Starting phenix.real_space_refine on Wed Apr 30 03:03:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vai_8653/04_2025/5vai_8653.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vai_8653/04_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_8653/04_2025/5vai_8653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vai_8653/04_2025/5vai_8653.map" model { file = "/net/cci-nas-00/data/ceres_data/5vai_8653/04_2025/5vai_8653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vai_8653/04_2025/5vai_8653.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 7} 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, 'GLU:plan': 1, 'ASP: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, 'GLU:plan': 2, 'ARG: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: 5.37, per 1000 atoms: 0.59 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.40 Time building geometry restraints manager: 2.75 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.660 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- 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 : 31.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.041 0.005 TRP R 120 HIS 0.021 0.004 HIS R 180 PHE 0.034 0.004 PHE A 312 TYR 0.024 0.004 TYR N 32 ARG 0.015 0.001 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.15063 ( 473) hydrogen bonds : angle 10.59459 ( 1341) SS BOND : bond 0.37475 ( 6) SS BOND : angle 6.39916 ( 12) covalent geometry : bond 0.00759 ( 9293) covalent geometry : angle 1.10919 (12612) *********************** 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 : 0.949 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: 0.8528 (p) REVERT: R 176 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7285 (ttm-80) REVERT: R 229 VAL cc_start: 0.9257 (t) cc_final: 0.9049 (p) REVERT: R 272 ILE cc_start: 0.8281 (tt) cc_final: 0.7955 (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: 0.7907 (t80) REVERT: P 15 ASP cc_start: 0.8876 (t0) cc_final: 0.8600 (t0) REVERT: A 11 ASP cc_start: 0.8495 (t0) cc_final: 0.8014 (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: 0.8344 (tp) REVERT: A 222 PHE cc_start: 0.7438 (t80) cc_final: 0.7217 (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: 0.7980 (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: 0.8608 (tp30) REVERT: A 318 TYR cc_start: 0.6146 (t80) cc_final: 0.5830 (t80) REVERT: A 344 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8688 (mm-30) REVERT: A 360 TYR cc_start: 0.8502 (m-10) cc_final: 0.8000 (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: 0.8301 (tm-30) REVERT: B 49 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7165 (mmt-90) REVERT: B 120 ILE cc_start: 0.8720 (mt) cc_final: 0.8420 (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: 0.8255 (t) REVERT: B 210 LEU cc_start: 0.9040 (tp) cc_final: 0.8785 (tp) REVERT: B 228 ASP cc_start: 0.7546 (m-30) cc_final: 0.7339 (m-30) REVERT: B 235 PHE cc_start: 0.7800 (t80) cc_final: 0.7377 (t80) REVERT: B 273 ILE cc_start: 0.9099 (mp) cc_final: 0.8801 (mp) REVERT: N 36 TRP cc_start: 0.6399 (m100) cc_final: 0.5998 (m100) REVERT: N 45 LEU cc_start: 0.8001 (mp) cc_final: 0.7592 (mt) REVERT: N 47 TRP cc_start: 0.8346 (t60) cc_final: 0.7128 (t60) REVERT: N 81 LEU cc_start: 0.9292 (tp) cc_final: 0.8906 (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: 0.2573 time to fit residues: 171.3555 Evaluate side-chains 341 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.0050 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 77 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.135133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117324 restraints weight = 27416.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.121043 restraints weight = 15699.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123572 restraints weight = 10139.494| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9299 Z= 0.190 Angle : 0.809 11.047 12624 Z= 0.430 Chirality : 0.048 0.195 1416 Planarity : 0.006 0.058 1612 Dihedral : 5.704 28.261 1277 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.72 % Rotamer: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1160 helix: -0.02 (0.23), residues: 426 sheet: -0.83 (0.33), residues: 216 loop : -0.50 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 31 HIS 0.008 0.002 HIS R 180 PHE 0.024 0.003 PHE A 246 TYR 0.028 0.003 TYR R 289 ARG 0.010 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05868 ( 473) hydrogen bonds : angle 7.14662 ( 1341) SS BOND : bond 0.00430 ( 6) SS BOND : angle 1.85171 ( 12) covalent geometry : bond 0.00409 ( 9293) covalent geometry : angle 0.80774 (12612) *********************** 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 437 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 2.013 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 180 HIS cc_start: 0.8289 (m-70) cc_final: 0.8074 (m90) REVERT: R 184 PHE cc_start: 0.9309 (m-10) cc_final: 0.9106 (m-80) REVERT: R 229 VAL cc_start: 0.9192 (t) cc_final: 0.8955 (p) REVERT: R 272 ILE cc_start: 0.8158 (tt) cc_final: 0.7887 (mt) REVERT: R 351 LYS cc_start: 0.8558 (tptt) cc_final: 0.7933 (tmtt) REVERT: A 28 