Starting phenix.real_space_refine on Tue May 13 00:13:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6q_36011/05_2025/8j6q_36011.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5876 2.51 5 N 1554 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 110 Unusual residues: {'3HR': 1, 'CLR': 2, 'IX8': 1, 'NAG': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.98, per 1000 atoms: 0.65 Number of scatterers: 9187 At special positions: 0 Unit cell: (106.02, 119.04, 113.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1688 8.00 N 1554 7.00 C 5876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 405 " - " ASN R 17 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.616A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.335A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.034A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.607A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.526A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.098A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'R' and resid 23 through 54 removed outlier: 3.877A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.671A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 removed outlier: 3.728A pdb=" N CYS R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.661A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 165 removed outlier: 3.672A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 170 through 174 removed outlier: 4.031A pdb=" N GLY R 173 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.523A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 removed outlier: 3.644A pdb=" N ARG R 222 " --> pdb=" O GLN R 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 222' Processing helix chain 'R' and resid 223 through 261 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 265 through 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 295 removed outlier: 4.461A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 5.945A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.455A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.787A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.836A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.066A 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: 3.518A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.657A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.547A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.958A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.860A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.525A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12 448 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1985 1.33 - 1.46: 2469 1.46 - 1.58: 4837 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9392 Sorted by residual: bond pdb=" C2 IX8 R 401 " pdb=" C25 IX8 R 401 " ideal model delta sigma weight residual 1.522 1.649 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C4 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C2 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.451 1.538 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C15 IX8 R 401 " pdb=" C16 IX8 R 401 " ideal model delta sigma weight residual 1.460 1.545 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C11 IX8 R 401 " pdb=" N10 IX8 R 401 " ideal model delta sigma weight residual 1.359 1.442 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12443 2.00 - 4.00: 207 4.00 - 6.00: 53 6.00 - 8.01: 12 8.01 - 10.01: 4 Bond angle restraints: 12719 Sorted by residual: angle pdb=" N CYS R 18 " pdb=" CA CYS R 18 " pdb=" C CYS R 18 " ideal model delta sigma weight residual 108.24 113.37 -5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 angle pdb=" C ASP S 73 " pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" CA GLN R 170 " pdb=" CB GLN R 170 " pdb=" CG GLN R 170 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 115.52 -5.24 1.55e+00 4.16e-01 1.14e+01 ... (remaining 12714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5174 17.82 - 35.64: 422 35.64 - 53.46: 55 53.46 - 71.28: 21 71.28 - 89.10: 6 Dihedral angle restraints: 5678 sinusoidal: 2343 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 52.96 40.04 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1322 0.089 - 0.179: 101 0.179 - 0.268: 6 0.268 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C2 IX8 R 401 " pdb=" C1 IX8 R 401 " pdb=" C25 IX8 R 401 " pdb=" N3 IX8 R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.86 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3 3HR R 403 " pdb=" C2 3HR R 403 " pdb=" C4 3HR R 403 " pdb=" O2 3HR R 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.73 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1427 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO S 75 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 38 " 0.006 2.00e-02 2.50e+03 1.36e-02 3.23e+00 pdb=" CG PHE R 38 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE R 38 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 38 