Starting phenix.real_space_refine on Sat Aug 23 01:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.map" model { file = "/net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jln_36401/08_2025/8jln_36401.cif" } resolution = 3.24 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= 0.037 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5814 2.51 5 N 1560 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "S" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1767 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.32, per 1000 atoms: 0.25 Number of scatterers: 9117 At special positions: 0 Unit cell: (107.95, 118.15, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 68 16.00 O 1674 8.00 N 1560 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.86 Conformation dependent library (CDL) restraints added in 341.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.978A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.546A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.086A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.864A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.995A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.623A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.262A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 50 removed outlier: 3.891A pdb=" N HIS R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 84 removed outlier: 3.503A pdb=" N SER R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 127 removed outlier: 3.914A pdb=" N THR R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER R 101 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 178 through 182 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 232 Processing helix chain 'R' and resid 247 through 277 removed outlier: 4.439A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 300 removed outlier: 3.559A pdb=" N ILE R 290 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.814A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 318 removed outlier: 3.572A pdb=" N MET R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.338A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.118A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 45 removed outlier: 4.060A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.333A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.617A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.607A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.754A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.991A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.573A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 59 removed outlier: 6.567A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.765A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 176 Processing sheet with id=AB5, first strand: chain 'S' and resid 189 through 190 409 hydrogen bonds defined for protein. 1179 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: 1.41 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 3889 1.40 - 1.58: 5330 1.58 - 1.76: 0 1.76 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 9322 Sorted by residual: bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.61e+00 bond pdb=" C01 UJF R 401 " pdb=" O01 UJF R 401 " ideal model delta sigma weight residual 1.370 1.396 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.42e+00 bond pdb=" C07 UJF R 401 " pdb=" O02 UJF R 401 " ideal model delta sigma weight residual 1.379 1.402 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.34e-02 5.57e+03 1.20e+00 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12416 2.01 - 4.03: 166 4.03 - 6.04: 27 6.04 - 8.06: 9 8.06 - 10.07: 1 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C LYS Y 20 " pdb=" N MET Y 21 " pdb=" CA MET Y 21 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.18e+01 angle pdb=" N VAL R 176 " pdb=" CA VAL R 176 " pdb=" C VAL R 176 " ideal model delta sigma weight residual 112.98 108.92 4.06 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.81 109.08 2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C ASP R 103 " pdb=" N ILE R 104 " pdb=" CA ILE R 104 " ideal model delta sigma weight residual 120.55 125.28 -4.73 1.60e+00 3.91e-01 8.74e+00 angle pdb=" CA MET Y 21 " pdb=" CB MET Y 21 " pdb=" CG MET Y 21 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 4949 18.14 - 36.29: 478 36.29 - 54.43: 81 54.43 - 72.57: 10 72.57 - 90.72: 9 Dihedral angle restraints: 5527 sinusoidal: 2176 harmonic: 3351 Sorted by residual: dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N ALA A 226 " pdb=" CA ALA A 226 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 911 0.034 - 0.068: 326 0.068 - 0.102: 116 0.102 - 0.136: 46 0.136 - 0.170: 4 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA MET Y 21 " pdb=" N MET Y 21 " pdb=" C MET Y 21 " pdb=" CB MET Y 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB ILE R 280 " pdb=" CA ILE R 280 " pdb=" CG1 ILE R 280 " pdb=" CG2 ILE R 280 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 350 " pdb=" CA THR A 350 " pdb=" OG1 THR A 350 " pdb=" CG2 THR A 350 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1400 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 310 " -0.014 2.00e-02 2.50e+03 1.55e-02 6.03e+00 pdb=" CG TRP R 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP R 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 310 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 310 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO S 151 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO S 107 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.024 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1441 2.76 - 3.31: 8896 3.31 - 3.86: 15061 3.86 - 4.41: 17457 4.41 - 4.96: 30913 Nonbonded interactions: 73768 