Starting phenix.real_space_refine on Thu Feb 13 15:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vai_8653/02_2025/5vai_8653.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vai_8653/02_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_8653/02_2025/5vai_8653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vai_8653/02_2025/5vai_8653.map" model { file = "/net/cci-nas-00/data/ceres_data/5vai_8653/02_2025/5vai_8653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vai_8653/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.79, per 1000 atoms: 0.64 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 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: 0.79 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: 2.41 Time building geometry restraints manager: 2.73 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: 1.170 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- 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 : 0.008 0.091 9293 Z= 0.504 Angle : 1.109 15.490 12612 Z= 0.625 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 *********************** 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 : 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: 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: 0.2511 time to fit residues: 167.5103 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 : 1.107 ------------------------------------------------------------------------------- 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 = 0.135129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117327 restraints weight = 27418.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.121058 restraints weight = 15697.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123593 restraints weight = 10140.409| |-----------------------------------------------------------------------------| 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 9293 Z= 0.272 Angle : 0.808 11.046 12612 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 *********************** 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 : 1.096 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: 0.8286 (m-70) cc_final: 0.8077 (m90) REVERT: R 184 PHE cc_start: 0.9307 (m-10) cc_final: 0.9106 (m-80) REVERT: R 229 VAL cc_start: 0.9192 (t) cc_final: 0.8954 (p) REVERT: R 272 ILE cc_start: 0.8162 (tt) cc_final: 0.7890 (mt) REVERT: R 351 LYS cc_start: 0.8557 (tptt) cc_final: 0.7932 (tmtt) REVERT: A 28 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6571 (ptpp) REVERT: A 32 LYS cc_start: 0.9174 (mttt) cc_final: 0.8953 (mttp) REVERT: A 229 ASP cc_start: 0.8121 (p0) cc_final: 0.7650 (p0) REVERT: A 237 CYS cc_start: 0.8652 (m) cc_final: 0.8155 (m) REVERT: A 271 ASN cc_start: 0.8460 (m110) cc_final: 0.7383 (m110) REVERT: A 273 PHE cc_start: 0.9122 (t80) cc_final: 0.8634 (t80) REVERT: A 279 ASN cc_start: 0.8779 (t0) cc_final: 0.8489 (t0) REVERT: A 283 ARG cc_start: 0.8449 (mtt180) cc_final: 0.8052 (ptp-170) REVERT: A 287 VAL cc_start: 0.8937 (t) cc_final: 0.8721 (t) REVERT: A 360 TYR cc_start: 0.8676 (m-10) cc_final: 0.8405 (m-10) REVERT: A 371 ASN cc_start: 0.8288 (p0) cc_final: 0.7968 (p0) REVERT: A 383 ILE cc_start: 0.9133 (tt) cc_final: 0.8716 (tp) REVERT: A 386 MET cc_start: 0.8161 (ttt) cc_final: 0.7918 (tmm) REVERT: A 388 LEU cc_start: 0.9237 (mm) cc_final: 0.8910 (mm) REVERT: B 6 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6733 (tm-30) REVERT: B 13 GLN cc_start: 0.8712 (tt0) cc_final: 0.8226 (pt0) REVERT: B 49 ARG cc_start: 0.7698 (mmt-90) cc_final: 0.7354 (mmt-90) REVERT: B 63 TRP cc_start: 0.8580 (m100) cc_final: 0.8248 (m100) REVERT: B 66 ASP cc_start: 0.8220 (p0) cc_final: 0.7981 (p0) REVERT: B 89 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8931 (mmmm) REVERT: B 120 ILE cc_start: 0.8654 (mt) cc_final: 0.8390 (mm) REVERT: B 148 CYS cc_start: 0.8627 (t) cc_final: 0.8365 (t) REVERT: B 153 ASP cc_start: 0.8267 (p0) cc_final: 0.7310 (p0) REVERT: B 210 LEU cc_start: 0.8999 (tp) cc_final: 0.8446 (tp) REVERT: B 220 GLN cc_start: 0.7956 (mp10) cc_final: 0.7380 (mp10) REVERT: B 235 PHE cc_start: 0.8035 (t80) cc_final: 0.7589 (t80) REVERT: B 246 ASP cc_start: 0.8262 (m-30) cc_final: 0.7938 (m-30) REVERT: B 251 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6167 (mtt90) REVERT: B 273 ILE cc_start: 0.9122 (mp) cc_final: 0.8695 (mp) REVERT: B 278 PHE cc_start: 0.7337 (m-80) cc_final: 0.7104 (m-80) REVERT: B 280 LYS cc_start: 0.8686 (tttt) cc_final: 0.7995 (tttm) REVERT: B 283 ARG cc_start: 0.8439 (tpt-90) cc_final: 0.8187 (tpt170) REVERT: B 325 MET cc_start: 0.8267 (tpp) cc_final: 0.7935 (tmm) REVERT: N 34 MET cc_start: 0.9163 (ttm) cc_final: 0.8815 (ttp) REVERT: N 47 TRP cc_start: 0.8258 (t60) cc_final: 0.6816 (t60) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2420 time to fit residues: 139.8365 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 : 1.046 ------------------------------------------------------------------------------- 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: 1.