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6572 (ptpp) REVERT: A 32 LYS cc_start: 0.9174 (mttt) cc_final: 0.8954 (mttp) REVERT: A 229 ASP cc_start: 0.8121 (p0) cc_final: 0.7652 (p0) REVERT: A 237 CYS cc_start: 0.8650 (m) cc_final: 0.8156 (m) REVERT: A 271 ASN cc_start: 0.8452 (m110) cc_final: 0.7388 (m110) REVERT: A 273 PHE cc_start: 0.9122 (t80) cc_final: 0.8634 (t80) REVERT: A 279 ASN cc_start: 0.8781 (t0) cc_final: 0.8490 (t0) REVERT: A 283 ARG cc_start: 0.8449 (mtt180) cc_final: 0.8053 (ptp-170) REVERT: A 287 VAL cc_start: 0.8945 (t) cc_final: 0.8729 (t) REVERT: A 360 TYR cc_start: 0.8681 (m-10) cc_final: 0.8405 (m-10) REVERT: A 371 ASN cc_start: 0.8304 (p0) cc_final: 0.7984 (p0) REVERT: A 383 ILE cc_start: 0.9135 (tt) cc_final: 0.8719 (tp) REVERT: A 386 MET cc_start: 0.8167 (ttt) cc_final: 0.7919 (tmm) REVERT: A 388 LEU cc_start: 0.9236 (mm) cc_final: 0.8910 (mm) REVERT: B 6 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 13 GLN cc_start: 0.8723 (tt0) cc_final: 0.8229 (pt0) REVERT: B 49 ARG cc_start: 0.7698 (mmt-90) cc_final: 0.7357 (mmt-90) REVERT: B 63 TRP cc_start: 0.8572 (m100) cc_final: 0.8247 (m100) REVERT: B 66 ASP cc_start: 0.8225 (p0) cc_final: 0.7984 (p0) REVERT: B 89 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8931 (mmmm) REVERT: B 120 ILE cc_start: 0.8655 (mt) cc_final: 0.8390 (mm) REVERT: B 148 CYS cc_start: 0.8628 (t) cc_final: 0.8365 (t) REVERT: B 153 ASP cc_start: 0.8265 (p0) cc_final: 0.7306 (p0) REVERT: B 210 LEU cc_start: 0.9004 (tp) cc_final: 0.8447 (tp) REVERT: B 220 GLN cc_start: 0.7960 (mp10) cc_final: 0.7383 (mp10) REVERT: B 235 PHE cc_start: 0.8032 (t80) cc_final: 0.7585 (t80) REVERT: B 246 ASP cc_start: 0.8277 (m-30) cc_final: 0.7946 (m-30) REVERT: B 251 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6167 (mtt90) REVERT: B 273 ILE cc_start: 0.9124 (mp) cc_final: 0.8692 (mp) REVERT: B 278 PHE cc_start: 0.7332 (m-80) cc_final: 0.7099 (m-80) REVERT: B 280 LYS cc_start: 0.8685 (tttt) cc_final: 0.7993 (tttm) REVERT: B 283 ARG cc_start: 0.8442 (tpt-90) cc_final: 0.8189 (tpt170) REVERT: B 325 MET cc_start: 0.8275 (tpp) cc_final: 0.7943 (tmm) REVERT: N 34 MET cc_start: 0.9164 (ttm) cc_final: 0.8815 (ttp) REVERT: N 47 TRP cc_start: 0.8251 (t60) cc_final: 0.6809 (t60) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2670 time to fit residues: 156.7425 Evaluate side-chains 351 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN 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 = 0.4190 r_free = 0.4190 target = 0.136977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.118750 restraints weight = 27786.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.122636 restraints weight = 15814.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.125313 restraints weight = 10133.715| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9299 Z= 0.163 Angle : 0.713 8.864 12624 Z= 0.383 Chirality : 0.045 0.174 1416 Planarity : 0.005 0.058 1612 Dihedral : 5.443 25.803 1277 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 0.32 % Allowed : 3.84 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1160 helix: -0.10 (0.23), residues: 434 sheet: -0.72 (0.35), residues: 203 loop : -0.47 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.008 0.002 HIS R 180 PHE 0.020 0.002 PHE R 321 TYR 0.044 0.002 TYR R 269 ARG 0.009 0.001 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 473) hydrogen bonds : angle 6.54029 ( 1341) SS BOND : bond 0.00966 ( 6) SS BOND : angle 1.63761 ( 12) covalent geometry : bond 0.00347 ( 9293) covalent geometry : angle 0.71133 (12612) *********************** 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 420 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 417 time to evaluate : 1.008 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 47 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: R 181 LEU cc_start: 0.9350 (mt) cc_final: 0.8955 (mt) REVERT: R 205 TYR cc_start: 0.8484 (t80) cc_final: 0.8245 (t80) REVERT: R 229 VAL cc_start: 0.9204 (t) cc_final: 0.8956 (p) REVERT: R 272 ILE cc_start: 0.8200 (tt) cc_final: 0.7964 (mt) REVERT: R 351 LYS cc_start: 0.8599 (tptt) cc_final: 0.7965 (tmtt) REVERT: R 397 MET cc_start: 0.8008 (mmp) cc_final: 0.7641 (mtp) REVERT: R 411 MET cc_start: 0.8266 (mmp) cc_final: 0.8026 (mmp) REVERT: A 28 LYS cc_start: 0.6848 (mmpt) cc_final: 0.6475 (ptpp) REVERT: A 32 LYS cc_start: 0.9163 (mttt) cc_final: 0.8939 (mttp) REVERT: A 44 LEU cc_start: 0.8710 (tp) cc_final: 0.8278 (tp) REVERT: A 229 ASP cc_start: 0.8131 (p0) cc_final: 0.7668 (p0) REVERT: A 241 VAL cc_start: 0.9103 (t) cc_final: 0.8769 (p) REVERT: A 270 LEU cc_start: 0.9523 (mt) cc_final: 0.9319 (mt) REVERT: A 279 ASN cc_start: 0.8804 (t0) cc_final: 0.8524 (t0) REVERT: A 283 ARG cc_start: 0.8278 (mtt180) cc_final: 0.8052 (ptp-170) REVERT: A 291 LEU cc_start: 0.9382 (mt) cc_final: 0.9074 (mt) REVERT: A 384 GLN cc_start: 0.9175 (pp30) cc_final: 0.8909 (pt0) REVERT: A 386 MET cc_start: 0.8136 (ttt) cc_final: 0.7645 (tpp) REVERT: B 6 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6693 (tm-30) REVERT: B 61 MET cc_start: 0.8993 (ppp) cc_final: 0.8280 (ppp) REVERT: B 63 