVERT: A 386 MET cc_start: 0.8098 (ttt) cc_final: 0.7564 (tmm) REVERT: A 388 LEU cc_start: 0.9168 (mm) cc_final: 0.8906 (mm) REVERT: B 49 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7510 (mmt-90) REVERT: B 61 MET cc_start: 0.9001 (ppp) cc_final: 0.8405 (ppp) REVERT: B 66 ASP cc_start: 0.8120 (p0) cc_final: 0.7915 (p0) REVERT: B 71 VAL cc_start: 0.9155 (m) cc_final: 0.8939 (m) REVERT: B 89 LYS cc_start: 0.9464 (mmmm) cc_final: 0.9021 (mmmm) REVERT: B 102 THR cc_start: 0.8806 (t) cc_final: 0.8434 (m) REVERT: B 120 ILE cc_start: 0.8679 (mt) cc_final: 0.8429 (mm) REVERT: B 153 ASP cc_start: 0.7737 (p0) cc_final: 0.7369 (p0) REVERT: B 170 ASP cc_start: 0.7422 (t0) cc_final: 0.7199 (t0) REVERT: B 210 LEU cc_start: 0.8713 (tp) cc_final: 0.8294 (tp) REVERT: B 220 GLN cc_start: 0.7897 (mp10) cc_final: 0.7366 (mp10) REVERT: B 235 PHE cc_start: 0.8065 (t80) cc_final: 0.7638 (t80) REVERT: B 264 TYR cc_start: 0.6920 (m-10) cc_final: 0.6411 (m-10) REVERT: B 278 PHE cc_start: 0.7312 (m-80) cc_final: 0.7007 (m-80) REVERT: B 293 ASN cc_start: 0.8058 (m-40) cc_final: 0.7814 (m-40) REVERT: B 297 TRP cc_start: 0.8177 (m100) cc_final: 0.7911 (m100) REVERT: B 325 MET cc_start: 0.8471 (tpp) cc_final: 0.8075 (tmm) REVERT: N 27 PHE cc_start: 0.8310 (p90) cc_final: 0.8096 (p90) REVERT: N 32 TYR cc_start: 0.8515 (m-80) cc_final: 0.8126 (m-10) REVERT: N 47 TRP cc_start: 0.8231 (t60) cc_final: 0.6694 (t60) REVERT: N 67 ARG cc_start: 0.7909 (ptp-110) cc_final: 0.7680 (ptp90) REVERT: N 68 PHE cc_start: 0.8733 (m-80) cc_final: 0.7870 (m-80) outliers start: 2 outliers final: 1 residues processed: 420 average time/residue: 0.1084 time to fit residues: 60.9127 Evaluate side-chains 342 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN R 240 ASN R 302 ASN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.136158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.118083 restraints weight = 27644.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.121875 restraints weight = 15823.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.124437 restraints weight = 10251.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.126176 restraints weight = 7214.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.127509 restraints weight = 5425.789| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9299 Z= 0.172 Angle : 0.724 8.883 12624 Z= 0.385 Chirality : 0.048 0.410 1416 Planarity : 0.005 0.057 1612 Dihedral : 5.416 25.614 1277 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 0.11 % Allowed : 3.84 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1160 helix: -0.19 (0.23), residues: 436 sheet: -0.55 (0.35), residues: 205 loop : -0.49 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 374 TYR 0.023 0.002 TYR A 391 PHE 0.032 0.003 PHE R 184 TRP 0.026 0.002 TRP B 169 HIS 0.009 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9293) covalent geometry : angle 0.72304 (12612) SS BOND : bond 0.00467 ( 6) SS BOND : angle 1.45528 ( 12) hydrogen bonds : bond 0.04975 ( 473) hydrogen bonds : angle 6.26309 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 180 HIS cc_start: 0.8874 (m-70) cc_final: 0.8495 (m-70) REVERT: R 181 LEU cc_start: 0.9145 (mt) cc_final: 0.8848 (mt) REVERT: R 205 TYR cc_start: 0.8415 (t80) cc_final: 0.8145 (t80) REVERT: R 262 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6493 (mm-30) REVERT: R 272 ILE cc_start: 0.8169 (tt) cc_final: 0.7931 (mt) REVERT: R 309 ILE cc_start: 0.7991 (tt) cc_final: 0.7776 (tt) REVERT: R 351 LYS cc_start: 0.8639 (tptt) cc_final: 0.7995 (tmtt) REVERT: R 411 MET cc_start: 0.8067 (mmp) cc_final: 0.7838 (mmp) REVERT: A 28 LYS cc_start: 0.6827 (mmpt) cc_final: 0.6564 (ptpp) REVERT: A 32 LYS cc_start: 0.9125 (mttt) cc_final: 0.8837 (mttt) REVERT: A 35 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7742 (mm-40) REVERT: A 229 ASP cc_start: 0.8159 (p0) cc_final: 0.7703 (p0) REVERT: A 279 ASN cc_start: 0.8866 (t0) cc_final: 0.8540 (t0) REVERT: A 