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE R 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 38 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 38 " 0.001 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 534 2.73 - 3.27: 8950 3.27 - 3.82: 16278 3.82 - 4.36: 20262 4.36 - 4.90: 34023 Nonbonded interactions: 80047 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.266 3.040 ... (remaining 80042 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.005 0.127 9398 Z= 0.219 Angle : 0.696 10.008 12732 Z= 0.355 Chirality : 0.048 0.446 1430 Planarity : 0.004 0.074 1595 Dihedral : 13.239 89.104 3507 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1137 helix: 1.12 (0.26), residues: 384 sheet: 0.12 (0.30), residues: 283 loop : -0.23 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.028 0.002 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 1.51826 ( 3) hydrogen bonds : bond 0.16774 ( 443) hydrogen bonds : angle 6.70476 ( 1242) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.21837 ( 10) covalent geometry : bond 0.00457 ( 9392) covalent geometry : angle 0.69478 (12719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.2994 time to fit residues: 219.9104 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 331 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120342 restraints weight = 9174.034| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3067 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9398 Z= 0.146 Angle : 0.545 8.350 12732 Z= 0.294 Chirality : 0.042 0.190 1430 Planarity : 0.004 0.066 1595 Dihedral : 7.049 89.157 1415 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 8.74 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1137 helix: 1.71 (0.27), residues: 381 sheet: 0.04 (0.30), residues: 279 loop : -0.20 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS R 189 PHE 0.013 0.001 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.004 0.000 ARG S 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.69040 ( 3) hydrogen bonds : bond 0.04484 ( 443) hydrogen bonds : angle 4.90522 ( 1242) SS BOND : bond 0.00495 ( 5) SS BOND : angle 1.24225 ( 10) covalent geometry : bond 0.00325 ( 9392) covalent geometry : angle 0.54361 (12719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.974 Fit side-chains REVERT: B 46 ARG cc_start: 0.7772 (mpp-170) cc_final: 0.7497 (mtm-85) REVERT: B 96 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7970 (mtt-85) REVERT: B 217 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7490 (pp-130) REVERT: G 36 ASP cc_start: 0.8236 (m-30) cc_final: 0.7935 (m-30) REVERT: S 160 ARG cc_start: 0.7596 (mtm110) cc_final: 0.6748 (mmm160) REVERT: S 202 ARG cc_start: 0.8314 (ptt-90) cc_final: 0.8046 (ptt-90) REVERT: R 102 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6969 (mm) REVERT: R 110 ASN cc_start: 0.8599 (m110) cc_final: 0.8328 (m110) outliers start: 13 outliers final: 2 residues processed: 148 average time/residue: 1.3512 time to fit residues: 212.1397 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109833 restraints weight = 9254.118| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.74 r_work: 0.3036 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9398 Z= 0.168 Angle : 0.553 7.180 12732 Z= 0.297 Chirality : 0.043 0.197 1430 Planarity : 0.004 0.065 1595 Dihedral : 6.593 82.098 1415 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.31 % Allowed : 11.86 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1137 helix: 1.81 (0.27), residues: 381 sheet: -0.11 (0.29), residues: 294 loop : -0.21 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 189 PHE 0.011 0.001 PHE R 276 TYR 0.026 0.002 TYR S 190 ARG 0.003 0.000 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.57570 ( 3) hydrogen bonds : bond 0.04332 ( 443) hydrogen bonds : angle 4.81528 ( 1242) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.27201 ( 10) covalent geometry : bond 0.00382 ( 9392) covalent geometry : angle 0.55148 (12719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.116 Fit side-chains REVERT: A 240 MET cc_start: 0.6212 (tpp) cc_final: 0.5894 (tpt) REVERT: A 306 GLN cc_start: 0.7915 (mm110) cc_final: 0.7483 (mp10) REVERT: B 46 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7480 (mtm-85) REVERT: G 36 ASP cc_start: 0.8290 (m-30) cc_final: 0.7903 (m-30) REVERT: S 89 GLU cc_start: 0.7842 (pm20) cc_final: 0.7420 (pp20) REVERT: S 160 ARG cc_start: 0.7598 (mtm110) cc_final: 0.6778 (mmm160) REVERT: S 202 ARG cc_start: 0.8296 (ptt-90) cc_final: 0.8041 (ptt-90) REVERT: R 110 ASN cc_start: 0.8610 (m110) cc_final: 0.8357 (m110) REVERT: R 253 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7045 (tpm170) outliers start: 13 outliers final: 4 residues processed: 149 average time/residue: 1.3457 time to fit residues: 213.0395 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 333 GLN B 268 ASN B 340 ASN S 186 GLN R 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120232 restraints weight = 9081.152| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.93 r_work: 0.3043 