TRP cc_start: 0.8557 (m100) cc_final: 0.8255 (m100) REVERT: B 66 ASP cc_start: 0.8185 (p0) cc_final: 0.7977 (p0) REVERT: B 89 LYS cc_start: 0.9388 (mmmm) cc_final: 0.8978 (mmmm) REVERT: B 120 ILE cc_start: 0.8655 (mt) cc_final: 0.8420 (mm) REVERT: B 148 CYS cc_start: 0.8776 (t) cc_final: 0.8442 (t) REVERT: B 153 ASP cc_start: 0.7783 (p0) cc_final: 0.7346 (p0) REVERT: B 170 ASP cc_start: 0.7478 (t0) cc_final: 0.7239 (t0) REVERT: B 210 LEU cc_start: 0.8757 (tp) cc_final: 0.8378 (tp) REVERT: B 220 GLN cc_start: 0.7989 (mp10) cc_final: 0.7391 (mp10) REVERT: B 235 PHE cc_start: 0.8012 (t80) cc_final: 0.7601 (t80) REVERT: B 262 MET cc_start: 0.7138 (mmm) cc_final: 0.6811 (mmm) REVERT: B 264 TYR cc_start: 0.7129 (m-80) cc_final: 0.6457 (m-80) REVERT: B 280 LYS cc_start: 0.8581 (tttt) cc_final: 0.8188 (tttm) REVERT: B 297 TRP cc_start: 0.8060 (m100) cc_final: 0.7813 (m100) REVERT: B 325 MET cc_start: 0.8427 (tpp) cc_final: 0.8048 (tmm) REVERT: N 27 PHE cc_start: 0.8431 (p90) cc_final: 0.8199 (p90) REVERT: N 32 TYR cc_start: 0.8477 (m-80) cc_final: 0.8132 (m-10) REVERT: N 45 LEU cc_start: 0.8018 (mt) cc_final: 0.7647 (mt) REVERT: N 47 TRP cc_start: 0.8230 (t60) cc_final: 0.6615 (t60) REVERT: N 67 ARG cc_start: 0.7971 (ptp-110) cc_final: 0.7680 (ptp90) REVERT: N 68 PHE cc_start: 0.8709 (m-80) cc_final: 0.7973 (m-80) outliers start: 3 outliers final: 1 residues processed: 419 average time/residue: 0.2627 time to fit residues: 145.1603 Evaluate side-chains 347 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 345 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.116111 restraints weight = 27834.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.119768 restraints weight = 15906.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.122319 restraints weight = 10286.388| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9299 Z= 0.214 Angle : 0.740 11.124 12624 Z= 0.398 Chirality : 0.048 0.379 1416 Planarity : 0.005 0.056 1612 Dihedral : 5.457 24.791 1277 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1160 helix: -0.16 (0.24), residues: 435 sheet: -0.73 (0.33), residues: 227 loop : -0.37 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 169 HIS 0.012 0.002 HIS R 180 PHE 0.028 0.003 PHE R 324 TYR 0.023 0.002 TYR A 391 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 473) hydrogen bonds : angle 6.31201 ( 1341) SS BOND : bond 0.00773 ( 6) SS BOND : angle 1.33376 ( 12) covalent geometry : bond 0.00447 ( 9293) covalent geometry : angle 0.73962 (12612) *********************** 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 391 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.184 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 181 LEU cc_start: 0.9284 (mt) cc_final: 0.8939 (mt) REVERT: R 205 TYR cc_start: 0.8446 (t80) cc_final: 0.8203 (t80) REVERT: R 272 ILE cc_start: 0.8241 (tt) cc_final: 0.8001 (mt) REVERT: R 351 LYS cc_start: 0.8656 (tptt) cc_final: 0.8014 (tmtt) REVERT: R 411 MET cc_start: 0.8188 (mmp) cc_final: 0.7915 (mmp) REVERT: A 28 LYS cc_start: 0.6797 (mmpt) cc_final: 0.6392 (ptpp) REVERT: A 35 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7903 (mm-40) REVERT: A 44 LEU cc_start: 0.8732 (tp) cc_final: 0.8278 (tp) REVERT: A 45 LEU cc_start: 0.9307 (tp) cc_final: 0.9035 (tp) REVERT: A 229 ASP cc_start: 0.8199 (p0) cc_final: 0.7734 (p0) REVERT: A 279 ASN cc_start: 0.8896 (t0) cc_final: 0.8629 (t0) REVERT: A 283 ARG cc_start: 0.8245 (mtt180) cc_final: 0.8013 (ptp-170) REVERT: A 295 ASP cc_start: 0.8332 (p0) cc_final: 0.7767 (p0) REVERT: A 309 GLU cc_start: 0.9324 (pt0) cc_final: 0.8747 (tp30) REVERT: A 335 THR cc_start: 0.8753 (m) cc_final: 0.8363 (p) REVERT: A 384 GLN cc_start: 0.9184 (pp30) cc_final: 0.8961 (pt0) REVERT: A 386 MET cc_start: 0.7989 (ttt) cc_final: 0.7706 (tpp) REVERT: B 6 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6629 (tm-30) REVERT: B 49 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.7482 (mmt90) REVERT: B 66 ASP cc_start: 0.8233 (p0) cc_final: 0.7965 (p0) REVERT: B 120 ILE cc_start: 0.8708 (mt) cc_final: 0.8460 (mm) REVERT: B 148 CYS cc_start: 0.8846 (t) cc_final: 0.8604 (t) REVERT: B 153 ASP cc_start: 0.7706 (p0) cc_final: 0.7466 (p0) REVERT: B 170 ASP cc_start: 0.7425 (t0) cc_final: 0.7186 (t0) REVERT: B 204 CYS cc_start: 0.8206 (m) cc_final: 0.7895 (m) REVERT: B 210 LEU cc_start: 0.8837 (tp) cc_final: 0.8377 (tp) REVERT: B 220 GLN cc_start: 0.7790 (mp10) cc_final: 0.7344 (mp10) REVERT: B 228 ASP cc_start: 0.7068 (m-30) cc_final: 0.6622 (m-30) REVERT: B 235 PHE cc_start: 0.8051 (t80) cc_final: 0.7725 (t80) REVERT: B 246 ASP cc_start: 0.8330 (m-30) cc_final: 0.8043 (m-30) REVERT: B 264 TYR cc_start: 0.7445 (m-80) cc_final: 0.6526 (m-80) REVERT: B 293 ASN cc_start: 0.8222 (m-40) cc_final: 0.8017 (m-40) REVERT: B 297 TRP cc_start: 0.8144 (m100) cc_final: 0.7649 (m100) REVERT: B 308 LEU cc_start: 0.7410 (mt) cc_final: 0.7100 (mt) REVERT: N 32 TYR cc_start: 0.8593 (m-80) cc_final: 0.8038 (m-10) REVERT: N 47 TRP cc_start: 0.8462 (t60) cc_final: 0.7225 (t60) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2622 time to fit residues: 138.6418 Evaluate side-chains 322 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN R 240 ASN ** A 23 ASN ** 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** ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.115939 restraints weight = 28048.