Starting phenix.real_space_refine on Wed Sep 17 12:01:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795.map" model { file = "/net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z68_39795/09_2025/8z68_39795_neut.cif" } resolution = 2.64 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= 0.001 sd= 0.022 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 50 5.16 5 C 5468 2.51 5 N 1470 2.21 5 O 1555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8543 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2456 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 338 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1730 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 276} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8543 At special positions: 0 Unit cell: (86.48, 118.68, 127.88, 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 50 16.00 O 1555 8.00 N 1470 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 13 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " 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 431.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.545A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.617A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.946A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.386A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.531A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.270A 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 208 through 212 removed outlier: 3.643A pdb=" N ASP S 211 " --> pdb=" O GLU S 208 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 208 through 212' Processing helix chain 'R' and resid 18 through 23 Processing helix chain 'R' and resid 23 through 36 Processing helix chain 'R' and resid 37 through 52 removed outlier: 4.755A pdb=" N LEU R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 83 removed outlier: 3.926A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 89 through 103 removed outlier: 4.209A pdb=" N SER R 93 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 125 Processing helix chain 'R' and resid 134 through 159 removed outlier: 4.384A pdb=" N TYR R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS R 159 " --> pdb=" O TYR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 192 Processing helix chain 'R' and resid 194 through 205 Processing helix chain 'R' and resid 207 through 212 Processing helix chain 'R' and resid 219 through 254 removed outlier: 3.650A pdb=" N GLN R 227 " --> pdb=" O LYS R 223 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 3.657A pdb=" N TRP R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 276 removed outlier: 3.540A pdb=" N ALA R 261 " --> pdb=" O SER R 257 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 296 removed outlier: 3.539A pdb=" N HIS R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG R 295 " --> pdb=" O GLU R 291 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP R 296 " --> pdb=" O THR R 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 290 through 296' Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.552A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.780A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.931A 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: 4.328A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.574A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.995A 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: 6.901A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.296A 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: 6.629A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.817A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.902A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.616A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 162 through 164 450 hydrogen bonds defined for protein. 