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.135512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117893 restraints weight = 27760.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121698 restraints weight = 15800.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.124330 restraints weight = 10104.309| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9293 Z= 0.245 Angle : 0.715 9.951 12612 Z= 0.384 Chirality : 0.045 0.172 1416 Planarity : 0.005 0.059 1612 Dihedral : 5.477 26.106 1277 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 0.32 % Allowed : 3.94 % Favored : 95.74 % 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: -0.11 (0.23), residues: 434 sheet: -0.72 (0.35), residues: 203 loop : -0.50 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 169 HIS 0.008 0.002 HIS R 48 PHE 0.020 0.002 PHE R 321 TYR 0.041 0.002 TYR R 269 ARG 0.010 0.001 ARG N 98 *********************** 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 416 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 413 time to evaluate : 0.986 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: R 47 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: R 181 LEU cc_start: 0.9349 (mt) cc_final: 0.8941 (mt) REVERT: R 229 VAL cc_start: 0.9215 (t) cc_final: 0.8972 (p) REVERT: R 272 ILE cc_start: 0.8222 (tt) cc_final: 0.7981 (mt) REVERT: R 351 LYS cc_start: 0.8587 (tptt) cc_final: 0.7945 (tmtt) REVERT: A 28 LYS cc_start: 0.6932 (mmpt) cc_final: 0.6541 (ptpp) REVERT: A 32 LYS cc_start: 0.9165 (mttt) cc_final: 0.8953 (mttp) REVERT: A 35 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7667 (mm-40) REVERT: A 44 LEU cc_start: 0.8728 (tp) cc_final: 0.8281 (tp) REVERT: A 229 ASP cc_start: 0.8149 (p0) cc_final: 0.7692 (p0) REVERT: A 233 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8566 (mttt) REVERT: A 271 ASN cc_start: 0.8381 (m110) cc_final: 0.7981 (m110) REVERT: A 279 ASN cc_start: 0.8782 (t0) cc_final: 0.8539 (t0) REVERT: A 283 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8082 (ptp-170) REVERT: A 289 LEU cc_start: 0.8652 (tp) cc_final: 0.8337 (tp) REVERT: A 291 LEU cc_start: 0.9393 (mt) cc_final: 0.9125 (mt) REVERT: A 383 ILE cc_start: 0.9087 (tt) cc_final: 0.8766 (tp) REVERT: A 384 GLN cc_start: 0.9167 (pp30) cc_final: 0.8865 (pt0) REVERT: A 386 MET cc_start: 0.8168 (ttt) cc_final: 0.7487 (tmm) REVERT: B 6 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6657 (tm-30) REVERT: B 61 MET cc_start: 0.9008 (ppp) cc_final: 0.8648 (ppp) REVERT: B 63 TRP cc_start: 0.8616 (m100) cc_final: 0.8274 (m100) REVERT: B 66 ASP cc_start: 0.8190 (p0) cc_final: 0.7965 (p0) REVERT: B 71 VAL cc_start: 0.9174 (m) cc_final: 0.8969 (m) REVERT: B 89 LYS cc_start: 0.9395 (mmmm) cc_final: 0.8870 (mmmm) REVERT: B 102 THR cc_start: 0.8662 (t) cc_final: 0.8358 (m) REVERT: B 120 ILE cc_start: 0.8677 (mt) cc_final: 0.8435 (mm) REVERT: B 148 CYS cc_start: 0.8822 (t) cc_final: 0.8514 (t) REVERT: B 153 ASP cc_start: 0.7771 (p0) cc_final: 0.7360 (p0) REVERT: B 170 ASP cc_start: 0.7537 (t0) cc_final: 0.7326 (t0) REVERT: B 204 CYS cc_start: 0.8325 (m) cc_final: 0.7902 (m) REVERT: B 210 LEU cc_start: 0.8764 (tp) cc_final: 0.8372 (tp) REVERT: B 220 GLN cc_start: 0.7909 (mp10) cc_final: 0.7297 (mp10) REVERT: B 229 ILE cc_start: 0.8374 (mt) cc_final: 0.7970 (mt) REVERT: B 235 PHE cc_start: 0.8125 (t80) cc_final: 0.7678 (t80) REVERT: B 262 MET cc_start: 0.7106 (mmm) cc_final: 0.6786 (mmm) REVERT: B 264 TYR cc_start: 0.7181 (m-80) cc_final: 0.6545 (m-80) REVERT: B 278 PHE cc_start: 0.7293 (m-80) cc_final: 0.7081 (m-80) REVERT: B 280 LYS cc_start: 0.8623 (tttt) cc_final: 0.8172 (tttm) REVERT: B 297 TRP cc_start: 0.8109 (m100) cc_final: 0.7873 (m100) REVERT: B 325 MET cc_start: 0.8458 (tpp) cc_final: 0.8089 (tmm) REVERT: N 27 PHE cc_start: 0.8464 (p90) cc_final: 0.8257 (p90) REVERT: N 32 TYR cc_start: 0.8486 (m-80) cc_final: 0.8051 (m-10) REVERT: N 47 TRP cc_start: 0.8245 (t60) cc_final: 0.6608 (t60) REVERT: N 67 ARG cc_start: 0.7979 (ptp-110) cc_final: 0.7686 (ptp90) REVERT: N 68 PHE cc_start: 0.8731 (m-80) cc_final: 0.7962 (m-80) outliers start: 3 outliers final: 1 residues processed: 415 average time/residue: 0.2437 time to fit residues: 134.8720 Evaluate side-chains 344 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 342 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 0.6980 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN R 302 ASN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.136752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118508 restraints weight = 27773.