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.119569 restraints weight = 16220.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.122039 restraints weight = 10552.179| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9299 Z= 0.182 Angle : 0.730 10.109 12624 Z= 0.393 Chirality : 0.047 0.358 1416 Planarity : 0.005 0.060 1612 Dihedral : 5.371 24.297 1277 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1160 helix: -0.06 (0.24), residues: 430 sheet: -0.49 (0.34), residues: 213 loop : -0.49 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 169 HIS 0.010 0.002 HIS A 357 PHE 0.036 0.003 PHE R 184 TYR 0.017 0.002 TYR A 339 ARG 0.004 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 473) hydrogen bonds : angle 6.19439 ( 1341) SS BOND : bond 0.00326 ( 6) SS BOND : angle 1.38385 ( 12) covalent geometry : bond 0.00387 ( 9293) covalent geometry : angle 0.72945 (12612) *********************** 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 384 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.074 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 38 LYS cc_start: 0.7978 (pttm) cc_final: 0.7343 (pttp) REVERT: R 180 HIS cc_start: 0.8838 (m-70) cc_final: 0.8572 (m-70) REVERT: R 181 LEU cc_start: 0.9136 (mt) cc_final: 0.8716 (mt) REVERT: R 205 TYR cc_start: 0.8470 (t80) cc_final: 0.8239 (t80) REVERT: R 272 ILE cc_start: 0.8287 (tt) cc_final: 0.8037 (mt) REVERT: R 351 LYS cc_start: 0.8749 (tptt) cc_final: 0.8046 (tmtt) REVERT: R 411 MET cc_start: 0.8267 (mmp) cc_final: 0.7994 (mmp) REVERT: A 28 LYS cc_start: 0.6994 (mmpt) cc_final: 0.6642 (ptpt) REVERT: A 35 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8051 (mm-40) REVERT: A 44 LEU cc_start: 0.8759 (tp) cc_final: 0.8369 (tp) REVERT: A 222 PHE cc_start: 0.7132 (t80) cc_final: 0.6433 (t80) REVERT: A 229 ASP cc_start: 0.8211 (p0) cc_final: 0.7760 (p0) REVERT: A 279 ASN cc_start: 0.8890 (t0) cc_final: 0.8644 (t0) REVERT: A 291 LEU cc_start: 0.9260 (mt) cc_final: 0.8974 (mt) REVERT: A 295 ASP cc_start: 0.8348 (p0) cc_final: 0.7837 (p0) REVERT: A 309 GLU cc_start: 0.9320 (pt0) cc_final: 0.8776 (tp30) REVERT: A 383 ILE cc_start: 0.8929 (tp) cc_final: 0.8694 (tp) REVERT: A 386 MET cc_start: 0.8134 (ttt) cc_final: 0.7619 (tpp) REVERT: B 6 GLN cc_start: 0.7115 (tm-30) cc_final: 0.6785 (tm-30) REVERT: B 49 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7409 (mmt90) REVERT: B 61 MET cc_start: 0.9061 (ppp) cc_final: 0.8450 (ppp) REVERT: B 66 ASP cc_start: 0.8223 (p0) cc_final: 0.7966 (p0) REVERT: B 71 VAL cc_start: 0.9186 (m) cc_final: 0.8787 (p) REVERT: B 89 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9125 (mmmm) REVERT: B 120 ILE cc_start: 0.8770 (mt) cc_final: 0.8511 (mm) REVERT: B 210 LEU cc_start: 0.8852 (tp) cc_final: 0.8511 (tp) REVERT: B 220 GLN cc_start: 0.7734 (mp10) cc_final: 0.7288 (mp10) REVERT: B 235 PHE cc_start: 0.7870 (t80) cc_final: 0.7441 (t80) REVERT: B 246 ASP cc_start: 0.8414 (m-30) cc_final: 0.8149 (m-30) REVERT: B 264 TYR cc_start: 0.7427 (m-80) cc_final: 0.6706 (m-80) REVERT: B 273 ILE cc_start: 0.9171 (mp) cc_final: 0.8687 (mp) REVERT: B 283 ARG cc_start: 0.8269 (tpt90) cc_final: 0.7859 (tpt90) REVERT: B 297 TRP cc_start: 0.8277 (m100) cc_final: 0.7930 (m100) REVERT: B 313 ASN cc_start: 0.7061 (t0) cc_final: 0.6670 (m110) REVERT: B 325 MET cc_start: 0.8411 (tpp) cc_final: 0.7712 (tmm) REVERT: N 32 TYR cc_start: 0.8567 (m-80) cc_final: 0.7993 (m-80) REVERT: N 47 TRP cc_start: 0.8379 (t60) cc_final: 0.7098 (t60) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2269 time to fit residues: 116.9010 Evaluate side-chains 318 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 278 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.134429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.116673 restraints weight = 27863.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.120299 restraints weight = 16127.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122752 restraints weight = 10527.470| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9299 Z= 0.170 Angle : 0.721 9.431 12624 Z= 0.386 Chirality : 0.048 0.329 1416 Planarity : 0.005 0.052 1612 Dihedral : 5.326 25.023 1277 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1160 helix: -0.00 (0.24), residues: 431 sheet: -0.70 (0.33), residues: 215 loop : -0.61 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.009 0.002 HIS A 357 PHE 0.039 0.003 PHE N 68 TYR 0.024 0.002 TYR A 391 ARG 0.007 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 473) hydrogen bonds : angle 6.05416 ( 1341) SS BOND : bond 0.00340 ( 6) SS BOND : angle 1.13655 ( 12) covalent geometry : bond 0.00363 ( 9293) covalent geometry : angle 0.72020 (12612) *********************** 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 394 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 1.004 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 176 ARG cc_start: 0.7931 (ttt180) cc_final: 