Starting phenix.real_space_refine on Thu Jul 2 22:29:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.cif Found real_map, /net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.map" model { file = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7evy_31341/07_2026/7evy_31341.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 5758 2.51 5 N 1521 2.21 5 O 1678 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9024 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'J8C': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.24 Number of scatterers: 9024 At special positions: 0 Unit cell: (91.485, 122.265, 134.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 F 3 9.00 O 1678 8.00 N 1521 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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 Links applied NAG-ASN " NAG D 402 " - " ASN D 30 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 353.6 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 35.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.655A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.511A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.727A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.679A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.039A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.584A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.520A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 4.081A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.500A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 50 through 73 removed outlier: 3.683A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 105 removed outlier: 3.965A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 85 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 148 removed outlier: 3.778A pdb=" N ALA D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 128 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 181 removed outlier: 3.846A pdb=" N SER D 171 " --> pdb=" O CYS D 167 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 234 removed outlier: 4.015A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 282 removed outlier: 3.972A pdb=" N VAL D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 293 through 314 removed outlier: 4.131A pdb=" N LEU D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 3.523A pdb=" N THR D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.528A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.946A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.506A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.923A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.686A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.520A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.615A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.082A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.747A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.731A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.506A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.063A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1507 1.32 - 1.44: 2479 1.44 - 1.57: 5127 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 9205 Sorted by residual: bond pdb=" C VAL D 258 " pdb=" O VAL D 258 " ideal model delta sigma weight residual 1.242 1.199 0.043 1.13e-02 7.83e+03 1.44e+01 bond pdb=" CA GLU A 289 " pdb=" CB GLU A 289 " ideal model delta sigma weight residual 1.528 1.571 -0.044 1.39e-02 5.18e+03 9.88e+00 bond pdb=" C ILE E 189 " pdb=" O ILE E 189 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.07e-02 8.73e+03 9.66e+00 bond pdb=" C LEU D 255 " pdb=" O LEU D 255 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" C LEU D 252 " pdb=" O LEU D 252 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.26e+00 ... (remaining 9200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12258 1.86 - 3.73: 156 3.73 - 5.59: 26 5.59 - 7.46: 10 7.46 - 9.32: 8 Bond angle restraints: 12458 Sorted by residual: angle pdb=" N ARG D 233 " pdb=" CA ARG D 233 " pdb=" C ARG D 233 " ideal model delta sigma weight residual 111.36 117.76 -6.40 1.09e+00 8.42e-01 3.45e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 113.12 118.89 -5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 110.97 115.78 -4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" C ARG D 238 " ideal model delta sigma weight residual 109.07 116.14 -7.07 1.61e+00 3.86e-01 1.93e+01 angle pdb=" N ILE E 189 " pdb=" CA ILE E 189 " pdb=" C ILE E 189 " ideal model delta sigma weight residual 107.18 114.39 -7.21 1.73e+00 3.34e-01 1.74e+01 ... (remaining 