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122323 restraints weight = 15875.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124999 restraints weight = 10220.556| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9293 Z= 0.226 Angle : 0.713 8.891 12612 Z= 0.383 Chirality : 0.047 0.386 1416 Planarity : 0.005 0.055 1612 Dihedral : 5.332 25.544 1277 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.05 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -0.61 (0.24), residues: 1160 helix: -0.12 (0.24), residues: 436 sheet: -0.63 (0.35), residues: 206 loop : -0.37 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.010 0.002 HIS R 180 PHE 0.034 0.002 PHE R 324 TYR 0.023 0.002 TYR A 391 ARG 0.007 0.001 ARG B 314 *********************** 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 404 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 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: symmetry clash revert: symmetry clash REVERT: R 180 HIS cc_start: 0.8929 (m-70) cc_final: 0.8709 (m-70) REVERT: R 181 LEU cc_start: 0.9283 (mt) cc_final: 0.8983 (mt) REVERT: R 205 TYR cc_start: 0.8416 (t80) cc_final: 0.8165 (t80) REVERT: R 229 VAL cc_start: 0.9246 (t) cc_final: 0.9020 (p) REVERT: R 262 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6412 (mm-30) REVERT: R 272 ILE cc_start: 0.8247 (tt) cc_final: 0.8006 (mt) REVERT: R 351 LYS cc_start: 0.8657 (tptt) cc_final: 0.7997 (tmtt) REVERT: R 397 MET cc_start: 0.7960 (mtm) cc_final: 0.7750 (ptm) REVERT: R 411 MET cc_start: 0.8138 (mmp) cc_final: 0.7894 (mmp) REVERT: A 25 LYS cc_start: 0.8018 (tptt) cc_final: 0.7406 (tptt) REVERT: A 28 LYS cc_start: 0.6835 (mmpt) cc_final: 0.6434 (ptpp) REVERT: A 35 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 44 LEU cc_start: 0.8720 (tp) cc_final: 0.8332 (tp) REVERT: A 45 LEU cc_start: 0.9262 (tp) cc_final: 0.9041 (tp) REVERT: A 229 ASP cc_start: 0.8112 (p0) cc_final: 0.7652 (p0) REVERT: A 279 ASN cc_start: 0.8853 (t0) cc_final: 0.8593 (t0) REVERT: A 283 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7945 (ptp-170) REVERT: A 295 ASP cc_start: 0.8393 (p0) cc_final: 0.7798 (p0) REVERT: A 309 GLU cc_start: 0.9322 (pt0) cc_final: 0.8745 (tp30) REVERT: A 335 THR cc_start: 0.8635 (m) cc_final: 0.8369 (p) REVERT: A 383 ILE cc_start: 0.9051 (tt) cc_final: 0.8707 (tp) REVERT: A 386 MET cc_start: 0.7999 (ttt) cc_final: 0.7680 (tmm) REVERT: A 388 LEU cc_start: 0.9221 (mm) cc_final: 0.8999 (mm) REVERT: B 6 GLN cc_start: 0.6945 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 49 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7461 (mmt90) REVERT: B 61 MET cc_start: 0.9054 (ppp) cc_final: 0.8458 (ppp) REVERT: B 63 TRP cc_start: 0.8595 (m100) cc_final: 0.8237 (m100) REVERT: B 66 ASP cc_start: 0.8244 (p0) cc_final: 0.7974 (p0) REVERT: B 71 VAL cc_start: 0.9166 (m) cc_final: 0.8534 (p) REVERT: B 120 ILE cc_start: 0.8673 (mt) cc_final: 0.8430 (mm) REVERT: B 148 CYS cc_start: 0.8804 (t) cc_final: 0.8554 (t) REVERT: B 153 ASP cc_start: 0.7728 (p0) cc_final: 0.7436 (p0) REVERT: B 170 ASP cc_start: 0.7439 (t0) cc_final: 0.7231 (t0) REVERT: B 210 LEU cc_start: 0.8797 (tp) cc_final: 0.8433 (tp) REVERT: B 220 GLN cc_start: 0.7687 (mp10) cc_final: 0.7272 (mp10) REVERT: B 235 PHE cc_start: 0.7994 (t80) cc_final: 0.7779 (t80) REVERT: B 262 MET cc_start: 0.6939 (mmm) cc_final: 0.6565 (mmm) REVERT: B 264 TYR cc_start: 0.7330 (m-80) cc_final: 0.6371 (m-80) REVERT: B 273 ILE cc_start: 0.9147 (mp) cc_final: 0.8911 (mp) REVERT: B 280 LYS cc_start: 0.8711 (tttt) cc_final: 0.8334 (tttm) REVERT: B 283 ARG cc_start: 0.8204 (tpt170) cc_final: 0.8001 (tpt170) REVERT: B 297 TRP cc_start: 0.8133 (m100) cc_final: 0.7618 (m100) REVERT: B 308 LEU cc_start: 0.7337 (mt) cc_final: 0.7053 (mt) REVERT: N 32 TYR cc_start: 0.8522 (m-80) cc_final: 0.7961 (m-10) REVERT: N 34 MET cc_start: 0.9139 (ttp) cc_final: 0.8569 (tpp) REVERT: N 46 GLU cc_start: 0.8055 (pm20) cc_final: 0.7835 (pm20) REVERT: N 81 LEU cc_start: 0.8728 (tp) cc_final: 0.8426 (tt) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2365 time to fit residues: 126.8677 Evaluate side-chains 337 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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: 20.0000 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.135815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.117679 restraints weight = 27803.