0.7664 (ttt180) REVERT: R 180 HIS cc_start: 0.8851 (m-70) cc_final: 0.8597 (m-70) REVERT: R 181 LEU cc_start: 0.9188 (mt) cc_final: 0.8791 (mt) REVERT: R 205 TYR cc_start: 0.8475 (t80) cc_final: 0.8261 (t80) REVERT: R 272 ILE cc_start: 0.8331 (tt) cc_final: 0.8100 (mt) REVERT: R 351 LYS cc_start: 0.8698 (tptt) cc_final: 0.7984 (tmtt) REVERT: R 411 MET cc_start: 0.8257 (mmp) cc_final: 0.7985 (mmp) REVERT: A 35 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7742 (mm-40) REVERT: A 44 LEU cc_start: 0.8704 (tp) cc_final: 0.8207 (tp) REVERT: A 229 ASP cc_start: 0.8260 (p0) cc_final: 0.7819 (p0) REVERT: A 271 ASN cc_start: 0.8348 (m110) cc_final: 0.7269 (m110) REVERT: A 273 PHE cc_start: 0.8967 (t80) cc_final: 0.8745 (t80) REVERT: A 279 ASN cc_start: 0.8942 (t0) cc_final: 0.8727 (t0) REVERT: A 295 ASP cc_start: 0.8334 (p0) cc_final: 0.7855 (p0) REVERT: A 309 GLU cc_start: 0.9315 (pt0) cc_final: 0.8737 (tp30) REVERT: A 386 MET cc_start: 0.8065 (ttt) cc_final: 0.7558 (tpp) REVERT: B 6 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6748 (tm-30) REVERT: B 16 ASN cc_start: 0.8753 (m-40) cc_final: 0.8501 (m-40) REVERT: B 49 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7573 (mmt90) REVERT: B 61 MET cc_start: 0.9062 (ppp) cc_final: 0.8471 (ppp) REVERT: B 66 ASP cc_start: 0.8228 (p0) cc_final: 0.7962 (p0) REVERT: B 89 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9128 (mmmm) REVERT: B 120 ILE cc_start: 0.8773 (mt) cc_final: 0.8510 (mm) REVERT: B 148 CYS cc_start: 0.9050 (t) cc_final: 0.8589 (t) REVERT: B 152 LEU cc_start: 0.8206 (mt) cc_final: 0.7714 (mt) REVERT: B 210 LEU cc_start: 0.8786 (tp) cc_final: 0.8421 (tp) REVERT: B 220 GLN cc_start: 0.7704 (mp10) cc_final: 0.7348 (mp10) REVERT: B 235 PHE cc_start: 0.7930 (t80) cc_final: 0.7427 (t80) REVERT: B 246 ASP cc_start: 0.8582 (m-30) cc_final: 0.8259 (m-30) REVERT: B 264 TYR cc_start: 0.7231 (m-80) cc_final: 0.6800 (m-80) REVERT: B 297 TRP cc_start: 0.8366 (m100) cc_final: 0.7998 (m100) REVERT: B 313 ASN cc_start: 0.7272 (t0) cc_final: 0.6700 (m110) REVERT: B 325 MET cc_start: 0.8404 (tpp) cc_final: 0.7639 (tmm) REVERT: G 24 ASN cc_start: 0.7208 (p0) cc_final: 0.6748 (t0) REVERT: N 27 PHE cc_start: 0.8325 (p90) cc_final: 0.8119 (p90) REVERT: N 28 THR cc_start: 0.8521 (t) cc_final: 0.8320 (t) REVERT: N 31 ASN cc_start: 0.8600 (m110) cc_final: 0.8135 (m110) REVERT: N 34 MET cc_start: 0.9100 (ttm) cc_final: 0.8816 (ttm) REVERT: N 47 TRP cc_start: 0.8358 (t60) cc_final: 0.7073 (t60) REVERT: N 81 LEU cc_start: 0.8586 (tp) cc_final: 0.8321 (tp) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.2947 time to fit residues: 156.4053 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 94 optimal weight: 0.0060 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 0.0070 chunk 111 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 302 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 384 GLN A 390 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.138768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.120377 restraints weight = 27885.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124151 restraints weight = 16155.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.126746 restraints weight = 10527.625| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9299 Z= 0.144 Angle : 0.696 9.252 12624 Z= 0.374 Chirality : 0.048 0.357 1416 Planarity : 0.005 0.059 1612 Dihedral : 5.245 26.190 1277 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1160 helix: -0.13 (0.24), residues: 447 sheet: -0.59 (0.32), residues: 229 loop : -0.45 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 36 HIS 0.009 0.002 HIS A 220 PHE 0.036 0.002 PHE R 184 TYR 0.026 0.002 TYR R 269 ARG 0.008 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 473) hydrogen bonds : angle 5.96739 ( 1341) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.57021 ( 12) covalent geometry : bond 0.00309 ( 9293) covalent geometry : angle 0.69503 (12612) *********************** 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 403 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.993 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: R 152 TYR cc_start: 0.7777 (t80) cc_final: 0.7238 (t80) REVERT: R 181 LEU cc_start: 0.9223 (mt) cc_final: 0.8979 (mt) REVERT: R 205 TYR cc_start: 0.8469 (t80) cc_final: 0.8258 (t80) REVERT: R 272 ILE cc_start: 0.8338 (tt) cc_final: 0.8129 (mt) REVERT: R 351 LYS cc_start: 0.8705 (tptt) cc_final: 0.7978 (tmtt) REVERT: R 397 MET cc_start: 0.7578 (mtp) cc_final: 0.7230 (mtp) REVERT: R 407 ASN cc_start: 0.7150 (p0) cc_final: 0.6767 (p0) REVERT: R 411 MET cc_start: 0.8206 (mmp) cc_final: 0.7984 (mmp) REVERT: A 28 LYS cc_start: 0.6994 (mmpt) cc_final: 0.6688 (mtmt) REVERT: A 32 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8403 (mttp) REVERT: A 45 LEU cc_start: 0.9165 (tp) cc_final: 0.8943 (tp) REVERT: A 229 ASP cc_start: 0.8211 (p0) cc_final: 0.7895 (p0) REVERT: A 241 VAL cc_start: 0.9006 (t) cc_final: 0.8549 (t) REVERT: A 273 PHE cc_start: 0.8935 (t80) cc_final: 0.8708 (t80) REVERT: A 279 ASN cc_start: 0.8898 (t0) cc_final: 0.8675 (t0) REVERT: A 295 ASP cc_start: 0.8303 (p0) cc_final: 0.7749 (p0) REVERT: A 309 GLU cc_start: 0.9325 (pt0) cc_final: 0.8662 (tp30) REVERT: A 384 GLN cc_start: 0.9230 (pt0) cc_final: 0.8851 (pt0) REVERT: A 388 LEU cc_start: 0.9285 (mm) cc_final: 0.9071 (mm) REVERT: B 6 GLN cc_start: 0.7222 (tm-30) cc_final: 0.6788 (tm-30) REVERT: B 66 ASP cc_start: 0.8181 (p0) cc_final: 0.7827 (p0) REVERT: B 68 ARG cc_start: 0.8310 (ttt90) cc_final: 0.7870 (mtp-110) REVERT: B 148 CYS cc_start: 0.8985 (t) cc_final: 0.8547 (t) REVERT: B 180 PHE cc_start: 0.8160 (m-80) cc_final: 0.7845 (m-10) REVERT: B 210 LEU cc_start: 0.8695 (tp) cc_final: 0.8463 (tp) REVERT: B 220 GLN cc_start: 0.7637 (mp10) cc_final: 0.7292 (mp10) REVERT: B 235 PHE cc_start: 0.7819 (t80) cc_final: 0.7349 (t80) REVERT: B 246 ASP cc_start: 0.8542 (m-30) cc_final: 0.8203 (m-30) REVERT: B 262 MET cc_start: 0.6956 (mmp) cc_final: 0.6673 (tpp) REVERT: B 273 ILE cc_start: 0.9200 (mp) cc_final: 0.8775 (mp) REVERT: B 297 TRP cc_start: 0.8448 (m100) cc_final: 0.8101 (m100) REVERT: B 325 MET cc_start: 0.8418 (tpp) cc_final: 0.7638 (tmm) REVERT: G 24 ASN cc_start: 0.7194 (p0) cc_final: 0.6713 (t0) REVERT: G 44 HIS cc_start: 0.8091 (m90) cc_final: 0.7607 (m90) REVERT: N 32 TYR cc_start: 0.8411 (m-80) cc_final: 0.8078 (m-10) REVERT: N 34 MET cc_start: 0.9096 (ttm) cc_final: 0.8781 (ttm) REVERT: N 46 GLU cc_start: 0.7991 (pm20) cc_final: 0.7778 (pm20) REVERT: N 67 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7803 (ptp90) REVERT: N 81 LEU cc_start: 0.8493 (tp) cc_final: 0.8210 (tp) REVERT: N 98 ARG cc_start: 0.7263 (ptm-80) cc_final: 0.6868 (ptm-80) REVERT: N 111 THR cc_start: 0.7175 (m) cc_final: 0.6808 (p) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2589 time to fit residues: 140.3199 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 : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.0050 chunk 110 optimal weight: 8.9990 chunk 89 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 213 GLN R 240 ASN A 23 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 384 GLN B 88 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.135198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117116 restraints weight = 28671.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.120781 restraints weight = 16471.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123252 restraints weight = 10709.153| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9299 Z= 0.183 Angle : 0.737 9.816 12624 Z= 0.397 Chirality : 0.048 0.297 1416 Planarity : 0.005 0.057 1612 Dihedral : 5.254 23.368 1277 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 0.11 % Allowed : 1.39 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1160 helix: -0.09 (0.23), residues: 445 sheet: -0.60 (0.33), residues: 225 loop : -0.56 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 36 HIS 0.012 0.002 HIS R 180 PHE 0.032 0.002 PHE R 184 TYR 0.024 0.002 TYR A 391 ARG 0.010 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 473) hydrogen bonds : angle 6.05762 ( 1341) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.52766 ( 12) covalent geometry : bond 0.00399 ( 9293) covalent geometry : angle 0.73544 (12612) *********************** 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 379 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 1.085 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: 0.7858 (t80) cc_final: 0.7378 (t80) REVERT: R 181 LEU cc_start: 0.9199 (mt) cc_final: 0.8883 (mt) REVERT: R 205 TYR cc_start: 0.8444 (t80) cc_final: 0.8223 (t80) REVERT: R 305 TYR cc_start: 0.7126 (m-80) cc_final: 0.6719 (m-80) REVERT: R 340 MET cc_start: 0.8018 (tpt) cc_final: 0.7577 (tpt) REVERT: R 351 LYS cc_start: 0.8762 (tptt) cc_final: 0.8540 (tptm) REVERT: R 397 MET cc_start: 0.7634 (mtp) cc_final: 0.7279 (mtp) REVERT: R 407 ASN cc_start: 0.7109 (p0) cc_final: 0.6906 (p0) REVERT: A 28 LYS cc_start: 0.6981 (mmpt) cc_final: 0.6735 (mtmt) REVERT: A 32 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8453 (mttp) REVERT: A 45 LEU cc_start: 0.9254 (tp) cc_final: 0.9035 (tp) REVERT: A 229 ASP cc_start: 0.8249 (p0) cc_final: 0.7947 (p0) REVERT: A 273 PHE cc_start: 0.8981 (t80) cc_final: 0.8757 (t80) REVERT: A 279 ASN cc_start: 0.9018 (t0) cc_final: 0.8815 (t0) REVERT: A 295 ASP cc_start: 0.8011 (p0) cc_final: 0.7550 (p0) REVERT: A 309 GLU cc_start: 0.9321 (pt0) cc_final: 0.8700 (tp30) REVERT: A 362 HIS cc_start: 0.7463 (m-70) cc_final: 0.7245 (m-70) REVERT: A 388 LEU cc_start: 0.9295 (mm) cc_final: 0.9073 (mm) REVERT: B 6 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 61 MET cc_start: 0.9070 (ppp) cc_final: 0.8332 (ppp) REVERT: B 66 ASP cc_start: 0.8246 (p0) cc_final: 0.7981 (p0) REVERT: B 120 ILE cc_start: 0.8823 (mt) cc_final: 0.8574 (mm) REVERT: B 180 PHE cc_start: 0.8139 (m-80) cc_final: 0.7809 (m-10) REVERT: B 210 LEU cc_start: 0.8776 (tp) cc_final: 0.8520 (tp) REVERT: B 220 GLN cc_start: 0.7677 (mp10) cc_final: 0.7292 (mp10) REVERT: B 235 PHE cc_start: 0.7922 (t80) cc_final: 0.7309 (t80) REVERT: B 246 ASP cc_start: 0.8643 (m-30) cc_final: 0.8262 (m-30) REVERT: B 273 ILE cc_start: 0.9213 (mp) cc_final: 0.8798 (mp) REVERT: B 283 ARG cc_start: 