283 ARG cc_start: 0.8308 (mtt180) cc_final: 0.8038 (mtt-85) REVERT: A 291 LEU cc_start: 0.9358 (mt) cc_final: 0.9070 (mt) REVERT: A 295 ASP cc_start: 0.8344 (p0) cc_final: 0.7834 (p0) REVERT: A 335 THR cc_start: 0.8669 (m) cc_final: 0.8296 (p) REVERT: A 383 ILE cc_start: 0.9117 (tt) cc_final: 0.8731 (tp) REVERT: A 386 MET cc_start: 0.8013 (ttt) cc_final: 0.7797 (tmm) REVERT: A 388 LEU cc_start: 0.9235 (mm) cc_final: 0.8924 (mm) REVERT: B 6 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6765 (tm-30) REVERT: B 49 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7347 (mmt-90) REVERT: B 66 ASP cc_start: 0.8166 (p0) cc_final: 0.7943 (p0) REVERT: B 71 VAL cc_start: 0.9142 (m) cc_final: 0.8461 (p) REVERT: B 89 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9047 (mmmm) REVERT: B 120 ILE cc_start: 0.8684 (mt) cc_final: 0.8441 (mm) REVERT: B 153 ASP cc_start: 0.7721 (p0) cc_final: 0.7189 (p0) REVERT: B 170 ASP cc_start: 0.7424 (t0) cc_final: 0.7219 (t0) REVERT: B 210 LEU cc_start: 0.8724 (tp) cc_final: 0.8324 (tp) REVERT: B 220 GLN cc_start: 0.7972 (mp10) cc_final: 0.7311 (mp10) REVERT: B 235 PHE cc_start: 0.8065 (t80) cc_final: 0.7826 (t80) REVERT: B 246 ASP cc_start: 0.8746 (m-30) cc_final: 0.8172 (m-30) REVERT: B 264 TYR cc_start: 0.6695 (m-10) cc_final: 0.6351 (m-10) REVERT: B 273 ILE cc_start: 0.9249 (mp) cc_final: 0.8972 (mp) REVERT: B 297 TRP cc_start: 0.8222 (m100) cc_final: 0.7684 (m100) REVERT: B 313 ASN cc_start: 0.7672 (m110) cc_final: 0.7288 (m110) REVERT: B 325 MET cc_start: 0.8372 (tpp) cc_final: 0.7997 (tmm) REVERT: B 337 LYS cc_start: 0.8457 (tppt) cc_final: 0.8114 (tppt) REVERT: N 32 TYR cc_start: 0.8615 (m-80) cc_final: 0.8085 (m-10) REVERT: N 34 MET cc_start: 0.9047 (ttp) cc_final: 0.8214 (tpp) REVERT: N 47 TRP cc_start: 0.8432 (t60) cc_final: 0.7880 (t60) REVERT: N 81 LEU cc_start: 0.8591 (tp) cc_final: 0.8305 (tt) outliers start: 1 outliers final: 1 residues processed: 412 average time/residue: 0.1042 time to fit residues: 58.2327 Evaluate side-chains 339 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN A 220 HIS A 271 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.120787 restraints weight = 27371.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.124662 restraints weight = 15581.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.127292 restraints weight = 9974.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.129116 restraints weight = 6943.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130431 restraints weight = 5136.280| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9299 Z= 0.149 Angle : 0.696 9.142 12624 Z= 0.369 Chirality : 0.046 0.380 1416 Planarity : 0.005 0.053 1612 Dihedral : 5.237 25.545 1277 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1160 helix: 0.05 (0.24), residues: 434 sheet: -0.44 (0.34), residues: 212 loop : -0.60 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.024 0.002 TYR N 117 PHE 0.033 0.002 PHE R 184 TRP 0.033 0.002 TRP A 281 HIS 0.008 0.002 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9293) covalent geometry : angle 0.69505 (12612) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.32428 ( 12) hydrogen bonds : bond 0.04860 ( 473) hydrogen bonds : angle 6.02118 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 38 LYS cc_start: 0.7874 (pttm) cc_final: 0.7467 (pttp) REVERT: R 181 LEU cc_start: 0.9164 (mt) cc_final: 0.8914 (mt) REVERT: R 205 TYR cc_start: 0.8428 (t80) cc_final: 0.8169 (t80) REVERT: R 262 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6488 (mm-30) REVERT: R 351 LYS cc_start: 0.8661 (tptt) cc_final: 0.7995 (tmtt) REVERT: R 397 MET cc_start: 0.7744 (mtp) cc_final: 0.7391 (mtp) REVERT: R 407 ASN cc_start: 0.6997 (p0) cc_final: 0.6729 (p0) REVERT: A 28 LYS cc_start: 0.6739 (mmpt) cc_final: 0.6403 (ptpp) REVERT: A 35 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 44 LEU cc_start: 0.8337 (tp) cc_final: 0.8001 (tp) REVERT: A 229 ASP cc_start: 0.8117 (p0) cc_final: 0.7590 (p0) REVERT: A 274 LYS cc_start: 0.8771 (tttt) cc_final: 0.8358 (tttt) REVERT: A 279 ASN cc_start: 0.8892 (t0) cc_final: 0.8669 (t0) REVERT: A 283 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7873 (ptp-170) REVERT: A 291 LEU cc_start: 0.9290 (mt) cc_final: 0.9061 (mt) REVERT: A 295 ASP cc_start: 0.8405 (p0) cc_final: 0.7931 (p0) REVERT: A 383 ILE cc_start: 0.9154 (tt) cc_final: 0.8656 (tp) REVERT: A 386 MET cc_start: 0.7964 (ttt) cc_final: 0.7627 (tmm) REVERT: A 388 LEU cc_start: 0.9234 (mm) cc_final: 0.8988 (mm) REVERT: B 6 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6934 (tm-30) REVERT: B 49 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7208 (mmt90) REVERT: B 89 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9055 (mmmm) REVERT: B 120 ILE cc_start: 0.8637 (mt) cc_final: 0.8378 (mm) REVERT: B 145 TYR cc_start: 0.8026 (p90) cc_final: 0.7191 (p90) REVERT: B 153 ASP cc_start: 0.7780 (p0) cc_final: 0.7320 (p0) REVERT: B 210 LEU cc_start: 0.8715 (tp) cc_final: 0.8346 (tp) REVERT: B 220 GLN cc_start: 0.7599 (mp10) cc_final: 0.7197 (mp10) REVERT: B 246 ASP cc_start: 0.8773 (m-30) cc_final: 0.8316 (m-30) REVERT: B 264 TYR cc_start: 0.6729 (m-10) cc_final: 0.6257 (m-10) REVERT: B 273 ILE cc_start: 0.9209 (mp) cc_final: 0.8761 (mp) REVERT: B 283 ARG cc_start: 0.8351 (tpt170) cc_final: 0.7597 (tpt90) REVERT: B 284 LEU cc_start: 0.8615 (mp) cc_final: 0.8380 (mp) REVERT: B 297 TRP cc_start: 0.8185 (m100) cc_final: 0.7531 (m100) REVERT: B 313 ASN cc_start: 0.7367 (m110) cc_final: 0.7164 (m-40) REVERT: B 337 LYS cc_start: 0.8477 (tppt) cc_final: 0.8023 (tppt) REVERT: N 32 TYR cc_start: 0.8495 (m-80) cc_final: 0.8097 (m-10) REVERT: N 34 MET cc_start: 0.9109 (ttp) cc_final: 0.8576 (tpp) REVERT: N 81 LEU cc_start: 0.8383 (tp) cc_final: 0.8088 (tp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1055 time to fit residues: 58.4242 Evaluate side-chains 329 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 213 GLN R 240 ASN R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.138442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120029 restraints weight = 27970.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.123957 restraints weight = 15885.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.126609 restraints weight = 10201.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.128435 restraints weight = 7122.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129647 restraints weight = 5321.084| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9299 Z= 0.148 Angle : 0.714 9.122 12624 Z= 0.379 Chirality : 0.047 0.325 1416 Planarity : 0.004 0.050 1612 Dihedral : 5.181 23.537 1277 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1160 helix: -0.12 (0.24), residues: 439 sheet: -0.44 (0.33), residues: 222 loop : -0.49 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 317 TYR 0.023 0.002 TYR A 391 PHE 0.030 0.002 PHE R 184 TRP 0.028 0.002 TRP A 281 HIS 0.006 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9293) covalent geometry : angle 0.71297 (12612) SS BOND : bond 0.00280 ( 6) SS BOND : angle 1.15612 ( 12) hydrogen bonds : bond 0.04736 ( 473) hydrogen bonds : angle 5.95807 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 159 LEU cc_start: 0.9087 (tp) cc_final: 0.8843 (tp) REVERT: R 176 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7633 (ttt180) REVERT: R 180 HIS cc_start: 0.8953 (m-70) cc_final: 0.8737 (m-70) REVERT: R 181 LEU cc_start: 0.9214 (mt) cc_final: 0.8910 (mt) REVERT: R 205 TYR cc_start: 0.8417 (t80) cc_final: 0.8164 (t80) REVERT: R 351 LYS cc_start: 0.8705 (tptt) cc_final: 0.8011 (tmtt) REVERT: R 397 MET cc_start: 0.7486 (mtp) cc_final: 0.7180 (mtp) REVERT: A 28 LYS cc_start: 0.6933 (mmpt) cc_final: 0.6632 (mtmt) REVERT: A 32 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8433 (mttp) REVERT: A 44 LEU cc_start: 0.8239 (tp) cc_final: 0.7734 (tp) REVERT: A 229 ASP cc_start: 0.8081 (p0) cc_final: 0.7654 (p0) REVERT: A 279 ASN cc_start: 0.8910 (t0) cc_final: 0.8546 (t0) REVERT: A 291 LEU cc_start: 0.9346 (mt) cc_final: 0.9080 (mt) REVERT: A 383 ILE cc_start: 0.9143 (tt) cc_final: 0.8822 (tp) REVERT: A 386 MET cc_start: 0.8002 (ttt) cc_final: 0.7575 (tpp) REVERT: A 388 LEU cc_start: 0.9242 (mm) cc_final: 0.8965 (mm) REVERT: B 6 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 18 ILE cc_start: 0.8548 (pt) cc_final: 0.8344 (pt) REVERT: B 49 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7391 (mmt90) REVERT: B 66 ASP cc_start: 0.8118 (p0) cc_final: 0.7869 (p0) REVERT: B 89 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9070 (mmmm) REVERT: B 120 ILE cc_start: 0.8669 (mt) cc_final: 0.8424 (mm) REVERT: B 145 TYR cc_start: 0.8146 (p90) cc_final: 0.7741 (p90) REVERT: B 153 ASP cc_start: 0.7792 (p0) cc_final: 0.7460 (p0) REVERT: B 210 LEU cc_start: 0.8682 (tp) cc_final: 0.8339 (tp) REVERT: B 220 GLN cc_start: 0.7691 (mp10) cc_final: 0.7208 (mp10) REVERT: B 235 PHE cc_start: 0.7811 (t80) cc_final: 0.7324 (t80) REVERT: B 246 ASP cc_start: 0.8769 (m-30) cc_final: 0.8352 (m-30) REVERT: B 264 TYR cc_start: 0.6922 (m-10) cc_final: 0.6110 (m-80) REVERT: B 273 ILE cc_start: 0.9156 (mp) cc_final: 0.8688 (mp) REVERT: B 283 ARG cc_start: 0.8449 (tpt170) cc_final: 0.8170 (tpt170) REVERT: B 297 TRP cc_start: 0.8145 (m100) cc_final: 0.7594 (m100) REVERT: B 308 LEU cc_start: 0.7430 (mt) cc_final: 0.7122 (mt) REVERT: B 337 LYS cc_start: 0.8565 (tppt) cc_final: 0.8108 (tppt) REVERT: B 339 TRP cc_start: 0.8043 (m100) cc_final: 0.7716 (m-90) REVERT: G 24 ASN cc_start: 0.7342 (p0) cc_final: 0.6867 (t0) REVERT: N 28 THR cc_start: 0.8211 (t) cc_final: 0.7954 (t) REVERT: N 31 ASN cc_start: 0.8713 (m110) cc_final: 0.8293 (m110) REVERT: N 32 TYR cc_start: 0.8503 (m-80) cc_final: 0.8085 (m-10) REVERT: N 34 MET cc_start: 0.9039 (ttp) cc_final: 0.8620 (tpp) REVERT: N 67 ARG cc_start: 0.7908 (ptp90) cc_final: 0.7691 (ptp90) REVERT: N 82 GLN cc_start: 0.6905 (mm110) cc_final: 0.6615 (mm110) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.0995 time to fit residues: 52.5828 Evaluate side-chains 326 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 340 ASN G 18 GLN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.136978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.118574 restraints weight = 28168.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122347 restraints weight = 16117.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.124991 restraints weight = 10457.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.126812 restraints weight = 7386.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.128068 restraints weight = 5563.938| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9299 Z= 0.154 Angle : 0.692 8.839 12624 Z= 0.368 Chirality : 0.046 0.262 1416 Planarity : 0.005 0.050 1612 Dihedral : 5.089 23.337 1277 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.05 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1160 helix: -0.21 (0.24), residues: 451 sheet: -0.40 (0.34), residues: 224 loop : -0.64 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 385 TYR 0.021 0.002 TYR A 391 PHE 0.031 0.002 PHE R 184 TRP 0.024 0.002 TRP A 281 HIS 0.008 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9293) covalent geometry : angle 0.69101 (12612) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.23361 ( 12) hydrogen bonds : bond 0.04636 ( 473) hydrogen bonds : angle 5.86821 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.9217 (mt) cc_final: 0.8972 (mt) REVERT: R 205 TYR cc_start: 0.8365 (t80) cc_final: 0.8105 (t80) REVERT: R 272 ILE cc_start: 0.8290 (tt) cc_final: 0.8052 (mt) REVERT: R 309 ILE cc_start: 0.7989 (tt) cc_final: 0.7759 (tt) REVERT: R 351 LYS cc_start: 0.8741 (tptt) cc_final: 0.8014 (tmtt) REVERT: R 397 MET cc_start: 0.7458 (mtp) cc_final: 0.7117 (mtp) REVERT: R 411 MET cc_start: 0.8188 (mmp) cc_final: 0.7983 (mmp) REVERT: P 27 