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.121462 restraints weight = 15975.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.124025 restraints weight = 10321.314| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9293 Z= 0.224 Angle : 0.697 9.648 12612 Z= 0.374 Chirality : 0.047 0.369 1416 Planarity : 0.005 0.052 1612 Dihedral : 5.248 24.566 1277 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.24), residues: 1160 helix: 0.06 (0.24), residues: 429 sheet: -0.39 (0.35), residues: 209 loop : -0.45 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 169 HIS 0.008 0.002 HIS A 357 PHE 0.030 0.002 PHE R 184 TYR 0.021 0.002 TYR N 117 ARG 0.006 0.001 ARG A 42 *********************** 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 393 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 38 LYS cc_start: 0.7751 (pttm) cc_final: 0.7432 (pttp) REVERT: R 181 LEU cc_start: 0.9125 (mt) cc_final: 0.8740 (mt) REVERT: R 187 PHE cc_start: 0.7964 (m-80) cc_final: 0.7754 (m-80) REVERT: R 205 TYR cc_start: 0.8452 (t80) cc_final: 0.8217 (t80) REVERT: R 262 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6247 (mm-30) REVERT: R 272 ILE cc_start: 0.8283 (tt) cc_final: 0.8040 (mt) REVERT: R 351 LYS cc_start: 0.8733 (tptt) cc_final: 0.8034 (tmtt) REVERT: A 28 LYS cc_start: 0.7010 (mmpt) cc_final: 0.6595 (mtmt) REVERT: A 32 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8418 (mttp) REVERT: A 35 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7879 (mm-40) REVERT: A 222 PHE cc_start: 0.7225 (t80) cc_final: 0.6561 (t80) REVERT: A 229 ASP cc_start: 0.8198 (p0) cc_final: 0.7748 (p0) REVERT: A 279 ASN cc_start: 0.8866 (t0) cc_final: 0.8595 (t0) REVERT: A 291 LEU cc_start: 0.9256 (mt) cc_final: 0.8992 (mt) REVERT: A 295 ASP cc_start: 0.8435 (p0) cc_final: 0.7974 (p0) REVERT: A 309 GLU cc_start: 0.9331 (pt0) cc_final: 0.8734 (tp30) REVERT: A 374 ARG cc_start: 0.8319 (ttt180) cc_final: 0.7918 (ptm160) REVERT: A 383 ILE cc_start: 0.9119 (tt) cc_final: 0.8611 (tp) REVERT: A 386 MET cc_start: 0.7996 (ttt) cc_final: 0.7653 (tmm) REVERT: A 388 LEU cc_start: 0.9252 (mm) cc_final: 0.9044 (mm) REVERT: B 6 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 49 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7332 (mmt90) REVERT: B 61 MET cc_start: 0.9093 (ppp) cc_final: 0.8451 (ppp) REVERT: B 63 TRP cc_start: 0.8644 (m100) cc_final: 0.8265 (m100) REVERT: B 66 ASP cc_start: 0.8232 (p0) cc_final: 0.8012 (p0) REVERT: B 71 VAL cc_start: 0.9155 (m) cc_final: 0.8743 (p) REVERT: B 89 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9021 (mmmm) REVERT: B 120 ILE cc_start: 0.8702 (mt) cc_final: 0.8449 (mm) REVERT: B 148 CYS cc_start: 0.8803 (t) cc_final: 0.8574 (t) REVERT: B 153 ASP cc_start: 0.7752 (p0) cc_final: 0.7312 (p0) REVERT: B 170 ASP cc_start: 0.7408 (t0) cc_final: 0.7183 (t0) REVERT: B 210 LEU cc_start: 0.8766 (tp) cc_final: 0.8439 (tp) REVERT: B 220 GLN cc_start: 0.7729 (mp10) cc_final: 0.7302 (mp10) REVERT: B 235 PHE cc_start: 0.7915 (t80) cc_final: 0.7490 (t80) REVERT: B 246 ASP cc_start: 0.8771 (m-30) cc_final: 0.8305 (m-30) REVERT: B 262 MET cc_start: 0.7089 (mmm) cc_final: 0.6551 (mmm) REVERT: B 264 TYR cc_start: 0.7224 (m-80) cc_final: 0.6385 (m-80) REVERT: B 273 ILE cc_start: 0.9183 (mp) cc_final: 0.8665 (mp) REVERT: B 283 ARG cc_start: 0.8174 (tpt170) cc_final: 0.7926 (tpt170) REVERT: B 284 LEU cc_start: 0.8614 (mp) cc_final: 0.8390 (mp) REVERT: B 297 TRP cc_start: 0.8138 (m100) cc_final: 0.7641 (m100) REVERT: B 313 ASN cc_start: 0.6920 (t0) cc_final: 0.6354 (m110) REVERT: N 32 TYR cc_start: 0.8549 (m-80) cc_final: 0.8046 (m-10) REVERT: N 36 TRP cc_start: 0.6483 (m100) cc_final: 0.6216 (m100) REVERT: N 47 TRP cc_start: 0.8206 (t60) cc_final: 0.7115 (t60) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.2302 time to fit residues: 120.5148 Evaluate side-chains 331 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 5.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 234 GLN R 240 ASN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.136379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.117878 restraints weight = 28513.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121621 restraints weight = 16432.