1272 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: 1.55 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1356 1.28 - 1.41: 2382 1.41 - 1.55: 4935 1.55 - 1.68: 0 1.68 - 1.81: 67 Bond restraints: 8740 Sorted by residual: bond pdb=" C ILE R 154 " pdb=" O ILE R 154 " ideal model delta sigma weight residual 1.237 1.155 0.081 1.12e-02 7.97e+03 5.26e+01 bond pdb=" C ASP R 67 " pdb=" O ASP R 67 " ideal model delta sigma weight residual 1.237 1.151 0.085 1.19e-02 7.06e+03 5.16e+01 bond pdb=" CA LYS R 223 " pdb=" C LYS R 223 " ideal model delta sigma weight residual 1.523 1.428 0.095 1.35e-02 5.49e+03 4.93e+01 bond pdb=" C THR R 30 " pdb=" O THR R 30 " ideal model delta sigma weight residual 1.237 1.160 0.076 1.19e-02 7.06e+03 4.13e+01 bond pdb=" C VAL R 31 " pdb=" O VAL R 31 " ideal model delta sigma weight residual 1.237 1.155 0.082 1.29e-02 6.01e+03 4.03e+01 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 11777 3.05 - 6.11: 114 6.11 - 9.16: 16 9.16 - 12.21: 8 12.21 - 15.27: 2 Bond angle restraints: 11917 Sorted by residual: angle pdb=" N THR R 152 " pdb=" CA THR R 152 " pdb=" C THR R 152 " ideal model delta sigma weight residual 113.55 101.27 12.28 1.26e+00 6.30e-01 9.50e+01 angle pdb=" C VAL R 26 " pdb=" CA VAL R 26 " pdb=" CB VAL R 26 " ideal model delta sigma weight residual 111.97 102.21 9.76 1.28e+00 6.10e-01 5.82e+01 angle pdb=" C ILE R 154 " pdb=" CA ILE R 154 " pdb=" CB ILE R 154 " ideal model delta sigma weight residual 112.02 102.38 9.64 1.31e+00 5.83e-01 5.41e+01 angle pdb=" N ALA R 147 " pdb=" CA ALA R 147 " pdb=" C ALA R 147 " ideal model delta sigma weight residual 111.07 103.73 7.34 1.07e+00 8.73e-01 4.70e+01 angle pdb=" CA TYR R 176 " pdb=" CB TYR R 176 " pdb=" CG TYR R 176 " ideal model delta sigma weight residual 113.90 102.29 11.61 1.80e+00 3.09e-01 4.16e+01 ... (remaining 11912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4605 17.95 - 35.90: 386 35.90 - 53.85: 73 53.85 - 71.80: 12 71.80 - 89.75: 5 Dihedral angle restraints: 5081 sinusoidal: 1758 harmonic: 3323 Sorted by residual: dihedral pdb=" N ARG R 213 " pdb=" C ARG R 213 " pdb=" CA ARG R 213 " pdb=" CB ARG R 213 " ideal model delta harmonic sigma weight residual 122.80 136.41 -13.61 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" N HIS R 175 " pdb=" C HIS R 175 " pdb=" CA HIS R 175 " pdb=" CB HIS R 175 " ideal model delta harmonic sigma weight residual 122.80 110.16 12.64 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" N VAL R 253 " pdb=" C VAL R 253 " pdb=" CA VAL R 253 " pdb=" CB VAL R 253 " ideal model delta harmonic sigma weight residual 123.40 135.30 -11.90 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 5078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1335 0.112 - 0.224: 34 0.224 - 0.336: 10 0.336 - 0.448: 0 0.448 - 0.560: 4 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA VAL R 253 " pdb=" N VAL R 253 " pdb=" C VAL R 253 " pdb=" CB VAL R 253 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA ARG R 213 " pdb=" N ARG R 213 " pdb=" C ARG R 213 " pdb=" CB ARG R 213 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CA THR R 30 " pdb=" N THR R 30 " pdb=" C THR R 30 " pdb=" CB THR R 30 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 1380 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 248 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C LEU R 248 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU R 248 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU R 249 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 223 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LYS R 223 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS R 223 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP R 224 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 176 " 0.034 2.00e-02 2.50e+03 2.22e-02 9.85e+00 pdb=" CG TYR R 176 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 176 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 176 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 176 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 176 " 0.007 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 263 2.69 - 3.24: 8316 3.24 - 3.80: 14088 3.80 - 4.35: 18444 4.35 - 4.90: 31056 Nonbonded interactions: 72167 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.138 3.040 nonbonded pdb=" O LEU R 272 " pdb=" OG1 THR R 275 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR R 102 " pdb=" OE1 GLU R 174 " model vdw 2.207 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O GLU B 130 " model vdw 2.235 3.040 ... (remaining 72162 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.009 0.095 8743 Z= 0.543 Angle : 0.797 15.268 11923 Z= 0.478 Chirality : 0.058 0.560 1383 Planarity : 0.005 0.072 1511 Dihedral : 14.044 89.752 2928 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.82 % Allowed : 6.69 % Favored : 92.49 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.19 (0.25), residues: 1122 helix: 1.15 (0.28), residues: 378 sheet: 0.02 (0.29), residues: 284 loop : -0.57 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.052 0.002 TYR R 176 PHE 0.027 0.002 PHE R 173 TRP 0.023 0.002 TRP B 169 HIS 0.008 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00863 ( 8740) covalent geometry : angle 0.79747 (11917) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.66988 ( 6) hydrogen bonds : bond 0.13675 ( 445) hydrogen bonds : angle 6.38731 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.326 Fit side-chains REVERT: A 243 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7903 (mptp) REVERT: A 265 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8290 (mtp-110) REVERT: A 310 ASP cc_start: 0.8253 (m-30) cc_final: 0.8019 (m-30) REVERT: A 331 ASP cc_start: 0.7718 (m-30) cc_final: 0.7492 (m-30) REVERT: B 219 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7970 (ttm-80) REVERT: B 269 ILE cc_start: 0.8226 (pt) cc_final: 0.7784 (pp) REVERT: G 38 MET cc_start: 0.7703 (mtm) cc_final: 0.7447 (ttm) REVERT: S 68 PHE cc_start: 0.7756 (m-10) cc_final: 0.7542 (m-10) REVERT: S 85 SER cc_start: 0.8538 (t) cc_final: 0.8334 (t) REVERT: S 181 SER cc_start: 0.8316 (t) cc_final: 0.8060 (p) REVERT: S 218 MET cc_start: 0.8576 (ttp) cc_final: 0.8206 (ttm) REVERT: R 81 VAL cc_start: 0.7966 (m) cc_final: 0.7738 (p) REVERT: R 106 TYR cc_start: 0.8226 (m-80) cc_final: 0.7803 (m-80) REVERT: R 132 PHE cc_start: 0.7873 (m-80) cc_final: 0.7455 (m-80) REVERT: R 179 GLN cc_start: 0.7058 (mm110) cc_final: 0.6858 (mt0) REVERT: R 200 LEU cc_start: 0.7432 (tp) cc_final: 0.7228 (tt) outliers start: 7 outliers final: 3 residues processed: 215 average time/residue: 0.4685 time to fit residues: 108.2880 Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 161 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN A 390 GLN B 62 HIS B 88 ASN B 119 ASN B 125 ASN B 293 ASN R 54 ASN R 125 HIS R 167 ASN R 269 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107856 restraints weight = 12534.419| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.53 r_work: 0.3421 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8743 Z= 0.204 Angle : 0.580 6.089 11923 Z= 0.314 Chirality : 0.043 0.199 1383 Planarity : 0.004 0.044 1511 Dihedral : 5.134 49.788 1236 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.70 % Allowed : 12.44 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.34 (0.25), residues: 1122 helix: 1.42 (0.28), residues: 382 sheet: 0.01 (0.29), residues: 289 loop : -0.58 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 241 TYR 0.038 0.002 TYR B 59 PHE 0.015 0.002 PHE R 111 TRP 0.022 0.002 TRP B 169 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8740) covalent geometry : angle 0.57985 (11917) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.11455 ( 6) hydrogen bonds : bond 0.04216 ( 445) hydrogen bonds : angle 5.10664 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 331 ASP cc_start: 0.7613 (m-30) cc_final: 0.7389 (m-30) REVERT: B 237 ASN cc_start: 0.7306 (t0) cc_final: 0.6974 (t0) REVERT: B 269 ILE cc_start: 0.8284 (pt) cc_final: 0.7883 (pp) REVERT: G 38 MET cc_start: 0.7786 (mtm) cc_final: 0.7535 (ttp) REVERT: S 85 SER cc_start: 0.8565 (t) cc_final: 0.8187 (p) REVERT: S 128 MET cc_start: 0.8784 (mmp) cc_final: 0.8577 (tpp) REVERT: S 192 SER cc_start: 0.8712 (t) cc_final: 0.8447 (p) REVERT: S 218 MET cc_start: 0.8567 (ttp) cc_final: 0.8232 (ttm) REVERT: R 132 PHE cc_start: 0.8194 (m-80) cc_final: 0.7783 (m-80) REVERT: R 156 PHE cc_start: 0.7734 (m-80) cc_final: 0.7339 (m-80) REVERT: R 247 