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9398 Z= 0.148 Angle : 0.530 7.154 12732 Z= 0.285 Chirality : 0.042 0.191 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.337 76.778 1415 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.71 % Allowed : 13.27 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1137 helix: 1.88 (0.27), residues: 381 sheet: -0.11 (0.29), residues: 290 loop : -0.18 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS R 189 PHE 0.022 0.001 PHE R 38 TYR 0.025 0.001 TYR S 190 ARG 0.005 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 1.52390 ( 3) hydrogen bonds : bond 0.04057 ( 443) hydrogen bonds : angle 4.69672 ( 1242) SS BOND : bond 0.00505 ( 5) SS BOND : angle 1.14424 ( 10) covalent geometry : bond 0.00335 ( 9392) covalent geometry : angle 0.52836 (12719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.042 Fit side-chains REVERT: A 186 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7165 (tt0) REVERT: A 240 MET cc_start: 0.6114 (tpp) cc_final: 0.5772 (tpt) REVERT: B 46 ARG cc_start: 0.7876 (mpp-170) cc_final: 0.7597 (mtm-85) REVERT: G 36 ASP cc_start: 0.8374 (m-30) cc_final: 0.7964 (m-30) REVERT: S 160 ARG cc_start: 0.7619 (mtm110) cc_final: 0.6868 (mmm160) REVERT: S 202 ARG cc_start: 0.8425 (ptt-90) cc_final: 0.8201 (ptt-90) REVERT: R 102 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7113 (mm) REVERT: R 110 ASN cc_start: 0.8602 (m110) cc_final: 0.8367 (m110) REVERT: R 253 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7020 (tpm170) outliers start: 17 outliers final: 6 residues processed: 142 average time/residue: 1.3455 time to fit residues: 202.9610 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119257 restraints weight = 9120.659| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.87 r_work: 0.3034 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9398 Z= 0.158 Angle : 0.536 7.143 12732 Z= 0.288 Chirality : 0.043 0.195 1430 Planarity : 0.004 0.062 1595 Dihedral : 6.219 70.953 1415 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 13.57 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1137 helix: 1.95 (0.27), residues: 379 sheet: -0.25 (0.29), residues: 285 loop : -0.10 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE R 38 TYR 0.026 0.002 TYR S 190 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.44351 ( 3) hydrogen bonds : bond 0.04052 ( 443) hydrogen bonds : angle 4.70657 ( 1242) SS BOND : bond 0.00516 ( 5) SS BOND : angle 1.15433 ( 10) covalent geometry : bond 0.00359 ( 9392) covalent geometry : angle 0.53469 (12719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.044 Fit side-chains REVERT: A 240 MET cc_start: 0.6108 (tpp) cc_final: 0.5807 (tpt) REVERT: A 306 GLN cc_start: 0.8052 (mm110) cc_final: 0.7626 (mp10) REVERT: B 46 ARG cc_start: 0.7886 (mpp-170) cc_final: 0.7595 (mtm-85) REVERT: G 36 ASP cc_start: 0.8383 (m-30) cc_final: 0.7992 (m-30) REVERT: G 38 MET cc_start: 0.8231 (mtp) cc_final: 0.7913 (mtp) REVERT: S 89 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: S 160 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7431 (mtm110) REVERT: S 202 ARG cc_start: 0.8443 (ptt-90) cc_final: 0.8197 (ptt-90) REVERT: R 42 LEU cc_start: 0.7978 (tp) cc_final: 0.7753 (tp) REVERT: R 102 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7169 (mm) REVERT: R 110 ASN cc_start: 0.8634 (m110) cc_final: 0.8416 (m110) REVERT: R 253 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7033 (tpm170) outliers start: 21 outliers final: 10 residues processed: 144 average time/residue: 1.2871 time to fit residues: 197.1772 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN S 186 GLN R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116857 restraints weight = 9052.982| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.94 r_work: 0.3015 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9398 Z= 0.172 Angle : 0.554 7.142 12732 Z= 0.297 Chirality : 0.043 0.199 1430 Planarity : 0.004 0.062 1595 Dihedral : 6.192 67.098 1415 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 14.37 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1137 helix: 1.93 (0.27), residues: 379 sheet: -0.20 (0.29), residues: 281 loop : -0.10 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.025 0.001 PHE R 38 TYR 0.026 0.002 TYR S 190 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.34762 ( 3) hydrogen bonds : bond 0.04102 ( 443) hydrogen bonds : angle 4.73005 ( 1242) SS BOND : bond 0.00508 ( 5) SS BOND : angle 1.16826 ( 10) covalent geometry : bond 0.00395 ( 9392) covalent geometry : angle 0.55326 (12719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.962 Fit side-chains REVERT: A 240 MET cc_start: 0.6022 (tpp) cc_final: 0.5746 (tpt) REVERT: A 306 GLN cc_start: 0.8062 (mm110) cc_final: 0.7624 (mp10) REVERT: B 46 ARG cc_start: 0.7905 (mpp-170) cc_final: 0.7604 (mtm-85) REVERT: B 172 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7379 (tm-30) REVERT: G 36 ASP cc_start: 0.8395 (m-30) cc_final: 0.8010 (m-30) REVERT: S 89 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: S 160 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7439 (mtm110) REVERT: S 202 ARG cc_start: 0.8442 (ptt-90) cc_final: 0.8181 (ptt-90) REVERT: R 102 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7235 (mm) REVERT: R 110 ASN cc_start: 0.8654 (m110) cc_final: 0.8424 (m110) REVERT: R 253 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6797 (tpm170) outliers start: 19 outliers final: 10 residues processed: 142 average time/residue: 1.3292 time to fit residues: 200.7156 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN S 186 GLN R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117942 restraints weight = 9171.743| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3031 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9398 Z= 0.151 Angle : 0.558 12.198 12732 Z= 0.295 Chirality : 0.042 0.191 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.280 62.928 1415 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.21 % Allowed : 14.77 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1137 helix: 2.00 (0.27), residues: 379 sheet: -0.27 (0.29), residues: 285 loop : -0.06 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.001 PHE R 38 TYR 0.026 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 1) link_NAG-ASN : angle 9.13028 ( 3) hydrogen bonds : bond 0.03939 ( 443) hydrogen bonds : angle 4.64870 ( 1242) SS BOND : bond 0.00403 ( 5) SS BOND : angle 0.89679 ( 10) covalent geometry : bond 0.00342 ( 9392) covalent geometry : angle 0.53961 (12719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.6160 (tpp) cc_final: 0.5897 (tpt) REVERT: A 306 GLN cc_start: 0.8023 (mm110) cc_final: 0.7586 (mp10) REVERT: B 46 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7574 (mtm-85) REVERT: B 172 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7327 (tm-30) REVERT: G 36 ASP cc_start: 0.8375 (m-30) cc_final: 0.8008 (m-30) REVERT: S 89 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: S 160 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7422 (mtm110) REVERT: S 202 ARG cc_start: 0.8414 (ptt-90) cc_final: 0.8148 (ptt-90) REVERT: R 102 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7216 (mm) REVERT: R 110 ASN cc_start: 0.8611 (m110) cc_final: 0.8403 (m110) REVERT: R 253 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.6777 (tpm170) outliers start: 22 outliers final: 11 residues processed: 149 average time/residue: 1.4182 time to fit residues: 224.3291 Evaluate side-chains 150 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 ASN B 340 ASN S 186 GLN R 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106251 restraints weight = 9250.543| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.75 r_work: 0.2987 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9398 Z= 0.229 Angle : 0.627 10.792 12732 Z= 0.331 Chirality : 0.045 0.213 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.415 61.417 1415 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.81 % Allowed : 15.18 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1137 helix: 1.87 (0.27), residues: 376 sheet: -0.31 (0.29), residues: 286 loop : -0.12 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS R 189 PHE 0.030 0.002 PHE R 38 TYR 0.026 0.002 TYR S 190 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 7.87787 ( 3) hydrogen bonds : bond 0.04418 ( 443) hydrogen bonds : angle 4.88736 ( 1242) SS BOND : bond 0.00546 ( 5) SS BOND : angle 1.24786 ( 10) covalent geometry : bond 0.00536 ( 9392) covalent geometry : angle 0.61456 (12719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.6153 (tpp) cc_final: 0.5590 (tpp) REVERT: A 306 GLN cc_start: 0.8133 (mm110) cc_final: 0.7758 (mm-40) REVERT: B 46 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7519 (mtm-85) REVERT: B 259 GLN cc_start: 0.8175 (tt0) cc_final: 0.7845 (tt0) REVERT: G 36 ASP cc_start: 0.8313 (m-30) cc_final: 0.7899 (m-30) REVERT: G 38 MET cc_start: 0.8261 (mtp) cc_final: 0.7984 (mtp) REVERT: S 89 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: S 160 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7395 (mtm110) REVERT: S 202 ARG cc_start: 0.8414 (ptt-90) cc_final: 0.8108 (ptt-90) REVERT: R 102 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7180 (mm) REVERT: R 110 ASN cc_start: 0.8677 (m110) cc_final: 0.8421 (m110) REVERT: R 232 PHE cc_start: 0.8187 (m-80) cc_final: 0.7897 (m-80) REVERT: R 253 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6710 (tpm170) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 1.3542 time to fit residues: 207.2526 Evaluate side-chains 150 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 268 ASN B 340 ASN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118807 restraints weight = 9115.771| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.96 r_work: 0.3047 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9398 Z= 0.130 Angle : 0.533 8.255 12732 Z= 0.285 Chirality : 0.042 0.186 1430 Planarity : 0.004 0.062 1595 Dihedral : 5.989 59.269 1415 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.31 % Allowed : 15.98 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1137 helix: 2.07 (0.27), residues: 378 sheet: -0.29 (0.29), residues: 284 loop : -0.07 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.028 0.001 PHE R 38 TYR 0.026 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 5.97622 ( 3) hydrogen bonds : bond 0.03823 ( 443) hydrogen bonds : angle 4.59298 ( 1242) SS BOND : bond 0.00437 ( 5) SS BOND : angle 0.92631 ( 10) covalent geometry : bond 0.00293 ( 9392) covalent geometry : angle 0.52441 (12719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 4 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6771 (m) REVERT: A 240 MET cc_start: 0.6204 (tpp) cc_final: 0.5678 (tpp) REVERT: A 306 GLN cc_start: 0.8002 (mm110) cc_final: 0.7561 (mp10) REVERT: B 46 ARG cc_start: 0.7886 (mpp-170) cc_final: 0.7538 (mtm-85) REVERT: B 259 GLN cc_start: 0.8027 (tt0) cc_final: 0.7707 (tt0) REVERT: G 36 ASP cc_start: 0.8325 (m-30) cc_final: 0.7905 (m-30) REVERT: S 89 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: S 160 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7383 (mtm110) REVERT: S 202 ARG cc_start: 0.8366 (ptt-90) cc_final: 0.8099 (ptt-90) REVERT: R 42 LEU cc_start: 0.7901 (tp) cc_final: 0.7691 (tp) REVERT: R 102 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7203 (mm) REVERT: R 110 ASN cc_start: 0.8534 (m110) cc_final: 0.8329 (m110) REVERT: R 216 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7526 (mtt-85) REVERT: R 253 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.6711 (tpm170) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 1.3783 time to fit residues: 210.7010 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN S 186 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 161 HIS R 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113462 restraints weight = 9228.617| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.00 r_work: 0.2967 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9398 Z= 0.282 Angle : 0.674 8.582 12732 Z= 0.356 Chirality : 0.047 0.227 1430 Planarity : 0.005 0.065 1595 Dihedral : 6.487 61.425 1415 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.31 % Allowed : 16.78 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1137 helix: 1.77 (0.27), residues: 375 sheet: -0.23 (0.29), residues: 289 loop : -0.19 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS R 189 PHE 0.031 0.002 PHE R 38 TYR 0.023 0.002 TYR S 190 ARG 0.008 0.001 ARG B 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 5.74988 ( 3) hydrogen bonds : bond 0.04671 ( 443) hydrogen bonds : angle 4.96957 ( 1242) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.40547 ( 10) covalent geometry : bond 0.00665 ( 9392) covalent geometry : angle 0.66754 (12719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.6227 (tpp) cc_final: 0.5667 (tpp) REVERT: A 306 GLN cc_start: 0.8203 (mm110) cc_final: 0.7792 (mm-40) REVERT: B 46 ARG cc_start: 0.7917 (mpp-170) cc_final: 0.7566 (mtm-85) REVERT: B 259 GLN cc_start: 0.8267 (tt0) cc_final: 0.7903 (tt0) REVERT: G 36 ASP cc_start: 0.8350 (m-30) cc_final: 0.7959 (m-30) REVERT: S 89 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: S 93 MET cc_start: 0.8753 (ttp) cc_final: 0.8538 (ttt) REVERT: S 160 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7406 (mtm110) REVERT: S 202 ARG cc_start: 0.8417 (ptt-90) cc_final: 0.8100 (ptt-90) REVERT: R 42 LEU cc_start: 0.7895 (tp) cc_final: 0.7671 (tp) REVERT: R 102 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7200 (mm) REVERT: R 110 ASN cc_start: 0.8739 (m110) cc_final: 0.8457 (m110) REVERT: R 232 PHE cc_start: 0.8245 (m-80) cc_final: 0.7955 (m-80) REVERT: R 253 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6711 (tpm170) outliers start: 13 outliers final: 5 residues processed: 143 average time/residue: 1.4399 time to fit residues: 217.8362 Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 111 optimal weight: 0.0030 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.0070 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121190 restraints weight = 9269.768| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.89 r_work: 0.3072 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9398 Z= 0.122 Angle : 0.532 7.715 12732 Z= 0.286 Chirality : 0.042 0.176 1430 Planarity : 0.004 0.063 1595 Dihedral : 5.973 58.840 1415 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 16.58 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1137 helix: 2.02 (0.27), residues: 378 sheet: -0.20 (0.30), residues: 287 loop : -0.07 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.028 0.001 PHE R 38 TYR 0.026 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 4.46324 ( 3) hydrogen bonds : bond 0.03764 ( 443) hydrogen bonds : angle 4.57284 ( 1242) SS BOND : bond 0.00456 ( 5) SS BOND : angle 0.92579 ( 10) covalent geometry : bond 0.00269 ( 9392) covalent geometry : angle 0.52722 (12719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7820.63 seconds wall clock time: 135 minutes 22.25 seconds (8122.25 seconds total)