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124166 restraints weight = 10683.038| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9293 Z= 0.251 Angle : 0.735 9.523 12612 Z= 0.393 Chirality : 0.048 0.302 1416 Planarity : 0.005 0.050 1612 Dihedral : 5.242 24.589 1277 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % 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: -0.73 (0.24), residues: 1160 helix: -0.10 (0.24), residues: 433 sheet: -0.58 (0.34), residues: 216 loop : -0.62 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.008 0.002 HIS A 357 PHE 0.036 0.002 PHE R 184 TYR 0.026 0.002 TYR A 391 ARG 0.007 0.001 ARG G 27 *********************** 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 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.9131 (mt) cc_final: 0.8749 (mt) REVERT: R 205 TYR cc_start: 0.8509 (t80) cc_final: 0.8289 (t80) REVERT: R 262 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6087 (mm-30) REVERT: R 272 ILE cc_start: 0.8348 (tt) cc_final: 0.8109 (mt) REVERT: R 351 LYS cc_start: 0.8753 (tptt) cc_final: 0.8038 (tmtt) REVERT: A 28 LYS cc_start: 0.7066 (mmpt) cc_final: 0.6663 (mtmt) REVERT: A 35 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7744 (mm-40) REVERT: A 229 ASP cc_start: 0.8209 (p0) cc_final: 0.7926 (p0) REVERT: A 279 ASN cc_start: 0.8896 (t0) cc_final: 0.8653 (t0) REVERT: A 295 ASP cc_start: 0.8276 (p0) cc_final: 0.7804 (p0) REVERT: A 309 GLU cc_start: 0.9335 (pt0) cc_final: 0.8744 (tp30) REVERT: A 381 ASP cc_start: 0.9099 (m-30) cc_final: 0.8802 (m-30) REVERT: A 383 ILE cc_start: 0.9101 (tt) cc_final: 0.8794 (tp) REVERT: A 388 LEU cc_start: 0.9248 (mm) cc_final: 0.8967 (mm) REVERT: B 6 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6660 (tm-30) REVERT: B 49 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7554 (mmt90) REVERT: B 61 MET cc_start: 0.9111 (ppp) cc_final: 0.8874 (ppp) REVERT: B 66 ASP cc_start: 0.8209 (p0) cc_final: 0.7822 (p0) REVERT: B 89 LYS cc_start: 0.9395 (mmmm) cc_final: 0.9137 (mmmm) REVERT: B 120 ILE cc_start: 0.8741 (mt) cc_final: 0.8464 (mm) REVERT: B 153 ASP cc_start: 0.7778 (p0) cc_final: 0.7398 (p0) REVERT: B 210 LEU cc_start: 0.8802 (tp) cc_final: 0.8551 (tp) REVERT: B 220 GLN cc_start: 0.7780 (mp10) cc_final: 0.7413 (mp10) REVERT: B 235 PHE cc_start: 0.7960 (t80) cc_final: 0.7420 (t80) REVERT: B 246 ASP cc_start: 0.8821 (m-30) cc_final: 0.8342 (m-30) REVERT: B 273 ILE cc_start: 0.9226 (mp) cc_final: 0.8793 (mp) REVERT: B 283 ARG cc_start: 0.8432 (tpt170) cc_final: 0.7929 (tpt170) REVERT: B 284 LEU cc_start: 0.8607 (mp) cc_final: 0.8406 (mp) REVERT: B 297 TRP cc_start: 0.8318 (m100) cc_final: 0.7767 (m100) REVERT: B 313 ASN cc_start: 0.6942 (t0) cc_final: 0.6683 (m110) REVERT: G 24 ASN cc_start: 0.7344 (p0) cc_final: 0.6839 (t0) REVERT: N 32 TYR cc_start: 0.8434 (m-80) cc_final: 0.7840 (m-80) REVERT: N 36 TRP cc_start: 0.6426 (m100) cc_final: 0.6167 (m100) REVERT: N 111 THR cc_start: 0.7157 (m) cc_final: 0.6719 (p) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2304 time to fit residues: 118.8953 Evaluate side-chains 328 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 302 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 176 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 = 0.4173 r_free = 0.4173 target = 0.135773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.117425 restraints weight = 28481.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.121092 restraints weight = 16425.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123610 restraints weight = 10725.716| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9293 Z= 0.229 Angle : 0.705 9.191 12612 Z= 0.380 Chirality : 0.048 0.295 1416 Planarity : 0.005 0.044 1612 Dihedral : 5.185 24.423 1277 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.91 % Favored : 94.91 % Rotamer: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.55 % 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: -0.59 (0.24), residues: 1160 helix: 0.05 (0.24), residues: 437 sheet: -0.65 (0.34), residues: 218 loop : -0.50 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.008 0.002 HIS B 183 PHE 0.030 0.002 PHE R 184 TYR 0.025 0.002 TYR R 269 ARG 0.011 0.001 ARG A 385 *********************** 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 386 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.9247 (mt) cc_final: 0.9031 (mt) REVERT: R 205 TYR cc_start: 0.8430 (t80) cc_final: 0.8170 (t80) REVERT: R 272 ILE cc_start: 0.8358 (tt) cc_final: 0.8151 (mt) REVERT: R 351 LYS cc_start: 0.8737 (tptt) cc_final: 0.7986 (tmtt) REVERT: R 397 MET cc_start: 0.7468 (mtp) cc_final: 0.7202 (mtp) REVERT: R 411 MET cc_start: 0.8306 (mmp) cc_final: 0.7942 (mmp) REVERT: A 28 LYS cc_start: 0.7036 (mmpt) cc_final: 0.6592 (mtmm) REVERT: A 35 