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 28 LYS cc_start: 0.7030 (mmpt) cc_final: 0.6775 (mtmt) REVERT: A 32 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8492 (mttp) REVERT: A 44 LEU cc_start: 0.8217 (tp) cc_final: 0.7632 (tp) REVERT: A 229 ASP cc_start: 0.8143 (p0) cc_final: 0.7746 (p0) REVERT: A 279 ASN cc_start: 0.8966 (t0) cc_final: 0.8630 (t0) REVERT: A 288 ILE cc_start: 0.8792 (tp) cc_final: 0.8592 (tp) REVERT: A 291 LEU cc_start: 0.9316 (mt) cc_final: 0.9061 (mt) REVERT: A 295 ASP cc_start: 0.8092 (p0) cc_final: 0.7322 (p0) REVERT: A 383 ILE cc_start: 0.9159 (tt) cc_final: 0.8813 (tp) REVERT: A 388 LEU cc_start: 0.9294 (mm) cc_final: 0.8980 (mm) REVERT: B 6 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 16 ASN cc_start: 0.8771 (m-40) cc_final: 0.8043 (m-40) REVERT: B 49 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7440 (mmt90) REVERT: B 57 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8306 (mtmm) REVERT: B 66 ASP cc_start: 0.8138 (p0) cc_final: 0.7904 (p0) REVERT: B 145 TYR cc_start: 0.8104 (p90) cc_final: 0.7639 (p90) REVERT: B 204 CYS cc_start: 0.8451 (m) cc_final: 0.7965 (m) REVERT: B 210 LEU cc_start: 0.8677 (tp) cc_final: 0.8472 (tp) REVERT: B 220 GLN cc_start: 0.7757 (mp10) cc_final: 0.7347 (mp10) REVERT: B 235 PHE cc_start: 0.7803 (t80) cc_final: 0.7416 (t80) REVERT: B 246 ASP cc_start: 0.8844 (m-30) cc_final: 0.8403 (m-30) REVERT: B 264 TYR cc_start: 0.7258 (m-10) cc_final: 0.6401 (m-80) REVERT: B 273 ILE cc_start: 0.9101 (mp) cc_final: 0.8670 (mp) REVERT: B 283 ARG cc_start: 0.8440 (tpt170) cc_final: 0.8030 (tpt170) REVERT: B 297 TRP cc_start: 0.8157 (m100) cc_final: 0.7624 (m100) REVERT: B 313 ASN cc_start: 0.7548 (m110) cc_final: 0.7323 (m110) REVERT: B 337 LYS cc_start: 0.8661 (tppt) cc_final: 0.8067 (tppt) REVERT: B 339 TRP cc_start: 0.7960 (m100) cc_final: 0.7705 (m-90) REVERT: G 24 ASN cc_start: 0.7347 (p0) cc_final: 0.6845 (t0) REVERT: N 32 TYR cc_start: 0.8464 (m-80) cc_final: 0.8104 (m-10) REVERT: N 34 MET cc_start: 0.9130 (ttp) cc_final: 0.8739 (tpp) REVERT: N 67 ARG cc_start: 0.8046 (ptp90) cc_final: 0.7782 (ptp90) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.0956 time to fit residues: 52.0127 Evaluate side-chains 326 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 67 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN R 240 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.138394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.120065 restraints weight = 27945.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.123909 restraints weight = 16147.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.126521 restraints weight = 10507.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.128337 restraints weight = 7415.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.129559 restraints weight = 5584.170| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9299 Z= 0.140 Angle : 0.698 9.649 12624 Z= 0.370 Chirality : 0.046 0.283 1416 Planarity : 0.005 0.054 1612 Dihedral : 5.084 23.230 1277 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1160 helix: 0.11 (0.25), residues: 441 sheet: -0.33 (0.35), residues: 221 loop : -0.61 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 336 TYR 0.022 0.002 TYR A 391 PHE 0.041 0.003 PHE R 184 TRP 0.048 0.003 TRP N 36 HIS 0.012 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9293) covalent geometry : angle 0.69692 (12612) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.43318 ( 12) hydrogen bonds : bond 0.04530 ( 473) hydrogen bonds : angle 5.84078 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 152 TYR cc_start: 0.7527 (t80) cc_final: 0.6782 (t80) REVERT: R 159 LEU cc_start: 0.9069 (tp) cc_final: 0.8805 (tp) REVERT: R 180 HIS cc_start: 0.8915 (m-70) cc_final: 0.8703 (m90) REVERT: R 181 LEU cc_start: 0.9205 (mt) cc_final: 0.8901 (mt) REVERT: R 184 PHE cc_start: 0.8447 (m-80) cc_final: 0.8165 (m-80) REVERT: R 205 TYR cc_start: 0.8352 (t80) cc_final: 0.8082 (t80) REVERT: R 351 LYS cc_start: 0.8737 (tptt) cc_final: 0.8405 (tptm) REVERT: R 397 MET cc_start: 0.7443 (mtp) cc_final: 0.6987 (ptm) REVERT: R 407 ASN cc_start: 0.7231 (p0) cc_final: 0.7003 (p0) REVERT: P 27 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8163 (mm-30) REVERT: A 11 ASP cc_start: 0.7836 (t0) cc_final: 0.7466 (t70) REVERT: A 32 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8482 (mttp) REVERT: A 44 LEU cc_start: 0.8115 (tp) cc_final: 0.7548 (tp) REVERT: A 279 ASN cc_start: 0.8896 (t0) cc_final: 0.8615 (t0) REVERT: A 291 LEU cc_start: 0.9246 (mt) cc_final: 0.9007 (mt) REVERT: A 295 ASP cc_start: 0.8067 (p0) cc_final: 0.7543 (p0) REVERT: A 381 ASP cc_start: 0.9140 (m-30) cc_final: 0.8864 (m-30) REVERT: A 388 LEU cc_start: 0.9370 (mm) cc_final: 0.9073 (mm) REVERT: B 6 GLN cc_start: 0.7312 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 16 ASN cc_start: 0.8189 (m110) cc_final: 0.7832 (m110) REVERT: B 66 ASP cc_start: 0.8105 (p0) cc_final: 0.7820 (p0) REVERT: B 89 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9171 (mmmm) REVERT: B 114 CYS cc_start: 0.8498 (p) cc_final: 0.7924 (p) REVERT: B 120 ILE cc_start: 0.8693 (mt) cc_final: 0.8399 (mm) REVERT: B 145 TYR cc_start: 0.8050 (p90) cc_final: 0.7805 (p90) REVERT: B 210 LEU cc_start: 0.8664 (tp) cc_final: 0.8455 (tp) REVERT: B 220 GLN cc_start: 0.7725 (mp10) cc_final: 0.7284 (mp10) REVERT: B 235 PHE cc_start: 0.7827 (t80) cc_final: 0.7336 (t80) REVERT: B 246 ASP cc_start: 0.8846 (m-30) cc_final: 0.8433 (m-30) REVERT: B 264 TYR cc_start: 0.7336 (m-10) cc_final: 0.6526 (m-80) REVERT: B 273 ILE cc_start: 0.9081 (mp) cc_final: 0.8617 (mp) REVERT: B 283 ARG cc_start: 0.8410 (tpt170) cc_final: 0.7571 (tpm170) REVERT: B 297 TRP cc_start: 0.8077 (m100) cc_final: 0.7558 (m100) REVERT: B 313 ASN cc_start: 0.7250 (m110) cc_final: 0.6930 (m-40) REVERT: B 337 LYS cc_start: 0.8612 (tppt) cc_final: 0.8035 (tppt) REVERT: G 24 ASN cc_start: 0.7179 (p0) cc_final: 0.6676 (t0) REVERT: G 44 HIS cc_start: 0.8222 (m170) cc_final: 0.8021 (m90) REVERT: N 31 ASN cc_start: 0.8272 (m110) cc_final: 0.7311 (t0) REVERT: N 32 TYR cc_start: 0.8409 (m-80) cc_final: 0.8065 (m-10) REVERT: N 34 MET cc_start: 0.9046 (ttp) cc_final: 0.8782 (tpp) REVERT: N 46 GLU cc_start: 0.7753 (pm20) cc_final: 0.7548 (pm20) REVERT: N 67 ARG cc_start: 0.8136 (ptp90) cc_final: 0.7826 (ptp90) REVERT: N 82 GLN cc_start: 0.7146 (mm110) cc_final: 0.6928 (mm110) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.0934 time to fit residues: 49.9050 Evaluate side-chains 321 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117648 restraints weight = 28193.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121349 restraints weight = 16320.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.123870 restraints weight = 10656.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.125651 restraints weight = 7568.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.126832 restraints weight = 5715.512| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9299 Z= 0.166 Angle : 0.721 8.775 12624 Z= 0.384 Chirality : 0.046 0.233 1416 Planarity : 0.005 0.044 1612 Dihedral : 5.135 26.005 1277 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1160 helix: 0.16 (0.25), residues: 436 sheet: -0.43 (0.34), residues: 230 loop : -0.55 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 228 TYR 0.024 0.002 TYR R 269 PHE 0.040 0.003 PHE R 184 TRP 0.033 0.003 TRP N 36 HIS 0.012 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9293) covalent geometry : angle 0.71826 (12612) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.99351 ( 12) hydrogen bonds : bond 0.04602 ( 473) hydrogen bonds : angle 5.87638 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 159 LEU cc_start: 0.9102 (tp) cc_final: 0.8833 (tp) REVERT: R 181 LEU cc_start: 0.9206 (mt) cc_final: 0.8899 (mt) REVERT: R 184 PHE cc_start: 0.8474 (m-80) cc_final: 0.8139 (m-80) REVERT: R 205 TYR cc_start: 0.8348 (t80) cc_final: 0.8085 (t80) REVERT: R 272 ILE cc_start: 0.8351 (tt) cc_final: 0.8098 (mt) REVERT: R 330 ILE cc_start: 0.7679 (mm) cc_final: 0.7374 (mm) REVERT: R 340 MET cc_start: 0.8026 (tpt) cc_final: 0.7569 (tpt) REVERT: R 351 LYS cc_start: 0.8761 (tptt) cc_final: 0.8519 (tptm) REVERT: R 397 MET cc_start: 0.7442 (mtp) cc_final: 0.7024 (mtp) REVERT: R 407 ASN cc_start: 0.7349 (p0) cc_final: 0.7072 (p0) REVERT: P 27 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 28 LYS cc_start: 0.7068 (mmpt) cc_final: 0.6737 (mtmm) REVERT: A 32 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8509 (mttp) REVERT: A 44 LEU cc_start: 0.8126 (tp) cc_final: 0.7548 (tp) REVERT: A 273 PHE cc_start: 0.8923 (t80) cc_final: 0.8580 (t80) REVERT: A 279 ASN cc_start: 0.8916 (t0) cc_final: 0.8639 (t0) REVERT: A 287 VAL cc_start: 0.9061 (t) cc_final: 0.8745 (t) REVERT: A 291 LEU cc_start: 0.9261 (mt) cc_final: 0.9029 (mt) REVERT: A 295 ASP cc_start: 0.7914 (p0) cc_final: 0.7489 (p0) REVERT: A 381 ASP cc_start: 0.9173 (m-30) cc_final: 0.8850 (m-30) REVERT: A 383 ILE cc_start: 0.9037 (tp) cc_final: 0.8808 (tp) REVERT: A 388 LEU cc_start: 0.9349 (mm) cc_final: 0.9076 (mm) REVERT: B 6 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6817 (tm-30) REVERT: B 66 ASP cc_start: 0.8153 (p0) cc_final: 0.7904 (p0) REVERT: B 89 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9209 (mmmm) REVERT: B 120 ILE cc_start: 0.8729 (mt) cc_final: 0.8467 (mm) REVERT: B 210 LEU cc_start: 0.8698 (tp) cc_final: 0.8449 (tp) REVERT: B 220 GLN cc_start: 0.7739 (mp10) cc_final: 0.7249 (mp10) REVERT: B 235 PHE cc_start: 0.7967 (t80) cc_final: 0.7478 (t80) REVERT: B 246 ASP cc_start: 0.8901 (m-30) cc_final: 0.8513 (m-30) REVERT: B 264 TYR cc_start: 0.7276 (m-10) cc_final: 0.6479 (m-80) REVERT: B 273 ILE cc_start: 0.9076 (mp) cc_final: 0.8699 (mp) REVERT: B 283 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7577 (tpm170) REVERT: B 297 TRP cc_start: 0.8218 (m100) cc_final: 0.7755 (m100) REVERT: B 337 LYS cc_start: 0.8731 (tppt) cc_final: 0.8416 (tppt) REVERT: G 24 ASN cc_start: 0.7253 (p0) cc_final: 0.6739 (t0) REVERT: N 31 ASN cc_start: 0.8303 (m110) cc_final: 0.7250 (t0) REVERT: N 32 TYR cc_start: 0.8452 (m-80) cc_final: 0.7995 (m-10) REVERT: N 47 TRP cc_start: 0.8196 (t60) cc_final: 0.7352 (t60) REVERT: N 67 ARG cc_start: 0.8190 (ptp90) cc_final: 0.7857 (ptp90) REVERT: N 111 THR cc_start: 0.7011 (m) cc_final: 0.6324 (p) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.0902 time to fit residues: 48.1601 Evaluate side-chains 303 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 0.0170 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.138325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.119652 restraints weight = 28265.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.123484 restraints weight = 16413.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.126074 restraints weight = 10749.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.127793 restraints weight = 7628.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.129118 restraints weight = 5844.920| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9299 Z= 0.153 Angle : 0.734 9.488 12624 Z= 0.389 Chirality : 0.047 0.222 1416 Planarity : 0.005 0.048 1612 Dihedral : 5.140 23.648 1277 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1160 helix: 0.23 (0.25), residues: 430 sheet: -0.40 (0.33), residues: 238 loop : -0.45 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 228 TYR 0.023 0.002 TYR A 391 PHE 0.040 0.002 PHE R 184 TRP 0.036 0.003 TRP N 36 HIS 0.012 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9293) covalent geometry : angle 0.73172 (12612) SS BOND : bond 0.00301 ( 6) SS BOND : angle 1.82358 ( 12) hydrogen bonds : bond 0.04566 ( 473) hydrogen bonds : angle 5.79423 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 159 LEU cc_start: 0.9100 (tp) cc_final: 0.8852 (tp) REVERT: R 181 LEU