12453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.71: 5237 24.71 - 49.42: 225 49.42 - 74.13: 18 74.13 - 98.83: 2 98.83 - 123.54: 4 Dihedral angle restraints: 5486 sinusoidal: 2166 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -138.12 52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" C30 J8C D 401 " pdb=" C32 J8C D 401 " pdb=" N31 J8C D 401 " pdb=" C33 J8C D 401 " ideal model delta sinusoidal sigma weight residual 218.96 95.42 123.54 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C20 J8C D 401 " pdb=" C21 J8C D 401 " pdb=" C22 J8C D 401 " pdb=" C23 J8C D 401 " ideal model delta sinusoidal sigma weight residual 55.47 -67.84 123.31 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1358 0.099 - 0.199: 64 0.199 - 0.298: 6 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 1429 Sorted by residual: chirality pdb=" CA MET E 192 " pdb=" N MET E 192 " pdb=" C MET E 192 " pdb=" CB MET E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C19 J8C D 401 " pdb=" C16 J8C D 401 " pdb=" C20 J8C D 401 " pdb=" C24 J8C D 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.85 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL D 258 " pdb=" N VAL D 258 " pdb=" C VAL D 258 " pdb=" CB VAL D 258 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1426 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.088 2.00e-02 2.50e+03 7.19e-02 6.46e+01 pdb=" C7 NAG D 402 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.067 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 231 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ARG D 231 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG D 231 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 232 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO E 236 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.031 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 93 2.63 - 3.20: 7701 3.20 - 3.76: 13149 3.76 - 4.33: 17834 4.33 - 4.90: 30952 Nonbonded interactions: 69729 Sorted by model distance: nonbonded pdb=" O3 NAG D 402 " pdb=" O7 NAG D 402 " model vdw 2.061 3.040 nonbonded pdb=" CD2 LEU D 276 " pdb=" F26 J8C D 401 " model vdw 2.164 3.410 nonbonded pdb=" OG SER A 293 " pdb=" OE2 GLU A 298 " model vdw 2.180 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.218 3.040 nonbonded pdb=" O LEU E 174 " pdb=" O ARG E 191 " model vdw 2.226 3.040 ... (remaining 69724 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.003 0.051 9209 Z= 0.185 Angle : 0.625 9.322 12467 Z= 0.353 Chirality : 0.047 0.497 1429 Planarity : 0.004 0.072 1555 Dihedral : 12.906 123.543 3335 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.91 % Allowed : 3.65 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1126 helix: 0.16 (0.24), residues: 381 sheet: -0.82 (0.30), residues: 274 loop : -2.37 (0.23), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 191 TYR 0.012 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.18 ( 9205) covalent geometry : angle 0.62345 / 0.35 (12458) SS BOND : bond 0.00489 / 0.24 ( 3) SS BOND : angle 0.44542 / 0.22 ( 6) hydrogen bonds : bond 0.12830 / 8.73 ( 399) hydrogen bonds : angle 4.49503 / 3.05 ( 1149) link_NAG-ASN : bond 0.01121 / 0.59 ( 1) link_NAG-ASN : angle 2.85033 / 1.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.359 Fit side-chains REVERT: A 25 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 240 MET cc_start: 0.8188 (tmm) cc_final: 0.7545 (pp-130) REVERT: A 242 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7092 (mtm-85) REVERT: A 276 GLU cc_start: 0.7420 (tp30) cc_final: 0.7120 (tp30) REVERT: A 289 GLU cc_start: 0.7787 (pm20) cc_final: 0.7407 (pp20) REVERT: A 302 TYR cc_start: 0.8241 (t80) cc_final: 0.8040 (t80) REVERT: B 226 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 268 ASN cc_start: 0.8253 (t0) cc_final: 0.8049 (t0) REVERT: B 303 ASP cc_start: 0.6919 (m-30) cc_final: 0.6404 (p0) REVERT: D 24 ILE cc_start: 0.7287 (mm) cc_final: 0.7072 (mt) REVERT: D 295 TYR cc_start: 0.6965 (m-80) cc_final: 0.6748 (m-80) REVERT: E 11 LEU cc_start: 0.8701 (tp) cc_final: 0.8418 (tm) REVERT: E 76 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8150 (pttt) REVERT: E 89 GLU cc_start: 0.8530 (pt0) cc_final: 0.8147 (tm-30) REVERT: E 204 SER cc_start: 0.8513 (t) cc_final: 0.7956 (p) REVERT: E 220 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6470 (mm-30) REVERT: E 234 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6562 (mt-10) outliers start: 9 outliers final: 7 residues processed: 209 average time/residue: 0.5899 time to fit residues: 131.2658 Evaluate side-chains 140 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 