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7798 (mm-40) REVERT: A 44 LEU cc_start: 0.8086 (tp) cc_final: 0.7718 (tp) REVERT: A 229 ASP cc_start: 0.8290 (p0) cc_final: 0.8063 (p0) REVERT: A 274 LYS cc_start: 0.8678 (tttp) cc_final: 0.8255 (tttt) REVERT: A 279 ASN cc_start: 0.8873 (t0) cc_final: 0.8654 (t0) REVERT: A 295 ASP cc_start: 0.8232 (p0) cc_final: 0.7748 (p0) REVERT: A 309 GLU cc_start: 0.9314 (pt0) cc_final: 0.8692 (tp30) REVERT: A 380 ARG cc_start: 0.8087 (tmm-80) cc_final: 0.7855 (tmm-80) REVERT: A 383 ILE cc_start: 0.9079 (tt) cc_final: 0.8775 (tp) REVERT: A 388 LEU cc_start: 0.9343 (mm) cc_final: 0.9047 (mm) REVERT: B 6 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6851 (tm-30) REVERT: B 61 MET cc_start: 0.9102 (ppp) cc_final: 0.8235 (ppp) REVERT: B 66 ASP cc_start: 0.8120 (p0) cc_final: 0.7880 (p0) REVERT: B 153 ASP cc_start: 0.7720 (p0) cc_final: 0.7458 (p0) REVERT: B 210 LEU cc_start: 0.8769 (tp) cc_final: 0.8499 (tp) REVERT: B 220 GLN cc_start: 0.7746 (mp10) cc_final: 0.7301 (mp10) REVERT: B 235 PHE cc_start: 0.7920 (t80) cc_final: 0.7505 (t80) REVERT: B 246 ASP cc_start: 0.8850 (m-30) cc_final: 0.8390 (m-30) REVERT: B 273 ILE cc_start: 0.9168 (mp) cc_final: 0.8720 (mp) REVERT: B 283 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7956 (tpt170) REVERT: B 297 TRP cc_start: 0.8380 (m100) cc_final: 0.7818 (m100) REVERT: B 313 ASN cc_start: 0.7150 (t0) cc_final: 0.6924 (m110) REVERT: G 24 ASN cc_start: 0.7211 (p0) cc_final: 0.6718 (t0) REVERT: G 50 LEU cc_start: 0.8603 (mm) cc_final: 0.8174 (mm) REVERT: N 27 PHE cc_start: 0.8270 (p90) cc_final: 0.7999 (p90) REVERT: N 31 ASN cc_start: 0.8650 (m-40) cc_final: 0.7423 (t0) REVERT: N 32 TYR cc_start: 0.8340 (m-80) cc_final: 0.7699 (m-80) REVERT: N 34 MET cc_start: 0.9092 (ttm) cc_final: 0.8768 (ttm) REVERT: N 81 LEU cc_start: 0.8629 (tp) cc_final: 0.8428 (tt) REVERT: N 111 THR cc_start: 0.7309 (m) cc_final: 0.7027 (p) outliers start: 1 outliers final: 1 residues processed: 385 average time/residue: 0.2498 time to fit residues: 129.7415 Evaluate side-chains 330 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 0.0570 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 33 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.138519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120011 restraints weight = 28625.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.123812 restraints weight = 16473.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126381 restraints weight = 10731.069| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9293 Z= 0.206 Angle : 0.713 9.044 12612 Z= 0.384 Chirality : 0.048 0.280 1416 Planarity : 0.005 0.054 1612 Dihedral : 5.118 24.090 1277 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -0.64 (0.24), residues: 1160 helix: -0.08 (0.24), residues: 453 sheet: -0.27 (0.34), residues: 211 loop : -0.67 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 36 HIS 0.011 0.002 HIS R 180 PHE 0.032 0.002 PHE R 184 TYR 0.024 0.002 TYR R 152 ARG 0.010 0.001 ARG A 385 *********************** 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 391 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 LEU cc_start: 0.9251 (mt) cc_final: 0.8978 (mt) REVERT: R 205 TYR cc_start: 0.8404 (t80) cc_final: 0.8151 (t80) REVERT: R 272 ILE cc_start: 0.8327 (tt) cc_final: 0.8103 (mt) REVERT: R 324 PHE cc_start: 0.7523 (t80) cc_final: 0.7316 (t80) REVERT: R 325 ILE cc_start: 0.8754 (mt) cc_final: 0.8543 (mt) REVERT: R 340 MET cc_start: 0.8048 (tpt) cc_final: 0.7621 (tpt) REVERT: R 351 LYS cc_start: 0.8779 (tptt) cc_final: 0.8552 (tptm) REVERT: R 397 MET cc_start: 0.7435 (mtp) cc_final: 0.7000 (ptm) REVERT: R 411 MET cc_start: 0.8367 (mmp) cc_final: 0.7999 (mmp) REVERT: A 11 ASP cc_start: 0.8195 (t70) cc_final: 0.7851 (t70) REVERT: A 28 LYS cc_start: 0.7016 (mmpt) cc_final: 0.6622 (mtmm) REVERT: A 44 LEU cc_start: 0.8062 (tp) cc_final: 0.7766 (tp) REVERT: A 279 ASN cc_start: 0.8891 (t0) cc_final: 0.8630 (t0) REVERT: A 295 ASP cc_start: 0.8286 (p0) cc_final: 0.7830 (p0) REVERT: A 309 GLU cc_start: 0.9325 (pt0) cc_final: 0.8681 (tp30) REVERT: A 388 LEU cc_start: 0.9375 (mm) cc_final: 0.9088 (mm) REVERT: B 6 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 61 MET cc_start: 0.9023 (ppp) cc_final: 0.8223 (ppp) REVERT: B 66 ASP cc_start: 0.8201 (p0) cc_final: 0.7846 (p0) REVERT: B 210 LEU cc_start: 0.8761 (tp) cc_final: 0.8536 (tp) REVERT: B 220 GLN cc_start: 0.7587 (mp10) cc_final: 0.7183 (mp10) REVERT: B 235 PHE cc_start: 0.7858 (t80) cc_final: 0.7452 (t80) REVERT: B 246 ASP cc_start: 0.8871 (m-30) cc_final: 0.8372 (m-30) REVERT: B 273 ILE