cc_start: 0.9224 (mt) cc_final: 0.8902 (mt) REVERT: R 184 PHE cc_start: 0.8456 (m-80) cc_final: 0.8071 (m-80) REVERT: R 205 TYR cc_start: 0.8384 (t80) cc_final: 0.8104 (t80) REVERT: R 272 ILE cc_start: 0.8335 (tt) cc_final: 0.8093 (mt) REVERT: R 351 LYS cc_start: 0.8752 (tptt) cc_final: 0.8513 (tptm) REVERT: R 397 MET cc_start: 0.7305 (mtp) cc_final: 0.6889 (ptm) REVERT: R 407 ASN cc_start: 0.7404 (p0) cc_final: 0.7097 (p0) REVERT: A 28 LYS cc_start: 0.7070 (mmpt) cc_final: 0.6774 (mtmm) REVERT: A 44 LEU cc_start: 0.8081 (tp) cc_final: 0.7589 (tp) REVERT: A 273 PHE cc_start: 0.9021 (t80) cc_final: 0.8740 (t80) REVERT: A 279 ASN cc_start: 0.8901 (t0) cc_final: 0.8590 (t0) REVERT: A 285 ILE cc_start: 0.9027 (mm) cc_final: 0.8645 (tp) REVERT: A 287 VAL cc_start: 0.9074 (t) cc_final: 0.8782 (t) REVERT: A 291 LEU cc_start: 0.9140 (mt) cc_final: 0.8826 (mt) REVERT: A 295 ASP cc_start: 0.7862 (p0) cc_final: 0.7466 (p0) REVERT: A 317 ARG cc_start: 0.8412 (pmt170) cc_final: 0.8207 (mpp-170) REVERT: A 343 ASP cc_start: 0.8359 (m-30) cc_final: 0.7859 (m-30) REVERT: A 381 ASP cc_start: 0.9105 (m-30) cc_final: 0.8841 (m-30) REVERT: A 388 LEU cc_start: 0.9374 (mm) cc_final: 0.9090 (mm) REVERT: B 6 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 49 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7754 (mmt90) REVERT: B 66 ASP cc_start: 0.8135 (p0) cc_final: 0.7849 (p0) REVERT: B 89 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9169 (mmmm) REVERT: B 120 ILE cc_start: 0.8717 (mt) cc_final: 0.8467 (mm) REVERT: B 153 ASP cc_start: 0.7647 (p0) cc_final: 0.7424 (p0) REVERT: B 220 GLN cc_start: 0.7730 (mp10) cc_final: 0.7265 (mp10) REVERT: B 235 PHE cc_start: 0.7922 (t80) cc_final: 0.7408 (t80) REVERT: B 264 TYR cc_start: 0.7367 (m-10) cc_final: 0.6461 (m-80) REVERT: B 283 ARG cc_start: 0.8183 (tpt170) cc_final: 0.7494 (tpm170) REVERT: B 297 TRP cc_start: 0.8188 (m100) cc_final: 0.7603 (m100) REVERT: B 303 ASP cc_start: 0.8732 (t70) cc_final: 0.8507 (t0) REVERT: B 307 VAL cc_start: 0.6928 (t) cc_final: 0.6697 (t) REVERT: B 337 LYS cc_start: 0.8670 (tppt) cc_final: 0.8450 (tppt) REVERT: G 24 ASN cc_start: 0.7157 (p0) cc_final: 0.6713 (t0) REVERT: G 50 LEU cc_start: 0.8577 (mm) cc_final: 0.8350 (mm) REVERT: N 31 ASN cc_start: 0.8315 (m110) cc_final: 0.7294 (t0) REVERT: N 32 TYR cc_start: 0.8282 (m-80) cc_final: 0.7966 (m-10) REVERT: N 38 ARG cc_start: 0.8450 (ptp90) cc_final: 0.7878 (ptp90) REVERT: N 47 TRP cc_start: 0.8205 (t60) cc_final: 0.7235 (t60) REVERT: N 67 ARG cc_start: 0.8227 (ptp90) cc_final: 0.7905 (ptp90) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.0928 time to fit residues: 49.1585 Evaluate side-chains 306 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118653 restraints weight = 27821.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.122307 restraints weight = 16259.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.124845 restraints weight = 10681.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.126623 restraints weight = 7582.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.127835 restraints weight = 5752.751| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9299 Z= 0.153 Angle : 0.723 8.921 12624 Z= 0.384 Chirality : 0.047 0.217 1416 Planarity : 0.005 0.070 1612 Dihedral : 5.056 22.297 1277 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.24), residues: 1160 helix: 0.30 (0.25), residues: 436 sheet: -0.18 (0.36), residues: 204 loop : -0.59 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 44 TYR 0.023 0.002 TYR A 391 PHE 0.042 0.002 PHE R 184 TRP 0.037 0.003 TRP N 36 HIS 0.016 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9293) covalent geometry : angle 0.72169 (12612) SS BOND : bond 0.00307 ( 6) SS BOND : angle 1.71853 ( 12) hydrogen bonds : bond 0.04516 ( 473) hydrogen bonds : angle 5.79187 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.89 seconds wall clock time: 34 minutes 16.56 seconds (2056.56 seconds total)