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7970 (tt) outliers start: 23 outliers final: 11 residues processed: 233 average time/residue: 0.4719 time to fit residues: 118.1579 Evaluate side-chains 223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 212 VAL Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 125 ASN S 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106983 restraints weight = 12519.962| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.53 r_work: 0.3411 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8743 Z= 0.187 Angle : 0.554 5.553 11923 Z= 0.300 Chirality : 0.043 0.184 1383 Planarity : 0.004 0.044 1511 Dihedral : 4.958 46.191 1233 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.93 % Allowed : 15.96 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 1122 helix: 1.59 (0.28), residues: 384 sheet: 0.02 (0.29), residues: 296 loop : -0.53 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 380 TYR 0.034 0.002 TYR B 59 PHE 0.015 0.002 PHE B 151 TRP 0.021 0.002 TRP B 169 HIS 0.008 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8740) covalent geometry : angle 0.55418 (11917) SS BOND : bond 0.00312 ( 3) SS BOND : angle 0.85148 ( 6) hydrogen bonds : bond 0.04205 ( 445) hydrogen bonds : angle 4.98851 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.337 Fit side-chains REVERT: A 331 ASP cc_start: 0.7665 (m-30) cc_final: 0.7450 (m-30) REVERT: B 269 ILE cc_start: 0.8310 (pt) cc_final: 0.7918 (pp) REVERT: G 38 MET cc_start: 0.7782 (mtm) cc_final: 0.7527 (ttp) REVERT: S 85 SER cc_start: 0.8564 (t) cc_final: 0.8185 (p) REVERT: S 128 MET cc_start: 0.8764 (mmp) cc_final: 0.8553 (tpp) REVERT: S 218 MET cc_start: 0.8589 (ttp) cc_final: 0.8257 (ttm) REVERT: R 132 PHE cc_start: 0.8213 (m-80) cc_final: 0.7810 (m-80) REVERT: R 173 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7512 (t80) outliers start: 25 outliers final: 9 residues processed: 232 average time/residue: 0.4472 time to fit residues: 112.0410 Evaluate side-chains 228 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 119 ASN B 125 ASN B 293 ASN R 159 HIS R 169 HIS ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 266 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105253 restraints weight = 12769.548| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.53 r_work: 0.3383 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8743 Z= 0.273 Angle : 0.605 5.886 11923 Z= 0.326 Chirality : 0.045 0.206 1383 Planarity : 0.004 0.045 1511 Dihedral : 5.128 42.582 1233 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.40 % Allowed : 18.08 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.27 (0.25), residues: 1122 helix: 1.42 (0.28), residues: 381 sheet: -0.02 (0.30), residues: 287 loop : -0.69 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.029 0.002 TYR B 59 PHE 0.020 0.002 PHE B 151 TRP 0.021 0.002 TRP B 169 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 8740) covalent geometry : angle 0.60459 (11917) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.22038 ( 6) hydrogen bonds : bond 0.04481 ( 445) hydrogen bonds : angle 5.07401 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.325 Fit side-chains REVERT: B 96 ARG cc_start: 0.8228 (ptp-170) cc_final: 0.7913 (mtt180) REVERT: B 188 MET cc_start: 0.8512 (mmm) cc_final: 0.8199 (mmp) REVERT: B 269 ILE cc_start: 0.8233 (pt) cc_final: 0.7845 (pp) REVERT: G 38 MET cc_start: 0.7836 (mtm) cc_final: 0.7593 (ttm) REVERT: S 69 THR cc_start: 0.8096 (t) cc_final: 0.7862 (m) REVERT: S 85 SER cc_start: 0.8566 (t) cc_final: 0.8182 (p) REVERT: S 128 MET cc_start: 0.8766 (mmp) cc_final: 0.8547 (tpp) REVERT: R 132 PHE cc_start: 0.8245 (m-80) cc_final: 0.7876 (m-80) REVERT: R 173 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7775 (t80) REVERT: R 182 GLN cc_start: 0.7693 (mt0) cc_final: 0.7471 (mt0) REVERT: R 249 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7697 (mt) outliers start: 29 outliers final: 15 residues processed: 227 average time/residue: 0.4767 time to fit residues: 116.6468 Evaluate side-chains 228 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 125 ASN B 293 ASN S 130 GLN R 