Starting phenix.real_space_refine on Tue Mar 3 20:57:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuy_32131/03_2026/7vuy_32131.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 65 5.16 5 C 5572 2.51 5 N 1458 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 8708 At special positions: 0 Unit cell: (116.833, 107.718, 105.232, 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 65 16.00 O 1613 8.00 N 1458 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 251.4 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.790A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.531A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.521A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.205A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 removed outlier: 4.601A pdb=" N LEU R 237 " --> pdb=" O LEU R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 252 through 280 removed outlier: 4.000A pdb=" N LEU R 256 " --> pdb=" O ASP R 252 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.552A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.508A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.792A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.184A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.871A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.933A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 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: 4.147A 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: 3.822A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.581A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.606A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.858A 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 52 removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A 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: 3.564A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.602A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.479A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.852A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A 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 removed outlier: 3.618A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.457A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR S 215 " --> pdb=" O THR S 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.499A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1248 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: 1.43 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2778 1.34 - 1.47: 2334 1.47 - 1.61: 3696 1.61 - 1.74: 1 1.74 - 1.87: 90 Bond restraints: 8899 Sorted by residual: bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.34e-02 1.83e+03 7.52e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.41e-02 5.03e+03 1.93e+01 bond pdb=" N ILE R 260 " pdb=" CA ILE R 260 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N ILE R 249 " pdb=" CA ILE R 249 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 ... (remaining 8894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11574 2.54 - 5.09: 406 5.09 - 7.63: 61 7.63 - 10.17: 18 10.17 - 12.72: 4 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.93 129.44 -8.51 1.06e+00 8.90e-01 6.45e+01 angle pdb=" O HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.71 113.17 7.54 9.40e-01 1.13e+00 6.44e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.12 -12.72 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 113.43 120.34 -6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" O GLN R 242 " pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 122.15 116.44 5.71 1.14e+00 7.69e-01 2.51e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4744 17.09 - 34.18: 453 34.18 - 51.27: 74 51.27 - 68.36: 12 68.36 - 85.45: 9 Dihedral angle restraints: 5292 sinusoidal: 2084 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+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 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1119 0.082 - 0.163: 220 0.163 - 0.245: 25 0.245 - 0.327: 4 0.327 - 0.408: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1369 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 261 " -0.045 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO R 262 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO S 41 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO G 55 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.038 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 30 2.42 - 3.04: 4893 3.04 - 3.66: 13333 3.66 - 4.28: 19997 4.28 - 4.90: 34031 Nonbonded interactions: 72284 Sorted by model distance: nonbonded pdb=" OE1 GLN R 181 " pdb=" CD1 TRP R 248 " model vdw 1.806 3.260 nonbonded pdb=" OE1 GLN R 181 " pdb=" NE1 TRP R 248 " model vdw 2.141 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 3.040 ... (remaining 72279 