Starting phenix.real_space_refine on Tue Mar 3 22:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908.map" model { file = "/net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hn8_34908/03_2026/8hn8_34908_neut.cif" } resolution = 3.0 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= -0.006 sd= 0.162 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 59 5.16 5 C 5673 2.51 5 N 1489 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8860 At special positions: 0 Unit cell: (94.64, 122.72, 131.04, 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 59 16.00 O 1639 8.00 N 1489 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 278.6 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.5% alpha, 21.7% 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 31 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.681A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 52' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.538A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A 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 270 through 280 removed outlier: 3.962A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.080A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.527A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.637A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.184A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.749A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 14 through 43 removed outlier: 3.560A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 78 removed outlier: 5.598A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 85 through 118 Processing helix chain 'R' and resid 118 through 125 removed outlier: 3.684A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.525A pdb=" N ILE R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 171 through 205 removed outlier: 5.302A pdb=" N VAL R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 4.038A pdb=" N ILE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR R 198 " --> pdb=" O ASN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 327 removed outlier: 3.541A pdb=" N LEU R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.792A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.744A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 344 " --> pdb=" O TYR R 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 364 through 374 removed outlier: 3.517A pdb=" N ALA R 368 " --> pdb=" O ARG R 364 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.580A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.076A 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 removed outlier: 4.132A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.244A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.982A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A 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: 6.512A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.651A 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: 4.207A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 10 through 12 removed outlier: 6.179A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.559A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148 418 hydrogen bonds defined for protein. 1194 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: 1.26 Time building geometry restraints manager: 0.86 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: 1432 1.32 - 1.44: 2575 1.44 - 1.57: 4970 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9062 Sorted by residual: bond pdb=" CG HSM R 401 " pdb=" ND1 HSM R 401 " ideal model delta sigma weight residual 1.383 1.258 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CD2 HSM R 401 " pdb=" NE2 HSM R 401 " ideal model delta sigma weight residual 1.376 1.293 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C LEU R 301 " pdb=" O LEU R 301 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" CA ALA R 298 " pdb=" CB ALA R 298 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.12e+01 bond pdb=" N ALA R 298 " pdb=" CA ALA R 298 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.92e+00 ... (remaining 9057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11917 1.48 - 2.95: 282 2.95 - 4.43: 55 4.43 - 5.91: 14 5.91 - 7.38: 5 Bond angle restraints: 12273 Sorted by residual: angle pdb=" N LEU R 293 " pdb=" CA LEU R 293 " pdb=" C LEU R 293 " ideal model delta sigma weight residual 111.28 104.04 7.24 1.09e+00 8.42e-01 4.41e+01 angle pdb=" CA LEU R 301 " pdb=" C LEU R 301 " pdb=" N ALA R 302 " ideal model delta sigma weight residual 117.04 122.25 -5.21 1.24e+00 6.50e-01 1.76e+01 angle pdb=" C LEU R 295 " pdb=" N LEU R 296 " pdb=" CA LEU R 296 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 108.14 113.31 -5.17 1.52e+00 4.33e-01 1.16e+01 angle pdb=" C LYS B 280 " pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4845 17.54 - 35.07: 414 35.07 - 52.61: 