104 ASN R 179 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107407 restraints weight = 12552.079| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.53 r_work: 0.3422 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8743 Z= 0.149 Angle : 0.538 7.990 11923 Z= 0.290 Chirality : 0.042 0.152 1383 Planarity : 0.004 0.046 1511 Dihedral : 4.898 41.083 1233 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.05 % Allowed : 19.48 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.38 (0.25), residues: 1122 helix: 1.62 (0.28), residues: 375 sheet: 0.02 (0.30), residues: 278 loop : -0.66 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 380 TYR 0.027 0.002 TYR R 268 PHE 0.020 0.002 PHE S 68 TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8740) covalent geometry : angle 0.53834 (11917) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.69495 ( 6) hydrogen bonds : bond 0.03825 ( 445) hydrogen bonds : angle 4.86060 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.320 Fit side-chains REVERT: A 29 GLN cc_start: 0.8390 (tp40) cc_final: 0.8127 (mm-40) REVERT: B 96 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7863 (mtt180) REVERT: B 188 MET cc_start: 0.8482 (mmm) cc_final: 0.8190 (mmp) REVERT: B 269 ILE cc_start: 0.8299 (pt) cc_final: 0.7907 (pp) REVERT: G 38 MET cc_start: 0.7730 (mtm) cc_final: 0.7486 (ttp) REVERT: S 85 SER cc_start: 0.8615 (t) cc_final: 0.8241 (p) REVERT: S 128 MET cc_start: 0.8774 (mmp) cc_final: 0.8546 (tpp) REVERT: R 132 PHE cc_start: 0.8222 (m-80) cc_final: 0.7864 (m-80) REVERT: R 173 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7721 (t80) outliers start: 26 outliers final: 13 residues processed: 219 average time/residue: 0.4728 time to fit residues: 111.5443 Evaluate side-chains 225 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 390 GLN B 125 ASN B 293 ASN S 130 GLN R 179 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106674 restraints weight = 12580.730| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.53 r_work: 0.3405 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8743 Z= 0.171 Angle : 0.552 8.365 11923 Z= 0.296 Chirality : 0.042 0.166 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.870 37.370 1233 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.40 % Allowed : 20.19 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.38 (0.25), residues: 1122 helix: 1.53 (0.28), residues: 381 sheet: -0.01 (0.30), residues: 283 loop : -0.60 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 380 TYR 0.021 0.002 TYR R 268 PHE 0.025 0.002 PHE S 68 TRP 0.017 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8740) covalent geometry : angle 0.55241 (11917) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.70939 ( 6) hydrogen bonds : bond 0.03940 ( 445) hydrogen bonds : angle 4.83674 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.338 Fit side-chains REVERT: B 59 TYR cc_start: 0.8086 (m-80) cc_final: 0.7702 (m-80) REVERT: B 188 MET cc_start: 0.8469 (mmm) cc_final: 0.8190 (mmp) REVERT: B 269 ILE cc_start: 0.8257 (pt) cc_final: 0.7862 (pp) REVERT: B 314 ARG cc_start: 0.8298 (ttt180) cc_final: 0.7962 (ttt180) REVERT: G 38 MET cc_start: 0.7733 (mtm) cc_final: 0.7475 (ttp) REVERT: S 85 SER cc_start: 0.8630 (t) cc_final: 0.8403 (t) REVERT: S 128 MET cc_start: 0.8782 (mmp) cc_final: 0.8558 (tpp) REVERT: R 33 VAL cc_start: 0.7960 (t) cc_final: 0.7745 (p) REVERT: R 132 PHE cc_start: 0.8212 (m-80) cc_final: 0.7827 (m-80) REVERT: R 173 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7745 (t80) REVERT: R 179 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7792 (mt0) outliers start: 29 outliers final: 15 residues processed: 226 average time/residue: 0.4746 time to fit residues: 115.4638 Evaluate side-chains 232 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 173 PHE Chi-restraints excluded: chain R residue 179 GLN Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 15 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 125 ASN S 130 GLN R 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106474 restraints weight = 12756.245| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.55 