191 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 110 ASN B 220 GLN B 237 ASN D 303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117432 restraints weight = 11065.136| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.60 r_work: 0.3279 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9209 Z= 0.115 Angle : 0.545 7.396 12467 Z= 0.278 Chirality : 0.041 0.155 1429 Planarity : 0.004 0.056 1555 Dihedral : 7.768 108.803 1298 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.05 % Allowed : 13.10 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1126 helix: 1.39 (0.26), residues: 390 sheet: -0.53 (0.30), residues: 275 loop : -2.08 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.016 0.001 TYR D 31 PHE 0.018 0.001 PHE D 237 TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9205) covalent geometry : angle 0.54437 / 0.28 (12458) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 0.69144 / 0.36 ( 6) hydrogen bonds : bond 0.03770 / 2.60 ( 399) hydrogen bonds : angle 3.57563 / 2.43 ( 1149) link_NAG-ASN : bond 0.00312 / 0.16 ( 1) link_NAG-ASN : angle 1.30561 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.338 Fit side-chains REVERT: A 25 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7047 (tm-30) REVERT: A 33 GLU cc_start: 0.8264 (pt0) cc_final: 0.7995 (pt0) REVERT: A 276 GLU cc_start: 0.7543 (tp30) cc_final: 0.7095 (tp30) REVERT: A 289 GLU cc_start: 0.7894 (pm20) cc_final: 0.7427 (pp20) REVERT: B 96 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7576 (mtt90) REVERT: B 118 ASP cc_start: 0.7683 (t0) cc_final: 0.7471 (t0) REVERT: B 197 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7034 (ttt-90) REVERT: B 214 ARG cc_start: 0.8506 (mmt90) cc_final: 0.8108 (mmt90) REVERT: B 226 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 259 GLN cc_start: 0.7543 (tt0) cc_final: 0.7298 (tt0) REVERT: B 268 ASN cc_start: 0.8163 (t0) cc_final: 0.7889 (t0) REVERT: B 303 ASP cc_start: 0.7044 (m-30) cc_final: 0.6205 (p0) REVERT: D 183 ASN cc_start: 0.7626 (t0) cc_final: 0.7178 (t0) REVERT: E 11 LEU cc_start: 0.8187 (tp) cc_final: 0.7880 (tm) REVERT: E 18 ARG cc_start: 0.7938 (pmm-80) cc_final: 0.7707 (pmm-80) REVERT: E 89 GLU cc_start: 0.8747 (pt0) cc_final: 0.8017 (tm-30) REVERT: E 93 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6297 (tpt) REVERT: E 204 SER cc_start: 0.7616 (t) cc_final: 0.7272 (p) REVERT: E 233 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7700 (mt) REVERT: E 234 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6615 (mt-10) outliers start: 30 outliers final: 16 residues processed: 151 average time/residue: 0.6716 time to fit residues: 107.2554 Evaluate side-chains 142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117195 restraints weight = 10920.173| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.55 r_work: 0.3277 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9209 Z= 0.103 Angle : 0.510 7.629 12467 Z= 0.263 Chirality : 0.040 0.137 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.865 107.285 1291 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.94 % Allowed : 15.43 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1126 helix: 1.77 (0.26), residues: 396 sheet: -0.31 (0.31), residues: 276 loop : -1.89 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.013 0.001 TYR D 295 PHE 0.011 0.001 PHE D 237 TRP 0.008 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9205) covalent geometry : angle 0.50958 / 0.26 (12458) SS BOND : bond 0.00366 / 0.18 ( 3) SS BOND : angle 0.74373 / 0.37 ( 6) hydrogen bonds : bond 0.03358 / 2.32 ( 399) hydrogen bonds : angle 3.44306 / 2.34 ( 1149) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 0.96492 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.362 Fit side-chains REVERT: A 25 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 33 GLU cc_start: 0.8183 (pt0) cc_final: 0.7924 (pt0) REVERT: A 240 MET cc_start: 0.7433 (ppp) cc_final: 0.6484 (pp-130) REVERT: A 276 GLU cc_start: 0.7636 (tp30) cc_final: 0.7249 (tp30) REVERT: A 318 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6797 (tt0) REVERT: B 96 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7685 (mtt90) REVERT: B 130 GLU cc_start: 0.6718 (mp0) cc_final: 0.6333 (mp0) REVERT: B 197 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7088 (ttt-90) REVERT: B 214 ARG cc_start: 0.8555 (mmt90) cc_final: 0.8166 (mmt90) REVERT: B 226 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 259 GLN cc_start: 0.7582 (tt0) cc_final: 0.7365 (tt0) REVERT: B 268 ASN cc_start: 0.8191 (t0) cc_final: 0.7880 (t0) REVERT: B 280 