53 52.61 - 70.15: 14 70.15 - 87.69: 11 Dihedral angle restraints: 5337 sinusoidal: 2082 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -160.93 74.93 1 1.00e+01 1.00e-02 7.10e+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 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CB GLU R 165 " pdb=" CG GLU R 165 " pdb=" CD GLU R 165 " pdb=" OE1 GLU R 165 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.076: 321 0.076 - 0.115: 88 0.115 - 0.153: 18 0.153 - 0.191: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA LEU R 296 " pdb=" N LEU R 296 " pdb=" C LEU R 296 " pdb=" CB LEU R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ARG R 299 " pdb=" N ARG R 299 " pdb=" C ARG R 299 " pdb=" CB ARG R 299 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU R 293 " pdb=" CB LEU R 293 " pdb=" CD1 LEU R 293 " pdb=" CD2 LEU R 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1369 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 301 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU R 301 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 301 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 334 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO R 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.020 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1325 2.76 - 3.30: 8050 3.30 - 3.83: 13942 3.83 - 4.37: 16368 4.37 - 4.90: 29837 Nonbonded interactions: 69522 Sorted by model distance: nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.225 3.120 nonbonded pdb=" OG SER S 134 " pdb=" OE1 GLU S 234 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.328 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.336 3.040 ... (remaining 69517 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: 1.250 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 0.125 9065 Z= 0.192 Angle : 0.590 7.382 12279 Z= 0.349 Chirality : 0.042 0.191 1372 Planarity : 0.003 0.041 1543 Dihedral : 13.370 87.685 3228 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.41 % Allowed : 0.21 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.55 (0.25), residues: 1102 helix: 1.69 (0.28), residues: 383 sheet: 0.46 (0.31), residues: 280 loop : -0.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.014 0.001 PHE R 169 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9062) covalent geometry : angle 0.58955 (12273) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.72654 ( 6) hydrogen bonds : bond 0.15579 ( 418) hydrogen bonds : angle 5.42055 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.308 Fit side-chains REVERT: A 309 ASP cc_start: 0.7096 (m-30) cc_final: 0.6716 (m-30) REVERT: R 125 GLN cc_start: 0.6974 (tt0) cc_final: 0.6418 (tt0) REVERT: R 297 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4287 (mtt180) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 0.5330 time to fit residues: 82.6551 Evaluate side-chains 106 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 297 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.148803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110751 restraints weight = 10367.601| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.27 r_work: 0.3118 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9065 Z= 0.252 Angle : 0.652 7.519 12279 Z= 0.349 Chirality : 0.047 0.211 1372 Planarity : 0.005 0.056 1543 Dihedral : 5.668 59.924 1220 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.49 % Allowed : 9.13 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1102 helix: 1.62 (0.27), residues: 379 sheet: 0.09 (0.29), residues: 293 loop : -1.05 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 204 TYR 0.031 0.002 TYR S 178 PHE 0.019 0.002 PHE R 169 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 9062) covalent geometry : angle 0.65229 (12273) SS BOND : bond 0.00484 ( 3) SS BOND : angle 0.70948 ( 6) hydrogen bonds : bond 0.06481 ( 418) hydrogen bonds : angle 4.65328 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.343 Fit side-chains REVERT: A 309 ASP cc_start: 0.7002 (m-30) cc_final: 0.6595 (m-30) REVERT: B 197 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.6787 (mtp-110) REVERT: B 217 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7478 (ppp) REVERT: R 31 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7067 (mm) REVERT: R 47 ARG cc_start: 0.8607 (mpt180) cc_final: 0.8229 (mpt180) REVERT: R 125 GLN cc_start: 0.7095 (tt0) cc_final: 0.6502 (tt0) REVERT: R 297 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.4769 (mtt180) REVERT: S 11 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7871 (tt) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.5449 time to fit residues: 71.0250 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117421 restraints weight = 10185.593| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.26 r_work: 0.3221 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9065 Z= 0.103 Angle : 0.490 