r_work: 0.3408 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8743 Z= 0.178 Angle : 0.553 7.057 11923 Z= 0.300 Chirality : 0.042 0.161 1383 Planarity : 0.004 0.045 1511 Dihedral : 4.867 34.809 1233 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.05 % Allowed : 20.31 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.38 (0.26), residues: 1122 helix: 1.53 (0.28), residues: 382 sheet: -0.02 (0.30), residues: 283 loop : -0.58 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 380 TYR 0.024 0.002 TYR R 155 PHE 0.025 0.002 PHE S 68 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8740) covalent geometry : angle 0.55253 (11917) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.74753 ( 6) hydrogen bonds : bond 0.03963 ( 445) hydrogen bonds : angle 4.82516 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.383 Fit side-chains REVERT: B 59 TYR cc_start: 0.8108 (m-80) cc_final: 0.7729 (m-80) REVERT: B 188 MET cc_start: 0.8512 (mmm) cc_final: 0.8225 (mmp) REVERT: B 269 ILE cc_start: 0.8258 (pt) cc_final: 0.7864 (pp) REVERT: G 38 MET cc_start: 0.7748 (mtm) cc_final: 0.7488 (ttp) REVERT: S 85 SER cc_start: 0.8640 (t) cc_final: 0.8408 (t) REVERT: S 128 MET cc_start: 0.8784 (mmp) cc_final: 0.8518 (tpp) REVERT: R 33 VAL cc_start: 0.7968 (t) cc_final: 0.7748 (p) REVERT: R 132 PHE cc_start: 0.8224 (m-80) cc_final: 0.7840 (m-80) REVERT: R 179 GLN cc_start: 0.7991 (mt0) cc_final: 0.7779 (mt0) outliers start: 26 outliers final: 18 residues processed: 220 average time/residue: 0.4397 time to fit residues: 104.1731 Evaluate side-chains 229 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 294 GLN A 390 GLN B 119 ASN B 125 ASN S 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105348 restraints weight = 12565.133| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.53 r_work: 0.3383 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8743 Z= 0.248 Angle : 0.597 7.075 11923 Z= 0.322 Chirality : 0.044 0.189 1383 Planarity : 0.004 0.046 1511 Dihedral : 5.021 31.180 1233 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 21.01 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1122 helix: 1.40 (0.28), residues: 381 sheet: -0.07 (0.29), residues: 292 loop : -0.63 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 380 TYR 0.023 0.002 TYR R 155 PHE 0.035 0.002 PHE S 68 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 8740) covalent geometry : angle 0.59639 (11917) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.94746 ( 6) hydrogen bonds : bond 0.04339 ( 445) hydrogen bonds : angle 4.95198 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.307 Fit side-chains REVERT: B 96 ARG cc_start: 0.8234 (ptp-170) cc_final: 0.7908 (mtt180) REVERT: B 188 MET cc_start: 0.8490 (mmm) cc_final: 0.8197 (mmp) REVERT: B 269 ILE cc_start: 0.8232 (pt) cc_final: 0.7838 (pp) REVERT: G 38 MET cc_start: 0.7785 (mtm) cc_final: 0.7548 (ttm) REVERT: S 85 SER cc_start: 0.8635 (t) cc_final: 0.8406 (t) REVERT: S 128 MET cc_start: 0.8781 (mmp) cc_final: 0.8509 (tpp) REVERT: R 33 VAL cc_start: 0.8022 (t) cc_final: 0.7810 (p) REVERT: R 132 PHE cc_start: 0.8251 (m-80) cc_final: 0.7915 (m-80) REVERT: R 179 GLN cc_start: 0.8070 (mt0) cc_final: 0.7838 (mt0) REVERT: R 235 VAL cc_start: 0.8529 (t) cc_final: 0.8328 (p) outliers start: 22 outliers final: 16 residues processed: 222 average time/residue: 0.4507 time to fit residues: 107.6900 Evaluate side-chains 231 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 125 ASN R 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106264 restraints weight = 12447.790| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.52 r_work: 0.3407 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8743 Z= 0.195 Angle : 0.575 7.383 11923 Z= 0.312 Chirality : 0.043 0.174 1383 Planarity : 0.004 0.047 1511 Dihedral : 4.935 28.425 1233 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.58 % Allowed : 20.66 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.25 (0.25), residues: 1122 helix: 1.45 (0.28), residues: 381 sheet: -0.14 (0.30), residues: 285 loop : -0.65 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 380 