cc_start: 0.9159 (mp) cc_final: 0.8736 (mp) REVERT: B 283 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7555 (tpt90) REVERT: B 297 TRP cc_start: 0.8346 (m100) cc_final: 0.7794 (m100) REVERT: B 313 ASN cc_start: 0.6907 (t0) cc_final: 0.6547 (m110) REVERT: G 24 ASN cc_start: 0.7231 (p0) cc_final: 0.6735 (t0) REVERT: N 31 ASN cc_start: 0.8647 (m-40) cc_final: 0.7430 (t0) REVERT: N 32 TYR cc_start: 0.8262 (m-80) cc_final: 0.7800 (m-10) REVERT: N 34 MET cc_start: 0.9062 (ttm) cc_final: 0.8609 (ttm) REVERT: N 38 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7556 (ptp90) REVERT: N 67 ARG cc_start: 0.8260 (ptp90) cc_final: 0.8055 (ptp90) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2180 time to fit residues: 115.5918 Evaluate side-chains 323 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 0.4980 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.119683 restraints weight = 28050.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.123434 restraints weight = 16496.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.126056 restraints weight = 10906.799| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9293 Z= 0.210 Angle : 0.720 9.122 12612 Z= 0.386 Chirality : 0.047 0.314 1416 Planarity : 0.005 0.047 1612 Dihedral : 5.085 22.802 1277 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % 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: -0.53 (0.24), residues: 1160 helix: 0.13 (0.25), residues: 441 sheet: -0.53 (0.34), residues: 213 loop : -0.55 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP N 36 HIS 0.009 0.001 HIS B 54 PHE 0.031 0.002 PHE R 184 TYR 0.024 0.002 TYR R 269 ARG 0.009 0.001 ARG A 385 *********************** 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 379 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.322 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: R 181 LEU cc_start: 0.9269 (mt) cc_final: 0.9060 (mt) REVERT: R 205 TYR cc_start: 0.8443 (t80) cc_final: 0.8207 (t80) REVERT: R 272 ILE cc_start: 0.8344 (tt) cc_final: 0.8111 (mt) REVERT: R 324 PHE cc_start: 0.7665 (t80) cc_final: 0.7443 (t80) REVERT: R 325 ILE cc_start: 0.8783 (mt) cc_final: 0.8575 (mt) REVERT: R 340 MET cc_start: 0.8160 (tpt) cc_final: 0.7735 (tpt) REVERT: R 351 LYS cc_start: 0.8754 (tptt) cc_final: 0.8538 (tptm) REVERT: R 397 MET cc_start: 0.7301 (mtp) cc_final: 0.6880 (mtp) REVERT: R 411 MET cc_start: 0.8345 (mmp) cc_final: 0.7977 (mmp) REVERT: P 27 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 11 ASP cc_start: 0.8316 (t70) cc_final: 0.8078 (t70) REVERT: A 28 LYS cc_start: 0.7089 (mmpt) cc_final: 0.6705 (mtmm) REVERT: A 32 LYS cc_start: 0.8829 (mttp) cc_final: 0.8458 (mptt) REVERT: A 274 LYS cc_start: 0.8648 (tttp) cc_final: 0.8319 (tttt) REVERT: A 279 ASN cc_start: 0.8868 (t0) cc_final: 0.8598 (t0) REVERT: A 295 ASP cc_start: 0.7893 (p0) cc_final: 0.7690 (p0) REVERT: A 309 GLU cc_start: 0.9367 (pt0) cc_final: 0.8700 (tp30) REVERT: A 388 LEU cc_start: 0.9343 (mm) cc_final: 0.9050 (mm) REVERT: B 6 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6862 (tm-30) REVERT: B 61 MET cc_start: 0.9034 (ppp) cc_final: 0.8219 (ppp) REVERT: B 66 ASP cc_start: 0.8256 (p0) cc_final: 0.7923 (p0) REVERT: B 120 ILE cc_start: 0.8709 (mt) cc_final: 0.8447 (mm) REVERT: B 152 LEU cc_start: 0.8149 (mt) cc_final: 0.7897 (mt) REVERT: B 220 GLN cc_start: 0.7665 (mp10) cc_final: 0.7275 (mp10) REVERT: B 235 PHE cc_start: 0.7947 (t80) cc_final: 0.7481 (t80) REVERT: B 246 ASP cc_start: 0.8782 (m-30) cc_final: 0.8258 (m-30) REVERT: B 273 ILE cc_start: 0.9174 (mp) cc_final: 0.8707 (mp) REVERT: B 283 ARG cc_start: 0.8467 (tpt170) cc_final: 0.7613 (tpt90) REVERT: B 297 TRP cc_start: 0.8432 (m100) cc_final: 0.7868 (m100) REVERT: G 24 ASN cc_start: 0.7291 (p0) cc_final: 0.6816 (t0) REVERT: N 31 ASN cc_start: 0.8643 (m-40) cc_final: 0.7378 (t0) REVERT: N 32 TYR cc_start: 0.8275 (m-80) cc_final: 0.7940 (m-10) REVERT: N 34 MET cc_start: 0.9071 (ttm) cc_final: 0.8795 (ttm) REVERT: N 38 ARG cc_start: 0.8080 (ptp90) cc_final: 0.7443 (ptp90) REVERT: N 46 GLU cc_start: 0.7757 (pm20) cc_final: 0.7515 (pm20) REVERT: N 67 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7787 (ptp90) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2197 time to fit residues: 112.7309 Evaluate side-chains 326 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 0.4980 chunk 6 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS G 18 GLN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.139135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120471 restraints weight = 28885.