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7376 (tmtt) REVERT: D 27 ARG cc_start: 0.8001 (ppp80) cc_final: 0.7638 (ptm-80) REVERT: D 68 LEU cc_start: 0.7022 (pp) cc_final: 0.6706 (mp) REVERT: D 183 ASN cc_start: 0.7651 (t0) cc_final: 0.7226 (t0) REVERT: E 11 LEU cc_start: 0.8166 (tp) cc_final: 0.7859 (tm) REVERT: E 89 GLU cc_start: 0.8719 (pt0) cc_final: 0.7993 (tm-30) REVERT: E 93 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6323 (tpt) REVERT: E 158 SER cc_start: 0.8498 (t) cc_final: 0.8149 (m) REVERT: E 204 SER cc_start: 0.7726 (t) cc_final: 0.7368 (p) REVERT: E 233 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7808 (mt) REVERT: E 234 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6667 (mt-10) outliers start: 29 outliers final: 12 residues processed: 142 average time/residue: 0.5829 time to fit residues: 87.9206 Evaluate side-chains 138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114898 restraints weight = 11050.880| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.60 r_work: 0.3235 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9209 Z= 0.115 Angle : 0.515 6.474 12467 Z= 0.266 Chirality : 0.040 0.155 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.501 106.334 1281 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.25 % Allowed : 16.85 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1126 helix: 1.95 (0.26), residues: 396 sheet: -0.28 (0.31), residues: 276 loop : -1.80 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.012 0.001 TYR D 31 PHE 0.012 0.001 PHE A 189 TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9205) covalent geometry : angle 0.51434 / 0.27 (12458) SS BOND : bond 0.00317 / 0.16 ( 3) SS BOND : angle 0.84272 / 0.40 ( 6) hydrogen bonds : bond 0.03485 / 2.39 ( 399) hydrogen bonds : angle 3.45163 / 2.33 ( 1149) link_NAG-ASN : bond 0.00109 / 0.06 ( 1) link_NAG-ASN : angle 0.87222 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.227 Fit side-chains REVERT: A 25 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 33 GLU cc_start: 0.8335 (pt0) cc_final: 0.8059 (pt0) REVERT: A 205 ARG cc_start: 0.8334 (mpt180) cc_final: 0.8069 (mmp80) REVERT: A 240 MET cc_start: 0.7164 (ppp) cc_final: 0.6094 (pp-130) REVERT: A 242 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6365 (mtp180) REVERT: A 276 GLU cc_start: 0.7750 (tp30) cc_final: 0.7372 (tp30) REVERT: A 318 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7007 (tt0) REVERT: B 96 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7850 (mtt90) REVERT: B 118 ASP cc_start: 0.7788 (t0) cc_final: 0.7585 (t0) REVERT: B 130 GLU cc_start: 0.6951 (mp0) cc_final: 0.6481 (mp0) REVERT: B 197 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7280 (ttt-90) REVERT: B 226 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 268 ASN cc_start: 0.8278 (t0) cc_final: 0.7961 (t0) REVERT: C 47 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: D 27 ARG cc_start: 0.8065 (ppp80) cc_final: 0.7719 (ptm-80) REVERT: D 68 LEU cc_start: 0.7119 (pp) cc_final: 0.6815 (mt) REVERT: D 80 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7117 (tpp) REVERT: D 150 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7473 (ptmm) REVERT: D 183 ASN cc_start: 0.7764 (t0) cc_final: 0.7345 (t0) REVERT: D 238 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5829 (ppt-90) REVERT: E 11 LEU cc_start: 0.8288 (tp) cc_final: 0.7966 (tm) REVERT: E 89 GLU cc_start: 0.8780 (pt0) cc_final: 0.8138 (tm-30) REVERT: E 93 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6742 (tpt) REVERT: E 158 SER cc_start: 0.8555 (t) cc_final: 0.8223 (m) REVERT: E 204 SER cc_start: 0.7872 (t) cc_final: 0.7494 (p) REVERT: E 233 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7871 (mt) REVERT: E 234 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6966 (mt-10) outliers start: 32 outliers final: 14 residues processed: 142 average time/residue: 0.6200 time to fit residues: 93.3660 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.162596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112224 restraints weight = 10863.876| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.45 r_work: 0.3231 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9209 Z= 0.126 Angle : 0.550 9.730 12467 Z= 0.280 Chirality : 0.041 0.165 1429 Planarity : 0.004 0.057 1555 Dihedral : 6.591 107.564 1281 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.25 % Allowed : 17.36 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.25), residues: 1126 helix: 2.07 (0.26), residues: 390 sheet: -0.36 (0.30), residues: 283 loop : -1.65 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 32 