TYR 0.022 0.002 TYR R 155 PHE 0.043 0.002 PHE S 68 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8740) covalent geometry : angle 0.57371 (11917) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.80156 ( 6) hydrogen bonds : bond 0.04079 ( 445) hydrogen bonds : angle 4.90027 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.487 Fit side-chains REVERT: A 29 GLN cc_start: 0.8432 (tp40) cc_final: 0.8175 (mm-40) REVERT: B 96 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.7890 (mtt180) REVERT: B 188 MET cc_start: 0.8507 (mmm) cc_final: 0.8219 (mmp) REVERT: B 269 ILE cc_start: 0.8265 (pt) cc_final: 0.7872 (pp) REVERT: G 38 MET cc_start: 0.7772 (mtm) cc_final: 0.7534 (ttm) REVERT: S 85 SER cc_start: 0.8656 (t) cc_final: 0.8423 (t) REVERT: S 128 MET cc_start: 0.8773 (mmp) cc_final: 0.8506 (tpp) REVERT: R 33 VAL cc_start: 0.8009 (t) cc_final: 0.7792 (p) REVERT: R 132 PHE cc_start: 0.8258 (m-80) cc_final: 0.7926 (m-80) REVERT: R 179 GLN cc_start: 0.8050 (mt0) cc_final: 0.7844 (mt0) outliers start: 22 outliers final: 16 residues processed: 220 average time/residue: 0.4594 time to fit residues: 109.0174 Evaluate side-chains 232 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 161 GLU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.119269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108697 restraints weight = 12289.784| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.50 r_work: 0.3439 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8743 Z= 0.135 Angle : 0.543 6.960 11923 Z= 0.295 Chirality : 0.042 0.153 1383 Planarity : 0.004 0.047 1511 Dihedral : 4.801 27.361 1233 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.00 % Allowed : 21.24 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.35 (0.25), residues: 1122 helix: 1.61 (0.28), residues: 379 sheet: -0.11 (0.30), residues: 284 loop : -0.65 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.021 0.002 TYR R 155 PHE 0.043 0.002 PHE S 68 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8740) covalent geometry : angle 0.54205 (11917) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.44856 ( 6) hydrogen bonds : bond 0.03752 ( 445) hydrogen bonds : angle 4.76765 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.316 Fit side-chains REVERT: B 96 ARG cc_start: 0.8148 (ptp-170) cc_final: 0.7799 (mtt180) REVERT: B 188 MET cc_start: 0.8450 (mmm) cc_final: 0.8175 (mmp) REVERT: B 269 ILE cc_start: 0.8258 (pt) cc_final: 0.7873 (pp) REVERT: G 38 MET cc_start: 0.7722 (mtm) cc_final: 0.7451 (ttp) REVERT: S 128 MET cc_start: 0.8753 (mmp) cc_final: 0.8480 (tpp) REVERT: R 132 PHE cc_start: 0.8187 (m-80) cc_final: 0.7827 (m-80) REVERT: R 173 PHE cc_start: 0.7676 (t80) cc_final: 0.7475 (t80) outliers start: 17 outliers final: 12 residues processed: 209 average time/residue: 0.4681 time to fit residues: 105.1049 Evaluate side-chains 214 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 71 optimal weight: 0.0570 chunk 88 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** R 269 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.118597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107978 restraints weight = 12358.033| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.52 r_work: 0.3421 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8743 Z= 0.161 Angle : 0.562 6.823 11923 Z= 0.304 Chirality : 0.042 0.169 1383 Planarity : 0.004 0.046 1511 Dihedral : 4.701 23.254 1230 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.64 % Allowed : 22.65 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.32 (0.25), residues: 1122 helix: 1.51 (0.28), residues: 382 sheet: -0.08 (0.30), residues: 283 loop : -0.64 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 380 TYR 0.021 0.002 TYR R 268 PHE 0.038 0.002 PHE S 68 TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8740) covalent geometry : angle 0.56125 (11917) SS BOND : bond 0.00201 ( 3) SS BOND : angle 1.48774 ( 6) hydrogen bonds : bond 0.03847 ( 445) hydrogen bonds : angle 4.77112 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.82 seconds wall clock time: 66 minutes 2.20 seconds (3962.20 seconds total)