0.8473 (tpt90) cc_final: 0.7907 (tpt90) REVERT: B 297 TRP cc_start: 0.8446 (m100) cc_final: 0.8109 (m100) REVERT: B 325 MET cc_start: 0.8421 (tpp) cc_final: 0.7948 (tmm) REVERT: G 21 MET cc_start: 0.5289 (ttm) cc_final: 0.5066 (ttm) REVERT: G 24 ASN cc_start: 0.7195 (p0) cc_final: 0.6608 (t0) REVERT: N 32 TYR cc_start: 0.8430 (m-80) cc_final: 0.8034 (m-10) REVERT: N 34 MET cc_start: 0.9039 (ttm) cc_final: 0.8749 (ttm) REVERT: N 46 GLU cc_start: 0.7976 (pm20) cc_final: 0.7738 (pm20) REVERT: N 47 TRP cc_start: 0.8346 (t60) cc_final: 0.7197 (t60) REVERT: N 67 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7802 (ptp90) REVERT: N 82 GLN cc_start: 0.6943 (mm110) cc_final: 0.6741 (mm-40) REVERT: N 98 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.6962 (ptm-80) REVERT: N 111 THR cc_start: 0.7321 (m) cc_final: 0.6915 (p) outliers start: 1 outliers final: 1 residues processed: 379 average time/residue: 0.3039 time to fit residues: 154.8435 Evaluate side-chains 318 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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 180 HIS ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 75 GLN B 225 HIS B 313 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117272 restraints weight = 28027.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.120887 restraints weight = 16416.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.123345 restraints weight = 10769.857| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9299 Z= 0.159 Angle : 0.712 9.228 12624 Z= 0.384 Chirality : 0.047 0.250 1416 Planarity : 0.005 0.046 1612 Dihedral : 5.220 21.751 1277 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.14 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1160 helix: 0.02 (0.24), residues: 437 sheet: -0.58 (0.33), residues: 223 loop : -0.67 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 36 HIS 0.010 0.002 HIS A 387 PHE 0.033 0.002 PHE R 184 TYR 0.029 0.002 TYR G 40 ARG 0.010 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 473) hydrogen bonds : angle 6.01119 ( 1341) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.65028 ( 12) covalent geometry : bond 0.00345 ( 9293) covalent geometry : angle 0.71026 (12612) *********************** 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 375 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.691 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 152 TYR cc_start: 0.7872 (t80) cc_final: 0.7421 (t80) REVERT: R 181 LEU cc_start: 0.9271 (mt) cc_final: 0.8964 (mt) REVERT: R 305 TYR cc_start: 0.6930 (m-80) cc_final: 0.6504 (m-80) REVERT: R 351 LYS cc_start: 0.8747 (tptt) cc_final: 0.8537 (tptm) REVERT: R 397 MET cc_start: 0.7550 (mtp) cc_final: 0.7126 (mtp) REVERT: R 402 TYR cc_start: 0.7279 (p90) cc_final: 0.7045 (p90) REVERT: R 411 MET cc_start: 0.8399 (mmp) cc_final: 0.8088 (mmp) REVERT: A 229 ASP cc_start: 0.8263 (p0) cc_final: 0.7927 (p0) REVERT: A 273 PHE cc_start: 0.8982 (t80) cc_final: 0.8763 (t80) REVERT: A 274 LYS cc_start: 0.8248 (tttm) cc_final: 0.7818 (tttp) REVERT: A 281 TRP cc_start: 0.8210 (m100) cc_final: 0.7832 (m100) REVERT: A 287 VAL cc_start: 0.9013 (t) cc_final: 0.8736 (t) REVERT: A 309 GLU cc_start: 0.9334 (pt0) cc_final: 0.8621 (tp30) REVERT: A 343 ASP cc_start: 0.8230 (m-30) cc_final: 0.7761 (m-30) REVERT: A 383 ILE cc_start: 0.8990 (tp) cc_final: 0.8782 (tp) REVERT: A 388 LEU cc_start: 0.9321 (mm) cc_final: 0.9095 (mm) REVERT: B 6 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 61 MET cc_start: 0.9058 (ppp) cc_final: 0.8344 (ppp) REVERT: B 66 ASP cc_start: 0.8225 (p0) cc_final: 0.7882 (p0) REVERT: B 120 ILE cc_start: 0.8828 (mt) cc_final: 0.8575 (mm) REVERT: B 180 PHE cc_start: 0.8158 (m-80) cc_final: 0.7899 (m-10) REVERT: B 210 LEU cc_start: 0.8724 (tp) cc_final: 0.8482 (tp) REVERT: B 220 GLN cc_start: 0.7634 (mp10) cc_final: 0.7286 (mp10) REVERT: B 228 ASP cc_start: 0.6738 (m-30) cc_final: 0.6486 (m-30) REVERT: B 235 PHE cc_start: 0.7933 (t80) cc_final: 0.7109 (t80) REVERT: B 246 ASP cc_start: 0.8662 (m-30) cc_final: 0.8281 (m-30) REVERT: B 251 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7647 (mtt180) REVERT: B 273 ILE cc_start: 0.9227 (mp) cc_final: 0.8766 (mp) REVERT: B 297 TRP cc_start: 0.8530 (m100) cc_final: 0.8173 (m100) REVERT: B 313 ASN cc_start: 0.7529 (m110) cc_final: 0.7325 (m-40) REVERT: B 325 MET cc_start: 0.8437 (tpp) cc_final: 0.7976 (tmm) REVERT: B 337 LYS cc_start: 0.8570 (tppt) cc_final: 0.8200 (tppp) REVERT: G 24 ASN cc_start: 0.7290 (p0) cc_final: 0.6796 (t0) REVERT: N 27 PHE cc_start: 0.8265 (p90) cc_final: 0.8025 (p90) REVERT: N 32 TYR cc_start: 0.8316 (m-80) cc_final: 0.7907 (m-10) REVERT: N 34 MET cc_start: 0.9055 (ttm) cc_final: 0.8778 (ttm) REVERT: N 46 GLU cc_start: 0.7947 (pm20) cc_final: 0.7606 (pm20) REVERT: N 47 TRP cc_start: 0.8387 (t60) cc_final: 0.7205 (t60) REVERT: N 67 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7918 (ptp90) REVERT: N 82 GLN cc_start: 0.7035 (mm110) cc_final: 0.6822 (mm110) REVERT: N 111 THR cc_start: 0.7250 (m) cc_final: 0.6865 (p) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2723 time to fit residues: 140.6113 Evaluate side-chains 317 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 213 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.136789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118260 restraints weight = 28280.