TYR 0.010 0.001 TYR D 31 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9205) covalent geometry : angle 0.54936 / 0.28 (12458) SS BOND : bond 0.00360 / 0.18 ( 3) SS BOND : angle 0.76851 / 0.37 ( 6) hydrogen bonds : bond 0.03573 / 2.46 ( 399) hydrogen bonds : angle 3.53431 / 2.40 ( 1149) link_NAG-ASN : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : angle 1.00456 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.344 Fit side-chains REVERT: A 25 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7112 (tm-30) REVERT: A 33 GLU cc_start: 0.8299 (pt0) cc_final: 0.7972 (pt0) REVERT: A 205 ARG cc_start: 0.8320 (mpt180) cc_final: 0.8049 (mmp80) REVERT: A 242 ARG cc_start: 0.6763 (mtp180) cc_final: 0.6454 (mtp85) REVERT: A 276 GLU cc_start: 0.7745 (tp30) cc_final: 0.7389 (tp30) REVERT: B 96 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7825 (mtt90) REVERT: B 118 ASP cc_start: 0.7640 (t0) cc_final: 0.7411 (t0) REVERT: B 130 GLU cc_start: 0.6908 (mp0) cc_final: 0.6435 (mp0) REVERT: B 197 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7293 (ttt-90) REVERT: B 214 ARG cc_start: 0.8511 (mmt90) cc_final: 0.8266 (mmt90) REVERT: B 226 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 259 GLN cc_start: 0.7554 (tt0) cc_final: 0.7310 (tt0) REVERT: B 268 ASN cc_start: 0.8182 (t0) cc_final: 0.7855 (t0) REVERT: D 27 ARG cc_start: 0.8027 (ppp80) cc_final: 0.7666 (ptm-80) REVERT: D 68 LEU cc_start: 0.7083 (pp) cc_final: 0.6813 (mt) REVERT: D 80 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6940 (tpp) REVERT: D 112 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7338 (tm) REVERT: D 150 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7559 (ptmm) REVERT: D 183 ASN cc_start: 0.7707 (t0) cc_final: 0.7299 (t0) REVERT: D 238 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5742 (ppt-90) REVERT: E 11 LEU cc_start: 0.8136 (tp) cc_final: 0.7810 (tm) REVERT: E 89 GLU cc_start: 0.8795 (pt0) cc_final: 0.8440 (pp20) REVERT: E 93 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6603 (tpt) REVERT: E 158 SER cc_start: 0.8426 (t) cc_final: 0.8129 (m) REVERT: E 204 SER cc_start: 0.7641 (t) cc_final: 0.7249 (p) REVERT: E 233 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7784 (mt) REVERT: E 234 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6968 (mt-10) outliers start: 32 outliers final: 15 residues processed: 139 average time/residue: 0.6082 time to fit residues: 89.6320 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110885 restraints weight = 11004.204| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.58 r_work: 0.3190 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9209 Z= 0.153 Angle : 0.578 8.869 12467 Z= 0.295 Chirality : 0.042 0.239 1429 Planarity : 0.004 0.058 1555 Dihedral : 6.709 109.453 1281 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.76 % Allowed : 17.26 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1126 helix: 2.03 (0.26), residues: 390 sheet: -0.49 (0.30), residues: 291 loop : -1.63 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.012 0.001 TYR D 31 PHE 0.014 0.001 PHE B 199 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 9205) covalent geometry : angle 0.57769 / 0.29 (12458) SS BOND : bond 0.00381 / 0.19 ( 3) SS BOND : angle 0.83108 / 0.41 ( 6) hydrogen bonds : bond 0.04050 / 2.78 ( 399) hydrogen bonds : angle 3.69796 / 2.51 ( 1149) link_NAG-ASN : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : angle 1.05922 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.346 Fit side-chains REVERT: A 25 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 33 GLU cc_start: 0.8336 (pt0) cc_final: 0.7989 (pt0) REVERT: A 205 ARG cc_start: 0.8284 (mpt180) cc_final: 0.8011 (mmp80) REVERT: A 209 LYS cc_start: 0.8557 (tttt) cc_final: 0.8328 (tttm) REVERT: A 242 ARG cc_start: 0.6848 (mtp180) cc_final: 0.6404 (mtp180) REVERT: A 245 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6736 (mp0) REVERT: A 276 GLU cc_start: 0.7795 (tp30) cc_final: 0.7591 (tp30) REVERT: B 42 ARG cc_start: 0.7551 (tpt170) cc_final: 0.7325 (mmp-170) REVERT: B 96 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7728 (mtt90) REVERT: B 118 ASP cc_start: 0.7649 (t0) cc_final: 0.7397 (t0) REVERT: B 130 GLU cc_start: 0.7070 (mp0) cc_final: 0.6613 (mp0) REVERT: B 197 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7369 (mtt-85) REVERT: B 214 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8193 (mmt90) REVERT: B 226 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 268 ASN cc_start: 0.8172 (t0) cc_final: 0.7850 (t0) REVERT: D 27 ARG cc_start: 0.7994 (ppp80) cc_final: 0.7620 (ptm-80) REVERT: D 68 LEU cc_start: 0.7164 (pp) cc_final: 0.6906 (mt) REVERT: D 80 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6974 (tpp) REVERT: D 150 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7540 (ptmm) REVERT: D 183 ASN cc_start: 0.7712 (t0) cc_final: 0.7342 (t0) REVERT: D 238 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5944 (ppt-90) REVERT: E 11 LEU cc_start: 0.8121 (tp) cc_final: 0.7793 (tm) REVERT: E 89 GLU cc_start: 0.8797 (pt0) cc_final: 0.8158 (tm-30) REVERT: E 93 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6581 (tpt) REVERT: E 158 SER cc_start: 0.8453 (t) cc_final: 0.8168 (m) REVERT: E 192 MET cc_start: 0.7453 (tpp) cc_final: 0.7190 (tpp) REVERT: E 204 SER cc_start: 0.7626 (t) cc_final: 0.7213 (p) REVERT: E 233 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7869 (mt) REVERT: E 234 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7077 (mt-10) outliers start: 37 outliers final: 14 residues processed: 146 average time/residue: 0.6415 time to fit residues: 99.1479 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.160483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109184 restraints weight = 11031.357| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.54 r_work: 0.3173 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9209 Z= 0.170 Angle : 0.599 8.932 12467 Z= 0.305 Chirality : 0.043 0.259 1429 Planarity : 0.004 0.059 1555 Dihedral : 6.800 110.596 1281 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.96 % Allowed : 18.78 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1126 helix: 2.00 (0.26), residues: 387 sheet: -0.64 (0.30), residues: 303 loop : -1.61 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 78 TYR 0.011 0.001 TYR D 31 PHE 0.016 0.001 PHE B 199 TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 9205) covalent geometry : angle 0.59834 / 0.31 (12458) SS BOND : bond 0.00427 / 0.22 ( 3) SS BOND : angle 0.91995 / 0.47 ( 6) hydrogen bonds : bond 0.04254 / 2.92 ( 399) hydrogen bonds : angle 3.78658 / 2.57 ( 1149) link_NAG-ASN : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : angle 1.05420 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.372 Fit side-chains REVERT: A 25 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 33 GLU cc_start: 0.8380 (pt0) cc_final: 0.8019 (pt0) REVERT: A 242 ARG cc_start: 0.6822 (mtp180) cc_final: 0.6412 (mtp85) REVERT: A 245 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6970 (mp0) REVERT: A 276 GLU cc_start: 0.7957 (tp30) cc_final: 0.7677 (tp30) REVERT: A 289 GLU cc_start: 0.7947 (pm20) cc_final: 0.7286 (pp20) REVERT: B 96 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7896 (mtt90) REVERT: B 130 GLU cc_start: 0.7147 (mp0) cc_final: 0.6682 (mp0) REVERT: B 197 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7238 (tpt-90) REVERT: B 226 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 268 ASN cc_start: 0.8203 (t0) cc_final: 0.7871 (t0) REVERT: D 27 ARG cc_start: 0.8050 (ppp80) cc_final: 0.7670 (ptm-80) REVERT: D 68 LEU cc_start: 0.7204 (pp) cc_final: 0.7002 (mt) REVERT: D 80 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7150 (tpp) REVERT: D 150 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7549 (ptmm) REVERT: D 183 ASN cc_start: 0.7883 (t0) cc_final: 0.7519 (t0) REVERT: D 238 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6068 (ppt-90) REVERT: E 11 LEU cc_start: 0.8161 (tp) cc_final: 0.7842 (tm) REVERT: E 89 GLU cc_start: 0.8806 (pt0) cc_final: 0.8153 (tm-30) REVERT: E 93 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6595 (tpt) REVERT: E 140 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.7984 (mtm) REVERT: E 158 SER cc_start: 0.8483 (t) cc_final: 0.8210 (m) REVERT: E 192 MET cc_start: 0.7437 (tpp) cc_final: 0.7157 (tpp) REVERT: E 204 SER cc_start: 0.7743 (t) cc_final: 0.7315 (p) REVERT: E 233 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7960 (mt) REVERT: E 234 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7191 (mt-10) outliers start: 39 outliers final: 17 residues processed: 151 average time/residue: 0.5566 time to fit residues: 89.1480 Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111327 restraints weight = 10963.244| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.58 r_work: 0.3199 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9209 Z= 0.130 Angle : 0.569 9.095 12467 Z= 0.291 Chirality : 0.042 0.285 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.647 110.076 1281 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 20.00 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1126 helix: 1.93 (0.26), residues: 397 sheet: -0.58 (0.30), residues: 301 loop : -1.54 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 78 TYR 0.012 0.001 TYR D 31 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9205) covalent geometry : angle 0.56911 / 0.29 (12458) SS BOND : bond 0.00351 / 0.18 ( 3) SS BOND : angle 0.77927 / 0.39 ( 6) hydrogen bonds : bond 0.03750 / 2.59 ( 399) hydrogen bonds : angle 3.69269 / 2.51 ( 1149) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 0.87133 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.354 Fit side-chains REVERT: A 25 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 33 GLU cc_start: 0.8349 (pt0) cc_final: 0.7998 (pt0) REVERT: A 232 LEU cc_start: 0.8708 (mt) cc_final: 0.8448 (mp) REVERT: A 242 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6301 (mtp85) REVERT: A 245 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6932 (mp0) REVERT: A 276 GLU cc_start: 0.7988 (tp30) cc_final: 0.7685 (tp30) REVERT: B 96 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7780 (mtt90) REVERT: B 118 ASP cc_start: 0.7934 (t0) cc_final: 0.7650 (t0) REVERT: B 130 GLU cc_start: 0.7003 (mp0) cc_final: 0.6517 (mp0) REVERT: B 197 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7346 (mtp180) REVERT: B 226 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8272 (mm-30) REVERT: B 268 ASN cc_start: 0.8220 (t0) cc_final: 0.7885 (t0) REVERT: D 27 ARG cc_start: 0.8021 (ppp80) cc_final: 0.7631 (ptm-80) REVERT: D 80 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7101 (tpp) REVERT: D 112 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7644 (tm) REVERT: D 150 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7574 (ptmm) REVERT: D 183 ASN cc_start: 0.7797 (t0) cc_final: 0.7331 (t0) REVERT: E 11 LEU cc_start: 0.8156 (tp) cc_final: 0.7802 (tm) REVERT: E 87 ARG cc_start: 0.6989 (mtt-85) cc_final: 0.6667 (mpt90) REVERT: E 89 GLU cc_start: 0.8795 (pt0) cc_final: 0.8143 (tm-30) REVERT: E 93 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6580 (tpt) REVERT: E 140 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8079 (mtm) REVERT: E 158 SER cc_start: 0.8512 (t) cc_final: 0.8258 (m) REVERT: E 204 SER cc_start: 0.7727 (t) cc_final: 0.7296 (p) REVERT: E 233 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mt) REVERT: E 234 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7133 (mt-10) outliers start: 29 outliers final: 16 residues processed: 146 average time/residue: 0.6561 time to fit residues: 101.5952 Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112157 restraints weight = 11005.270| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.55 r_work: 0.3209 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9209 Z= 0.125 Angle : 0.575 9.810 12467 Z= 0.292 Chirality : 0.041 0.302 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.548 109.600 1281 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.64 % Allowed : 20.81 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1126 helix: 2.01 (0.26), residues: 397 sheet: -0.61 (0.30), residues: 298 loop : -1.44 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 78 TYR 0.016 0.001 TYR D 31 PHE 0.012 0.001 PHE B 199 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 9205) covalent geometry : angle 0.57435 / 0.29 (12458) SS BOND : bond 0.00333 / 0.17 ( 3) SS BOND : angle 0.74500 / 0.37 ( 6) hydrogen bonds : bond 0.03593 / 2.48 ( 399) hydrogen bonds : angle 3.67350 / 2.49 ( 1149) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 0.86408 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.418 Fit side-chains REVERT: A 25 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 33 GLU cc_start: 0.8262 (pt0) cc_final: 0.7891 (pt0) REVERT: A 232 LEU cc_start: 0.8651 (mt) cc_final: 0.8384 (mp) REVERT: A 242 ARG cc_start: 0.6686 (mtp180) cc_final: 0.6277 (mtp85) REVERT: A 245 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7021 (mp0) REVERT: A 276 GLU cc_start: 0.7954 (tp30) cc_final: 0.7657 (tp30) REVERT: B 96 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7761 (mtt90) REVERT: B 118 ASP cc_start: 0.7816 (t0) cc_final: 0.7507 (t0) REVERT: B 130 GLU cc_start: 0.6892 (mp0) cc_final: 0.6400 (mp0) REVERT: B 197 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7283 (mtp180) REVERT: B 226 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8229 (mm-30) REVERT: B 268 ASN cc_start: 0.8176 (t0) cc_final: 0.7841 (t0) REVERT: D 27 ARG cc_start: 0.8080 (ppp80) cc_final: 0.7682 (ptm-80) REVERT: D 80 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6968 (tpp) REVERT: D 103 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 150 LYS cc_start: 0.8181 (ptpt) cc_final: 0.7531 (ptmm) REVERT: D 183 ASN cc_start: 0.7784 (t0) cc_final: 0.7287 (t0) REVERT: D 197 LEU cc_start: 0.7721 (mt) cc_final: 0.7519 (mt) REVERT: E 11 LEU cc_start: 0.8103 (tp) cc_final: 0.7766 (tm) REVERT: E 87 ARG cc_start: 0.6954 (mtt-85) cc_final: 0.6670 (mpt90) REVERT: E 89 GLU cc_start: 0.8796 (pt0) cc_final: 0.8141 (tm-30) REVERT: E 93 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6548 (tpt) REVERT: E 140 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: E 158 SER cc_start: 0.8439 (t) cc_final: 0.8196 (m) REVERT: E 204 SER cc_start: 0.7625 (t) cc_final: 0.7202 (p) REVERT: E 233 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7853 (mt) REVERT: E 234 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7042 (mt-10) outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 0.6133 time to fit residues: 88.9524 Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 62 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113898 restraints weight = 10987.085| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.56 r_work: 0.3233 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9209 Z= 0.114 Angle : 0.557 9.585 12467 Z= 0.284 Chirality : 0.041 0.303 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.290 108.584 1281 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 21.12 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1126 helix: 2.13 (0.26), residues: 394 sheet: -0.54 (0.30), residues: 298 loop : -1.39 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 78 TYR 0.017 0.001 TYR D 31 PHE 0.011 0.001 PHE B 199 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 9205) covalent geometry : angle 0.55715 / 0.28 (12458) SS BOND : bond 0.00300 / 0.15 ( 3) SS BOND : angle 0.64967 / 0.33 ( 6) hydrogen bonds : bond 0.03323 / 2.30 ( 399) hydrogen bonds : angle 3.60981 / 2.45 ( 1149) link_NAG-ASN : bond 0.00091 / 0.05 ( 1) link_NAG-ASN : angle 0.83686 / 0.45 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 33 GLU cc_start: 0.8220 (pt0) cc_final: 0.7856 (pt0) REVERT: A 242 ARG cc_start: 0.6598 (mtp180) cc_final: 0.6150 (mtp85) REVERT: A 245 GLU cc_start: 0.7207 (mm-30) cc_final: 0.7004 (mp0) REVERT: A 276 GLU cc_start: 0.7905 (tp30) cc_final: 0.7610 (tp30) REVERT: B 96 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7760 (mtt90) REVERT: B 118 ASP cc_start: 0.7750 (t0) cc_final: 0.7444 (t0) REVERT: B 130 GLU cc_start: 0.6775 (mp0) cc_final: 0.6264 (mp0) REVERT: B 197 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7311 (mtp180) REVERT: B 226 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 268 ASN cc_start: 0.8181 (t0) cc_final: 0.7830 (t0) REVERT: D 27 ARG cc_start: 0.8105 (ppp80) cc_final: 0.7718 (ptm-80) REVERT: D 80 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6927 (tpp) REVERT: D 183 ASN cc_start: 0.7814 (t0) cc_final: 0.7051 (t0) REVERT: E 11 LEU cc_start: 0.8002 (tp) cc_final: 0.7672 (tm) REVERT: E 89 GLU cc_start: 0.8796 (pt0) cc_final: 0.8449 (pp20) REVERT: E 93 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6549 (tpt) REVERT: E 140 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7925 (mtm) REVERT: E 158 SER cc_start: 0.8458 (t) cc_final: 0.8234 (m) REVERT: E 204 SER cc_start: 0.7651 (t) cc_final: 0.7236 (p) REVERT: E 233 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7828 (mt) REVERT: E 234 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6993 (mt-10) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 0.5185 time to fit residues: 78.4930 Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113929 restraints weight = 10845.088| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.53 r_work: 0.3237 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9209 Z= 0.117 Angle : 0.559 9.345 12467 Z= 0.286 Chirality : 0.041 0.290 1429 Planarity : 0.004 0.056 1555 Dihedral : 6.242 108.571 1281 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.64 % Allowed : 21.32 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1126 helix: 2.14 (0.26), residues: 394 sheet: -0.52 (0.30), residues: 299 loop : -1.37 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.019 0.001 TYR D 31 PHE 0.019 0.001 PHE D 65 TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9205) covalent geometry : angle 0.55866 / 0.29 (12458) SS BOND : bond 0.00319 / 0.16 ( 3) SS BOND : angle 0.67643 / 0.33 ( 6) hydrogen bonds : bond 0.03331 / 2.30 ( 399) hydrogen bonds : angle 3.59923 / 2.45 ( 1149) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 0.84888 / 0.46 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.42 seconds wall clock time: 55 minutes 35.48 seconds (3335.48 seconds total)