6.349 12279 Z= 0.261 Chirality : 0.041 0.161 1372 Planarity : 0.004 0.040 1543 Dihedral : 5.057 59.595 1220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.97 % Allowed : 11.10 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.60 (0.25), residues: 1102 helix: 2.08 (0.27), residues: 382 sheet: 0.07 (0.30), residues: 288 loop : -0.88 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.012 0.001 PHE S 27 TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9062) covalent geometry : angle 0.49005 (12273) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.72524 ( 6) hydrogen bonds : bond 0.04299 ( 418) hydrogen bonds : angle 4.28952 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.335 Fit side-chains REVERT: A 20 ASP cc_start: 0.8138 (m-30) cc_final: 0.7923 (m-30) REVERT: A 252 SER cc_start: 0.7078 (m) cc_final: 0.6848 (m) REVERT: A 255 ASN cc_start: 0.7953 (m-40) cc_final: 0.7515 (m110) REVERT: A 305 CYS cc_start: 0.7840 (m) cc_final: 0.6760 (m) REVERT: A 309 ASP cc_start: 0.6990 (m-30) cc_final: 0.6520 (m-30) REVERT: A 354 PHE cc_start: 0.8313 (t80) cc_final: 0.8004 (t80) REVERT: B 170 ASP cc_start: 0.7834 (t70) cc_final: 0.7631 (t0) REVERT: B 215 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: R 125 GLN cc_start: 0.6947 (tt0) cc_final: 0.6449 (tt0) REVERT: R 297 ARG cc_start: 0.5249 (OUTLIER) cc_final: 0.4700 (mtt180) REVERT: S 11 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7917 (tt) outliers start: 19 outliers final: 7 residues processed: 121 average time/residue: 0.5466 time to fit residues: 70.5762 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116303 restraints weight = 10455.226| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.31 r_work: 0.3217 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9065 Z= 0.113 Angle : 0.492 6.455 12279 Z= 0.261 Chirality : 0.041 0.186 1372 Planarity : 0.004 0.041 1543 Dihedral : 4.885 59.170 1220 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 12.45 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.67 (0.25), residues: 1102 helix: 2.17 (0.27), residues: 383 sheet: 0.10 (0.30), residues: 288 loop : -0.87 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.019 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9062) covalent geometry : angle 0.49144 (12273) SS BOND : bond 0.00362 ( 3) SS BOND : angle 0.64694 ( 6) hydrogen bonds : bond 0.04331 ( 418) hydrogen bonds : angle 4.19229 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8134 (m-30) cc_final: 0.7918 (m-30) REVERT: A 252 SER cc_start: 0.6983 (m) cc_final: 0.6754 (m) REVERT: A 305 CYS cc_start: 0.7841 (m) cc_final: 0.7181 (m) REVERT: B 65 THR cc_start: 0.8035 (m) cc_final: 0.7762 (m) REVERT: B 197 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.6555 (mtp-110) REVERT: B 268 ASN cc_start: 0.8143 (m110) cc_final: 0.7915 (m110) REVERT: G 58 GLU cc_start: 0.7818 (tp30) cc_final: 0.7573 (mm-30) REVERT: R 47 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8159 (mpt180) REVERT: R 125 GLN cc_start: 0.6925 (tt0) cc_final: 0.6403 (tt0) REVERT: R 297 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.4924 (mtt180) REVERT: R 322 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: S 11 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7847 (tt) outliers start: 24 outliers final: 11 residues processed: 126 average time/residue: 0.5407 time to fit residues: 73.0248 Evaluate side-chains 125 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115859 restraints weight = 10368.924| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.24 r_work: 0.3207 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9065 Z= 0.132 Angle : 0.505 6.660 12279 Z= 0.270 Chirality : 0.042 0.199 1372 Planarity : 0.004 0.041 1543 Dihedral : 4.774 59.163 1220 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.11 % Allowed : 12.66 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.55 (0.25), residues: 1102 helix: 2.04 (0.27), residues: 389 sheet: 0.03 (0.30), residues: 290 loop : -0.96 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9062) covalent geometry : angle 0.50520 (12273) SS BOND : bond 0.00389 ( 3) SS BOND : angle 0.57866 ( 6) hydrogen bonds : bond 0.04574 ( 418) hydrogen bonds : angle 4.20896 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8124 (m-30) cc_final: 0.7907 (m-30) REVERT: A 255 ASN cc_start: 0.7895 (m-40) cc_final: 0.7441 (m110) REVERT: A 305 CYS cc_start: 0.7772 (m) cc_final: 0.6764 (m) REVERT: A 309 ASP cc_start: 0.6906 (m-30) cc_final: 0.6457 (m-30) REVERT: B 65 THR cc_start: 0.8006 (m) cc_final: 0.7739 (m) REVERT: B 197 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.6564 (mtp-110) REVERT: B 234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: B 268 ASN cc_start: 0.8162 (m110) cc_final: 0.7922 (m110) REVERT: G 58 GLU cc_start: 0.7850 (tp30) cc_final: 0.7588 (mm-30) REVERT: R 47 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8228 (mpt180) REVERT: R 125 GLN cc_start: 0.6969 (tt0) cc_final: 0.6542 (tt0) REVERT: R 297 ARG cc_start: 0.5397 (OUTLIER) cc_final: 0.4798 (mtt180) REVERT: R 322 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6965 (m-80) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 0.5265 time to fit residues: 74.5080 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115300 restraints weight = 10274.021| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.26 r_work: 0.3190 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9065 Z= 0.131 Angle : 0.507 6.867 12279 Z= 0.270 Chirality : 0.042 0.202 1372 Planarity : 0.004 0.041 1543 Dihedral : 4.718 59.779 1220 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 13.17 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.57 (0.25), residues: 1102 helix: 2.05 (0.27), residues: 390 sheet: 0.08 (0.30), residues: 288 loop : -0.97 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.012 0.001 PHE S 27 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9062) covalent geometry : angle 0.50654 (12273) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.54605 ( 6) hydrogen bonds : bond 0.04552 ( 418) hydrogen bonds : angle 4.19789 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 255 ASN cc_start: 0.7970 (m-40) cc_final: 0.7543 (m110) REVERT: A 305 CYS cc_start: 0.7898 (m) cc_final: 0.6939 (m) REVERT: A 309 ASP cc_start: 0.7019 (m-30) cc_final: 0.6586 (m-30) REVERT: B 65 THR cc_start: 0.8054 (m) cc_final: 0.7791 (m) REVERT: B 197 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.6644 (mtp-110) REVERT: B 268 ASN cc_start: 0.8200 (m110) cc_final: 0.7973 (m110) REVERT: G 58 GLU cc_start: 0.7981 (tp30) cc_final: 0.7700 (mm-30) REVERT: R 47 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8322 (mpt180) REVERT: R 125 GLN cc_start: 0.7051 (tt0) cc_final: 0.6651 (tt0) REVERT: R 297 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.4905 (mtt180) REVERT: R 322 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7070 (m-80) outliers start: 31 outliers final: 19 residues processed: 133 average time/residue: 0.4938 time to fit residues: 70.5857 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** R 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116059 restraints weight = 10441.490| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.30 r_work: 0.3208 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9065 Z= 0.117 Angle : 0.498 6.872 12279 Z= 0.264 Chirality : 0.042 0.212 1372 Planarity : 0.003 0.040 1543 Dihedral : 4.651 59.732 1220 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 13.38 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.63 (0.25), residues: 1102 helix: 2.12 (0.27), residues: 390 sheet: 0.10 (0.30), residues: 288 loop : -0.95 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.018 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9062) covalent geometry : angle 0.49784 (12273) SS BOND : bond 0.00351 ( 3) SS BOND : angle 0.52610 ( 6) hydrogen bonds : bond 0.04324 ( 418) hydrogen bonds : angle 4.16638 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8076 (m-30) cc_final: 0.7862 (m-30) REVERT: A 305 CYS cc_start: 0.7926 (m) cc_final: 0.6912 (m) REVERT: A 309 ASP cc_start: 0.6997 (m-30) cc_final: 0.6549 (m-30) REVERT: B 65 THR cc_start: 0.8010 (m) cc_final: 0.7737 (m) REVERT: B 197 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.6575 (mtp-110) REVERT: G 58 GLU cc_start: 0.7988 (tp30) cc_final: 0.7695 (mm-30) REVERT: R 125 GLN cc_start: 0.6981 (tt0) cc_final: 0.6489 (tt0) REVERT: R 294 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5610 (tt0) REVERT: R 297 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4812 (mtt180) REVERT: R 322 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7009 (m-80) outliers start: 31 outliers final: 19 residues processed: 130 average time/residue: 0.5222 time to fit residues: 72.6723 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117942 restraints weight = 10288.576| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.28 r_work: 0.3236 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9065 Z= 0.101 Angle : 0.477 6.733 12279 Z= 0.253 Chirality : 0.041 0.215 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.497 58.896 1220 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.49 % Allowed : 14.42 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.77 (0.26), residues: 1102 helix: 2.29 (0.27), residues: 385 sheet: 0.09 (0.30), residues: 293 loop : -0.85 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.016 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9062) covalent geometry : angle 0.47711 (12273) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.53433 ( 6) hydrogen bonds : bond 0.03973 ( 418) hydrogen bonds : angle 4.09126 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8102 (m-30) cc_final: 0.7877 (m-30) REVERT: A 305 CYS cc_start: 0.7931 (m) cc_final: 0.6937 (m) REVERT: A 309 ASP cc_start: 0.7006 (m-30) cc_final: 0.6561 (m-30) REVERT: G 58 GLU cc_start: 0.7965 (tp30) cc_final: 0.7700 (mm-30) REVERT: R 125 GLN cc_start: 0.6934 (tt0) cc_final: 0.6565 (tt0) REVERT: R 297 ARG cc_start: 0.5488 (OUTLIER) cc_final: 0.4825 (mtt180) REVERT: R 322 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: S 150 SER cc_start: 0.7855 (m) cc_final: 0.7248 (p) outliers start: 24 outliers final: 16 residues processed: 133 average time/residue: 0.5531 time to fit residues: 78.6623 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 70 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117507 restraints weight = 10280.740| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.27 r_work: 0.3230 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9065 Z= 0.110 Angle : 0.487 6.258 12279 Z= 0.260 Chirality : 0.041 0.237 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.486 58.366 1220 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.49 % Allowed : 14.94 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1102 helix: 2.27 (0.27), residues: 387 sheet: 0.11 (0.30), residues: 293 loop : -0.85 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.017 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9062) covalent geometry : angle 0.48741 (12273) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.51261 ( 6) hydrogen bonds : bond 0.04075 ( 418) hydrogen bonds : angle 4.08319 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8129 (m-30) cc_final: 0.7900 (m-30) REVERT: A 305 CYS cc_start: 0.7951 (m) cc_final: 0.6936 (m) REVERT: A 309 ASP cc_start: 0.7039 (m-30) cc_final: 0.6592 (m-30) REVERT: G 58 GLU cc_start: 0.7988 (tp30) cc_final: 0.7763 (mm-30) REVERT: R 125 GLN cc_start: 0.6984 (tt0) cc_final: 0.6614 (tt0) REVERT: R 297 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.4851 (mtt180) REVERT: R 322 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: S 150 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7292 (p) outliers start: 24 outliers final: 17 residues processed: 127 average time/residue: 0.5422 time to fit residues: 73.6013 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 76 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118196 restraints weight = 10303.109| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.28 r_work: 0.3240 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9065 Z= 0.104 Angle : 0.483 6.003 12279 Z= 0.256 Chirality : 0.041 0.249 1372 Planarity : 0.003 0.038 1543 Dihedral : 4.440 58.610 1220 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 15.66 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.83 (0.26), residues: 1102 helix: 2.35 (0.27), residues: 385 sheet: 0.11 (0.30), residues: 294 loop : -0.82 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.016 0.001 TYR S 178 PHE 0.011 0.001 PHE S 27 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9062) covalent geometry : angle 0.48316 (12273) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.52756 ( 6) hydrogen bonds : bond 0.03938 ( 418) hydrogen bonds : angle 4.04349 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8094 (m-30) cc_final: 0.7859 (m-30) REVERT: A 305 CYS cc_start: 0.7969 (m) cc_final: 0.6972 (m) REVERT: A 309 ASP cc_start: 0.7027 (m-30) cc_final: 0.6575 (m-30) REVERT: G 58 GLU cc_start: 0.7991 (tp30) cc_final: 0.7750 (mm-30) REVERT: R 47 ARG cc_start: 0.8467 (mpt180) cc_final: 0.8094 (mmt-90) REVERT: R 125 GLN cc_start: 0.6936 (tt0) cc_final: 0.6568 (tt0) REVERT: R 163 GLU cc_start: 0.7036 (tt0) cc_final: 0.6220 (tp30) REVERT: R 297 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.4805 (mtt180) REVERT: R 322 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: S 150 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7262 (p) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.5226 time to fit residues: 71.1314 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115206 restraints weight = 10271.540| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.24 r_work: 0.3199 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9065 Z= 0.144 Angle : 0.520 5.452 12279 Z= 0.278 Chirality : 0.043 0.268 1372 Planarity : 0.004 0.039 1543 Dihedral : 4.604 59.009 1220 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.18 % Allowed : 15.87 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.61 (0.25), residues: 1102 helix: 2.11 (0.27), residues: 391 sheet: 0.01 (0.30), residues: 296 loop : -0.93 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.022 0.001 TYR S 178 PHE 0.012 0.001 PHE S 27 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9062) covalent geometry : angle 0.51997 (12273) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.48842 ( 6) hydrogen bonds : bond 0.04637 ( 418) hydrogen bonds : angle 4.16119 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.20 seconds wall clock time: 58 minutes 2.51 seconds (3482.51 seconds total)