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: 0.530 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.450 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.010 0.203 8903 Z= 0.422 Angle : 1.122 12.716 12071 Z= 0.609 Chirality : 0.068 0.408 1372 Planarity : 0.007 0.073 1514 Dihedral : 13.835 85.451 3212 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.42 % Allowed : 0.95 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.23), residues: 1098 helix: -0.35 (0.24), residues: 367 sheet: -1.40 (0.29), residues: 285 loop : -1.50 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG R 220 TYR 0.027 0.003 TYR R 113 PHE 0.027 0.003 PHE R 183 TRP 0.015 0.002 TRP B 332 HIS 0.017 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00961 ( 8899) covalent geometry : angle 1.11900 (12063) SS BOND : bond 0.01831 ( 4) SS BOND : angle 3.52826 ( 8) hydrogen bonds : bond 0.16318 ( 426) hydrogen bonds : angle 7.64678 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7986 (mpp) cc_final: 0.7597 (mmt) REVERT: A 305 CYS cc_start: 0.7550 (m) cc_final: 0.7300 (m) REVERT: B 6 GLN cc_start: 0.7374 (pp30) cc_final: 0.7009 (pp30) REVERT: B 15 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7922 (mmmt) REVERT: B 290 ASP cc_start: 0.7987 (m-30) cc_final: 0.7762 (m-30) outliers start: 4 outliers final: 2 residues processed: 177 average time/residue: 0.6231 time to fit residues: 116.5372 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS A 52 GLN A 188 HIS A 306 GLN A 322 HIS A 331 ASN B 110 ASN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136497 restraints weight = 11042.078| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.52 r_work: 0.3666 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8903 Z= 0.185 Angle : 0.655 7.644 12071 Z= 0.342 Chirality : 0.044 0.245 1372 Planarity : 0.004 0.049 1514 Dihedral : 6.912 77.281 1267 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.42 % Allowed : 13.38 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.89 (0.25), residues: 1098 helix: 0.87 (0.26), residues: 371 sheet: -1.31 (0.30), residues: 273 loop : -1.27 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.018 0.002 TYR R 113 PHE 0.018 0.001 PHE R 183 TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8899) covalent geometry : angle 0.65310 (12063) SS BOND : bond 0.00927 ( 4) SS BOND : angle 1.83574 ( 8) hydrogen bonds : bond 0.04606 ( 426) hydrogen bonds : angle 5.51073 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: R 34 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7762 (p) REVERT: R 220 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7185 (ttt-90) REVERT: R 257 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.4641 (t80) REVERT: A 51 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7500 (mmtt) REVERT: A 240 MET cc_start: 0.6249 (tpt) cc_final: 0.6043 (mmt) REVERT: A 305 CYS cc_start: 0.7875 (m) cc_final: 0.7530 (m) REVERT: B 6 GLN cc_start: 0.7177 (pp30) cc_final: 0.6763 (pp30) REVERT: B 290 ASP cc_start: 0.8414 (m-30) cc_final: 0.8147 (m-30) REVERT: S 62 ASP cc_start: 0.8294 (m-30) cc_final: 0.8069 (m-30) outliers start: 23 outliers final: 9 residues processed: 159 average time/residue: 0.5076 time to fit residues: 86.4926 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 88 ASN B 259 GLN S 13 GLN S 174 GLN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.181001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142658 restraints weight = 10847.105| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.51 r_work: 0.3753 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8903 Z= 0.109 Angle : 0.572 9.277 12071 Z= 0.292 Chirality : 0.041 0.201 1372 Planarity : 0.003 0.041 1514 Dihedral : 5.933 78.623 1263 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.11 % Allowed : 16.97 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.37 (0.25), residues: 1098 helix: 1.48 (0.27), residues: 372 sheet: -1.12 (0.30), residues: 280 loop : -1.06 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.019 0.001 TYR R 113 PHE 0.025 0.001 PHE R 94 TRP 0.021 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8899) covalent geometry : angle 0.57084 (12063) SS BOND : bond 0.00841 ( 4) SS BOND : angle 1.23142 ( 8) hydrogen bonds : bond 0.03807 ( 426) hydrogen bonds : angle 4.94769 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.259 Fit side-chains REVERT: R 83 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7606 (mm) REVERT: R 208 ARG cc_start: 0.7472 (tpt-90) cc_final: 0.7058 (tpt90) REVERT: A 51 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7580 (mmtt) REVERT: A 193 ASP cc_start: 0.7784 (m-30) cc_final: 0.7126 (t0) REVERT: A 305 CYS cc_start: 0.7805 (m) cc_final: 0.7400 (m) REVERT: B 6 GLN cc_start: 0.7243 (pp30) cc_final: 0.6818 (pp30) REVERT: B 35 ASN cc_start: 0.8363 (t0) cc_final: 0.7841 (p0) REVERT: B 246 ASP cc_start: 0.8385 (m-30) cc_final: 0.8180 (m-30) REVERT: B 258 ASP cc_start: 0.7698 (t70) cc_final: 0.7078 (t70) REVERT: G 21 MET cc_start: 0.6393 (tmt) cc_final: 0.6153 (tmt) outliers start: 20 outliers final: 6 residues processed: 171 average time/residue: 0.5239 time to fit residues: 95.7482 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN A 188 HIS B 75 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.176235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137010 restraints weight = 11141.199| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.51 r_work: 0.3676 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8903 Z= 0.175 Angle : 0.609 9.020 12071 Z= 0.314 Chirality : 0.044 0.175 1372 Planarity : 0.004 0.040 1514 Dihedral : 5.842 79.772 1263 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.69 % Allowed : 17.39 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.25 (0.26), residues: 1098 helix: 1.61 (0.27), residues: 376 sheet: -1.07 (0.30), residues: 274 loop : -1.04 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.015 0.002 TYR S 178 PHE 0.017 0.001 PHE R 94 TRP 0.015 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8899) covalent geometry : angle 0.60731 (12063) SS BOND : bond 0.00904 ( 4) SS BOND : angle 1.80891 ( 8) hydrogen bonds : bond 0.04178 ( 426) hydrogen bonds : angle 4.98843 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.275 Fit side-chains REVERT: R 226 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7713 (mm) REVERT: R 257 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4493 (t80) REVERT: A 51 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7611 (mmtt) REVERT: A 193 ASP cc_start: 0.8074 (m-30) cc_final: 0.7227 (t0) REVERT: A 282 PRO cc_start: 0.7430 (Cg_endo) cc_final: 0.7165 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7907 (m) cc_final: 0.7537 (m) REVERT: A 349 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8135 (tmmt) REVERT: B 6 GLN cc_start: 0.7169 (pp30) cc_final: 0.6734 (pp30) REVERT: B 35 ASN cc_start: 0.8383 (t0) cc_final: 0.7874 (p0) REVERT: B 46 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8135 (mmm-85) outliers start: 35 outliers final: 16 residues processed: 175 average time/residue: 0.5185 time to fit residues: 97.1111 Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN B 44 GLN B 340 ASN S 13 GLN S 159 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.172604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132285 restraints weight = 11064.679| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.54 r_work: 0.3599 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8903 Z= 0.239 Angle : 0.672 8.929 12071 Z= 0.345 Chirality : 0.046 0.182 1372 Planarity : 0.004 0.042 1514 Dihedral : 6.022 81.013 1263 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.21 % Allowed : 19.60 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.35 (0.25), residues: 1098 helix: 1.57 (0.26), residues: 374 sheet: -1.21 (0.30), residues: 268 loop : -1.08 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.019 0.002 TYR R 113 PHE 0.015 0.002 PHE R 94 TRP 0.013 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 8899) covalent geometry : angle 0.67000 (12063) SS BOND : bond 0.01123 ( 4) SS BOND : angle 2.11800 ( 8) hydrogen bonds : bond 0.04568 ( 426) hydrogen bonds : angle 5.16291 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.340 Fit side-chains REVERT: R 226 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7667 (mm) REVERT: R 230 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 25 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 51 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7656 (mmtt) REVERT: A 193 ASP cc_start: 0.8132 (m-30) cc_final: 0.7667 (m-30) REVERT: A 282 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.7317 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7873 (m) cc_final: 0.7504 (m) REVERT: A 349 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8129 (tmmt) REVERT: B 6 GLN cc_start: 0.7151 (pp30) cc_final: 0.6728 (pp30) REVERT: B 35 ASN cc_start: 0.8451 (t0) cc_final: 0.7939 (p0) REVERT: B 46 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: B 246 ASP cc_start: 0.8650 (m-30) cc_final: 0.8421 (m-30) REVERT: B 262 MET cc_start: 0.8720 (mmt) cc_final: 0.8386 (tpp) outliers start: 40 outliers final: 22 residues processed: 180 average time/residue: 0.5332 time to fit residues: 102.4284 Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140917 restraints weight = 10937.702| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.48 r_work: 0.3729 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8903 Z= 0.116 Angle : 0.600 10.293 12071 Z= 0.302 Chirality : 0.042 0.170 1372 Planarity : 0.003 0.039 1514 Dihedral : 5.529 79.958 1263 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.37 % Allowed : 22.13 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.11 (0.26), residues: 1098 helix: 1.83 (0.27), residues: 378 sheet: -1.14 (0.29), residues: 285 loop : -0.94 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 61 TYR 0.023 0.001 TYR R 113 PHE 0.013 0.001 PHE A 189 TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8899) covalent geometry : angle 0.59922 (12063) SS BOND : bond 0.00535 ( 4) SS BOND : angle 1.22624 ( 8) hydrogen bonds : bond 0.03698 ( 426) hydrogen bonds : angle 4.72450 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.321 Fit side-chains REVERT: R 226 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7690 (mm) REVERT: A 193 ASP cc_start: 0.8086 (m-30) cc_final: 0.7166 (t0) REVERT: A 282 PRO cc_start: 0.7454 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7952 (m) cc_final: 0.7555 (m) REVERT: B 6 GLN cc_start: 0.7121 (pp30) cc_final: 0.6703 (pp30) REVERT: B 35 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7950 (p0) REVERT: B 46 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.8093 (mmm-85) REVERT: B 246 ASP cc_start: 0.8568 (m-30) cc_final: 0.8276 (m-30) REVERT: S 206 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7547 (mpp-170) outliers start: 32 outliers final: 16 residues processed: 177 average time/residue: 0.5024 time to fit residues: 95.1699 Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.173662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134327 restraints weight = 11104.859| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.49 r_work: 0.3627 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8903 Z= 0.220 Angle : 0.686 10.160 12071 Z= 0.348 Chirality : 0.045 0.181 1372 Planarity : 0.004 0.039 1514 Dihedral : 5.858 81.271 1263 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.48 % Allowed : 22.87 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.17 (0.26), residues: 1098 helix: 1.82 (0.26), residues: 374 sheet: -1.07 (0.30), residues: 276 loop : -1.10 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 67 TYR 0.021 0.002 TYR S 103 PHE 0.015 0.002 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8899) covalent geometry : angle 0.68389 (12063) SS BOND : bond 0.01048 ( 4) SS BOND : angle 1.99361 ( 8) hydrogen bonds : bond 0.04381 ( 426) hydrogen bonds : angle 5.01313 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.311 Fit side-chains REVERT: R 226 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7752 (mm) REVERT: R 257 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.4277 (t80) REVERT: A 51 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7539 (mmtt) REVERT: A 193 ASP cc_start: 0.8135 (m-30) cc_final: 0.7174 (t0) REVERT: A 305 CYS cc_start: 0.7901 (m) cc_final: 0.7534 (m) REVERT: B 6 GLN cc_start: 0.7126 (pp30) cc_final: 0.6692 (pp30) REVERT: B 35 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 46 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8134 (mmm-85) REVERT: S 206 ARG cc_start: 0.7856 (mpp-170) cc_final: 0.7637 (mpp-170) outliers start: 33 outliers final: 17 residues processed: 167 average time/residue: 0.5158 time to fit residues: 92.0740 Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135206 restraints weight = 11003.681| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.48 r_work: 0.3630 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8903 Z= 0.199 Angle : 0.684 10.519 12071 Z= 0.345 Chirality : 0.045 0.179 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.830 81.406 1263 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.79 % Allowed : 23.18 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.21 (0.26), residues: 1098 helix: 1.75 (0.26), residues: 376 sheet: -1.18 (0.29), residues: 288 loop : -1.02 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 148 TYR 0.024 0.002 TYR R 113 PHE 0.015 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8899) covalent geometry : angle 0.68211 (12063) SS BOND : bond 0.00919 ( 4) SS BOND : angle 1.86775 ( 8) hydrogen bonds : bond 0.04252 ( 426) hydrogen bonds : angle 4.96015 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.359 Fit side-chains REVERT: R 226 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7730 (mm) REVERT: A 51 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7526 (mmtt) REVERT: A 193 ASP cc_start: 0.8144 (m-30) cc_final: 0.7190 (t0) REVERT: A 305 CYS cc_start: 0.7885 (m) cc_final: 0.7516 (m) REVERT: B 6 GLN cc_start: 0.7103 (pp30) cc_final: 0.6695 (pp30) REVERT: B 46 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8098 (mmm-85) REVERT: B 234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 246 ASP cc_start: 0.8563 (m-30) cc_final: 0.8167 (m-30) REVERT: S 46 GLU cc_start: 0.7001 (pt0) cc_final: 0.6791 (pt0) REVERT: S 206 ARG cc_start: 0.7747 (mpp-170) cc_final: 0.7486 (mpp-170) outliers start: 