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121977 restraints weight = 16416.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124544 restraints weight = 10742.885| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6643 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= 0.153 Angle : 0.728 8.933 12624 Z= 0.391 Chirality : 0.047 0.240 1416 Planarity : 0.005 0.088 1612 Dihedral : 5.218 21.496 1277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1160 helix: 0.07 (0.24), residues: 442 sheet: -0.63 (0.34), residues: 225 loop : -0.60 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.010 0.002 HIS A 387 PHE 0.034 0.002 PHE R 184 TYR 0.023 0.002 TYR A 391 ARG 0.023 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 473) hydrogen bonds : angle 5.96443 ( 1341) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.55911 ( 12) covalent geometry : bond 0.00339 ( 9293) covalent geometry : angle 0.72686 (12612) ********************** 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 369 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.030 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 152 TYR cc_start: 0.7790 (t80) cc_final: 0.7250 (t80) REVERT: R 181 LEU cc_start: 0.9268 (mt) cc_final: 0.8967 (mt) REVERT: R 305 TYR cc_start: 0.7301 (m-80) cc_final: 0.6892 (m-80) REVERT: R 397 MET cc_start: 0.7477 (mtp) cc_final: 0.7036 (mtp) REVERT: R 402 TYR cc_start: 0.7269 (p90) cc_final: 0.6973 (p90) REVERT: R 411 MET cc_start: 0.8360 (mmp) cc_final: 0.8157 (mmp) REVERT: A 44 LEU cc_start: 0.8453 (tp) cc_final: 0.8093 (tp) REVERT: A 229 ASP cc_start: 0.8344 (p0) cc_final: 0.8038 (p0) REVERT: A 273 PHE cc_start: 0.8937 (t80) cc_final: 0.8715 (t80) REVERT: A 274 LYS cc_start: 0.8196 (tttm) cc_final: 0.7901 (tmtt) REVERT: A 279 ASN cc_start: 0.8984 (t0) cc_final: 0.8751 (t0) REVERT: A 281 TRP cc_start: 0.8188 (m100) cc_final: 0.7890 (m100) REVERT: A 287 VAL cc_start: 0.8950 (t) cc_final: 0.8672 (t) REVERT: A 309 GLU cc_start: 0.9366 (pt0) cc_final: 0.8631 (tp30) REVERT: A 383 ILE cc_start: 0.8991 (tp) cc_final: 0.8783 (tp) REVERT: A 384 GLN cc_start: 0.9220 (pt0) cc_final: 0.8818 (pt0) REVERT: A 388 LEU cc_start: 0.9355 (mm) cc_final: 0.9107 (mm) REVERT: B 6 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6939 (tm-30) REVERT: B 61 MET cc_start: 0.9037 (ppp) cc_final: 0.8329 (ppp) REVERT: B 66 ASP cc_start: 0.8159 (p0) cc_final: 0.7870 (p0) REVERT: B 120 ILE cc_start: 0.8815 (mt) cc_final: 0.8563 (mm) REVERT: B 210 LEU cc_start: 0.8741 (tp) cc_final: 0.8538 (tp) REVERT: B 220 GLN cc_start: 0.7663 (mp10) cc_final: 0.7322 (mp10) REVERT: B 235 PHE cc_start: 0.8021 (t80) cc_final: 0.7477 (t80) REVERT: B 246 ASP cc_start: 0.8625 (m-30) cc_final: 0.8222 (m-30) REVERT: B 273 ILE cc_start: 0.9208 (mp) cc_final: 0.8759 (mp) REVERT: B 297 TRP cc_start: 0.8616 (m100) cc_final: 0.8339 (m100) REVERT: B 313 ASN cc_start: 0.7465 (m110) cc_final: 0.7004 (m-40) REVERT: B 325 MET cc_start: 0.8460 (tpp) cc_final: 0.7656 (tmm) REVERT: B 337 LYS cc_start: 0.8381 (tppt) cc_final: 0.8116 (tppp) REVERT: G 24 ASN cc_start: 0.7272 (p0) cc_final: 0.6788 (t0) REVERT: N 27 PHE cc_start: 0.8274 (p90) cc_final: 0.7905 (p90) REVERT: N 34 MET cc_start: 0.9081 (ttm) cc_final: 0.8770 (ttm) REVERT: N 46 GLU cc_start: 0.8009 (pm20) cc_final: 0.7475 (pm20) REVERT: N 47 TRP cc_start: 0.8316 (t60) cc_final: 0.7179 (t60) REVERT: N 67 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7959 (ptp90) REVERT: N 82 GLN cc_start: 0.6789 (mm110) cc_final: 0.6436 (mm110) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2313 time to fit residues: 117.3323 Evaluate side-chains 310 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 16 ASN B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.135103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117034 restraints weight = 28385.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120647 restraints weight = 16606.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.123157 restraints weight = 10874.288| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.6784 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= 0.174 Angle : 0.748 9.955 12624 Z= 0.406 Chirality : 0.047 0.235 1416 Planarity : 0.005 0.067 1612 Dihedral : 5.210 20.149 1277 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1160 helix: 0.08 (0.25), residues: 430 sheet: -0.59 (0.34), residues: 228 loop : -0.59 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP N 36 HIS 0.013 0.002 HIS R 48 PHE 0.033 0.002 PHE R 184 TYR 0.027 0.002 TYR R 269 ARG 0.013 0.001 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 473) hydrogen bonds : angle 5.97861 ( 1341) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.96750 ( 12) covalent geometry : bond 0.00384 ( 9293) covalent geometry : angle 0.74570 (12612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.24 seconds wall clock time: 76 minutes 15.34 seconds (4575.34 seconds total)