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.124240 restraints weight = 16898.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.126767 restraints weight = 11146.490| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9293 Z= 0.220 Angle : 0.741 9.145 12612 Z= 0.395 Chirality : 0.048 0.253 1416 Planarity : 0.005 0.046 1612 Dihedral : 5.104 22.162 1277 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % 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: -0.56 (0.24), residues: 1160 helix: 0.03 (0.25), residues: 445 sheet: -0.37 (0.34), residues: 206 loop : -0.59 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 36 HIS 0.009 0.002 HIS A 387 PHE 0.030 0.002 PHE R 184 TYR 0.022 0.002 TYR A 391 ARG 0.009 0.001 ARG A 385 ********************** 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 373 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 TYR cc_start: 0.8361 (t80) cc_final: 0.8109 (t80) REVERT: R 272 ILE cc_start: 0.8367 (tt) cc_final: 0.8109 (mt) REVERT: R 292 GLU cc_start: 0.7827 (pm20) cc_final: 0.7273 (pm20) REVERT: R 302 ASN cc_start: 0.7620 (t0) cc_final: 0.7406 (t0) REVERT: R 325 ILE cc_start: 0.8782 (mt) cc_final: 0.8575 (mt) REVERT: R 351 LYS cc_start: 0.8774 (tptt) cc_final: 0.8560 (tptm) REVERT: R 397 MET cc_start: 0.7278 (mtp) cc_final: 0.6866 (ptm) REVERT: R 402 TYR cc_start: 0.7219 (p90) cc_final: 0.6900 (p90) REVERT: R 411 MET cc_start: 0.8306 (mmp) cc_final: 0.7955 (mmp) REVERT: P 27 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 11 ASP cc_start: 0.8134 (t70) cc_final: 0.7922 (t70) REVERT: A 28 LYS cc_start: 0.7004 (mmpt) cc_final: 0.6755 (mtmm) REVERT: A 32 LYS cc_start: 0.8829 (mttp) cc_final: 0.8399 (mptt) REVERT: A 44 LEU cc_start: 0.8095 (tp) cc_final: 0.7475 (tp) REVERT: A 279 ASN cc_start: 0.8814 (t0) cc_final: 0.8517 (t0) REVERT: A 285 ILE cc_start: 0.9038 (mm) cc_final: 0.8696 (tp) REVERT: A 309 GLU cc_start: 0.9348 (pt0) cc_final: 0.8696 (tp30) REVERT: A 314 GLU cc_start: 0.8015 (pm20) cc_final: 0.7782 (pm20) REVERT: A 362 HIS cc_start: 0.7274 (m-70) cc_final: 0.7062 (m-70) REVERT: A 388 LEU cc_start: 0.9346 (mm) cc_final: 0.9062 (mm) REVERT: B 6 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6756 (tm-30) REVERT: B 61 MET cc_start: 0.9007 (ppp) cc_final: 0.8182 (ppp) REVERT: B 66 ASP cc_start: 0.8217 (p0) cc_final: 0.7852 (p0) REVERT: B 120 ILE cc_start: 0.8721 (mt) cc_final: 0.8464 (mm) REVERT: B 220 GLN cc_start: 0.7691 (mp10) cc_final: 0.7348 (mp10) REVERT: B 235 PHE cc_start: 0.7910 (t80) cc_final: 0.7445 (t80) REVERT: B 246 ASP cc_start: 0.8786 (m-30) cc_final: 0.8268 (m-30) REVERT: B 273 ILE cc_start: 0.9181 (mp) cc_final: 0.8755 (mp) REVERT: B 283 ARG cc_start: 0.8362 (tpt170) cc_final: 0.7529 (tpt90) REVERT: B 297 TRP cc_start: 0.8340 (m100) cc_final: 0.7810 (m100) REVERT: B 313 ASN cc_start: 0.7270 (m110) cc_final: 0.6709 (m-40) REVERT: G 24 ASN cc_start: 0.7203 (p0) cc_final: 0.6761 (t0) REVERT: N 31 ASN cc_start: 0.8646 (m-40) cc_final: 0.7332 (t0) REVERT: N 32 TYR cc_start: 0.8215 (m-80) cc_final: 0.7819 (m-10) REVERT: N 34 MET cc_start: 0.9022 (ttm) cc_final: 0.8639 (ttm) REVERT: N 38 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7537 (ptp90) REVERT: N 46 GLU cc_start: 0.7646 (pm20) cc_final: 0.7413 (pm20) REVERT: N 67 ARG cc_start: 0.8217 (ptp90) cc_final: 0.7831 (ptp90) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2238 time to fit residues: 113.3349 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 : 0.867 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 6.9990 chunk 113 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN A 239 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4205 r_free = 0.4205 target = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.119943 restraints weight = 28179.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.123677 restraints weight = 16527.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126261 restraints weight = 10867.561| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9293 Z= 0.225 Angle : 0.756 8.733 12612 Z= 0.405 Chirality : 0.048 0.250 1416 Planarity : 0.005 0.046 1612 Dihedral : 5.272 54.014 1277 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.48 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.52 (0.24), residues: 1160 helix: 0.12 (0.25), residues: 441 sheet: -0.41 (0.34), residues: 213 loop : -0.58 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.009 0.002 HIS R 48 PHE 0.029 0.002 PHE R 184 TYR 0.024 0.002 TYR A 391 ARG 0.009 0.001 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.21 seconds wall clock time: 66 minutes 2.26 seconds (3962.26 seconds total)