36 outliers final: 23 residues processed: 172 average time/residue: 0.5471 time to fit residues: 100.1697 Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS A 188 HIS B 13 GLN B 44 GLN B 75 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.172547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132436 restraints weight = 11078.212| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.53 r_work: 0.3605 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8903 Z= 0.219 Angle : 0.703 10.332 12071 Z= 0.357 Chirality : 0.045 0.181 1372 Planarity : 0.004 0.040 1514 Dihedral : 5.917 81.796 1263 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.11 % Allowed : 23.18 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.29 (0.26), residues: 1098 helix: 1.68 (0.26), residues: 375 sheet: -1.14 (0.29), residues: 282 loop : -1.11 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.024 0.002 TYR R 113 PHE 0.015 0.001 PHE A 189 TRP 0.014 0.002 TRP R 248 HIS 0.009 0.001 HIS R 144 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8899) covalent geometry : angle 0.70086 (12063) SS BOND : bond 0.01019 ( 4) SS BOND : angle 2.37579 ( 8) hydrogen bonds : bond 0.04385 ( 426) hydrogen bonds : angle 5.03960 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.278 Fit side-chains REVERT: R 58 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7149 (mpt180) REVERT: R 160 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7309 (tp) REVERT: A 51 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7553 (mmtt) REVERT: A 193 ASP cc_start: 0.8151 (m-30) cc_final: 0.7694 (m-30) REVERT: A 305 CYS cc_start: 0.7858 (m) cc_final: 0.7491 (m) REVERT: B 6 GLN cc_start: 0.7089 (pp30) cc_final: 0.6687 (pp30) REVERT: B 46 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8119 (mmm-85) REVERT: B 234 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: B 246 ASP cc_start: 0.8594 (m-30) cc_final: 0.8227 (m-30) outliers start: 39 outliers final: 26 residues processed: 168 average time/residue: 0.5405 time to fit residues: 96.9737 Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 58 ARG Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136243 restraints weight = 11043.954| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.46 r_work: 0.3663 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8903 Z= 0.174 Angle : 0.686 10.320 12071 Z= 0.346 Chirality : 0.044 0.177 1372 Planarity : 0.004 0.040 1514 Dihedral : 5.757 81.437 1263 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.48 % Allowed : 24.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.22 (0.26), residues: 1098 helix: 1.76 (0.26), residues: 376 sheet: -1.15 (0.29), residues: 287 loop : -1.05 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.026 0.002 TYR R 113 PHE 0.015 0.001 PHE A 189 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8899) covalent geometry : angle 0.68380 (12063) SS BOND : bond 0.00857 ( 4) SS BOND : angle 2.02953 ( 8) hydrogen bonds : bond 0.04089 ( 426) hydrogen bonds : angle 4.90461 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.294 Fit side-chains REVERT: R 58 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6986 (mpt180) REVERT: A 51 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7536 (mmtt) REVERT: A 193 ASP cc_start: 0.8109 (m-30) cc_final: 0.7167 (t0) REVERT: A 297 GLU cc_start: 0.7928 (pm20) cc_final: 0.7599 (mm-30) REVERT: A 305 CYS cc_start: 0.7962 (m) cc_final: 0.7589 (m) REVERT: B 6 GLN cc_start: 0.7104 (pp30) cc_final: 0.6692 (pp30) REVERT: B 46 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7932 (m-80) outliers start: 33 outliers final: 21 residues processed: 168 average time/residue: 0.5084 time to fit residues: 91.2873 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 58 ARG Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138187 restraints weight = 10986.810| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.50 r_work: 0.3703 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8903 Z= 0.135 Angle : 0.661 11.675 12071 Z= 0.328 Chirality : 0.043 0.174 1372 Planarity : 0.004 0.040 1514 Dihedral : 5.586 80.960 1263 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.21 % Allowed : 25.50 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.07 (0.26), residues: 1098 helix: 1.89 (0.26), residues: 377 sheet: -1.07 (0.29), residues: 285 loop : -0.99 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.026 0.001 TYR R 113 PHE 0.014 0.001 PHE R 244 TRP 0.019 0.001 TRP S 47 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8899) covalent geometry : angle 0.65950 (12063) SS BOND : bond 0.00653 ( 4) SS BOND : angle 1.66205 ( 8) hydrogen bonds : bond 0.03765 ( 426) hydrogen bonds : angle 4.73278 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.10 seconds wall clock time: 61 minutes 54.72 seconds (3714.72 seconds total)