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU A 21 " pdb=" OG SER S 52 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.288 3.040 ... (remaining 73763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.002 0.032 9325 Z= 0.137 Angle : 0.637 10.073 12625 Z= 0.365 Chirality : 0.043 0.170 1403 Planarity : 0.004 0.051 1597 Dihedral : 14.364 90.715 3358 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.25), residues: 1136 helix: 1.76 (0.27), residues: 396 sheet: -0.03 (0.34), residues: 246 loop : -1.73 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 23 TYR 0.014 0.001 TYR S 103 PHE 0.020 0.001 PHE S 80 TRP 0.042 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9322) covalent geometry : angle 0.63731 (12619) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.56103 ( 6) hydrogen bonds : bond 0.14960 ( 409) hydrogen bonds : angle 5.86706 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.334 Fit side-chains REVERT: B 42 ARG cc_start: 0.7311 (ptm-80) cc_final: 0.6910 (tmt170) REVERT: R 262 ILE cc_start: 0.7961 (tt) cc_final: 0.7675 (tt) REVERT: S 20 LEU cc_start: 0.6905 (mt) cc_final: 0.6616 (mt) REVERT: Y 21 MET cc_start: 0.5427 (pmm) cc_final: 0.4650 (mtp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0865 time to fit residues: 18.8136 Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 35 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.210533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132098 restraints weight = 10095.289| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.91 r_work: 0.3384 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9325 Z= 0.203 Angle : 0.658 8.573 12625 Z= 0.344 Chirality : 0.047 0.167 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.873 71.331 1264 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.42 % Allowed : 8.80 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.40 (0.25), residues: 1136 helix: 1.54 (0.26), residues: 400 sheet: -0.32 (0.34), residues: 252 loop : -1.83 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.018 0.002 TYR S 190 PHE 0.032 0.002 PHE R 165 TRP 0.028 0.002 TRP R 310 HIS 0.007 0.002 HIS S 167 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9322) covalent geometry : angle 0.65756 (12619) SS BOND : bond 0.00418 ( 3) SS BOND : angle 1.11212 ( 6) hydrogen bonds : bond 0.07134 ( 409) hydrogen bonds : angle 4.80621 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7305 (tt0) cc_final: 0.6878 (tm-30) REVERT: B 42 ARG cc_start: 0.7472 (ptm-80) cc_final: 0.6985 (tmt170) REVERT: B 138 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 153 ASP cc_start: 0.8245 (t0) cc_final: 0.7910 (t0) REVERT: B 212 ASP cc_start: 0.7695 (t0) cc_final: 0.7383 (p0) REVERT: B 247 ASP cc_start: 0.8275 (t70) cc_final: 0.7940 (t0) REVERT: R 91 PHE cc_start: 0.8365 (m-80) cc_final: 0.8144 (m-80) REVERT: S 20 LEU cc_start: 0.6882 (mt) cc_final: 0.6585 (mt) REVERT: S 172 THR cc_start: 0.8205 (m) cc_final: 0.7692 (t) REVERT: S 233 LEU cc_start: 0.4911 (tp) cc_final: 0.4645 (tp) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.0902 time to fit residues: 19.6495 Evaluate side-chains 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 0.0770 chunk 73 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 20 ASN R 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.214798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139233 restraints weight = 9684.667| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.37 r_work: 0.3402 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9325 Z= 0.117 Angle : 0.550 10.046 12625 Z= 0.285 Chirality : 0.043 0.216 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.671 73.509 1264 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.11 % Allowed : 13.04 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.25), residues: 1136 helix: 1.84 (0.26), residues: 396 sheet: -0.32 (0.33), residues: 257 loop : -1.82 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.015 0.001 TYR S 190 PHE 0.028 0.001 PHE B 199 TRP 0.023 0.001 TRP R 310 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9322) covalent geometry : angle 0.54966 (12619) SS BOND : bond 0.00324 ( 3) SS BOND : angle 0.64157 ( 6) hydrogen bonds : bond 0.05141 ( 409) hydrogen bonds : angle 4.44011 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7373 (tt0) cc_final: 0.6912 (tm-30) REVERT: B 42 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.7016 (tmt170) REVERT: B 153 ASP cc_start: 0.7798 (t0) cc_final: 0.7534 (t0) REVERT: B 212 ASP cc_start: 0.7639 (t0) cc_final: 0.7197 (p0) REVERT: B 247 ASP cc_start: 0.8320 (t70) cc_final: 0.7874 (t0) REVERT: R 23 ARG cc_start: 0.8095 (mpt-90) cc_final: 0.7860 (mpt180) REVERT: R 69 ASP cc_start: 0.7661 (m-30) cc_final: 0.7429 (m-30) REVERT: S 20 LEU cc_start: 0.7007 (mt) cc_final: 0.6675 (mt) REVERT: S 172 THR cc_start: 0.8114 (m) cc_final: 0.7654 (t) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.0868 time to fit residues: 16.9159 Evaluate side-chains 129 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.210727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143263 restraints weight = 9218.196| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.28 r_work: 0.3387 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9325 Z= 0.152 Angle : 0.566 7.862 12625 Z= 0.297 Chirality : 0.043 0.157 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.699 77.655 1264 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.82 % Allowed : 15.07 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1136 helix: 1.80 (0.26), residues: 399 sheet: -0.37 (0.33), residues: 259 loop : -1.80 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.016 0.001 TYR A 37 PHE 0.035 0.002 PHE R 165 TRP 0.024 0.001 TRP R 310 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9322) covalent geometry : angle 0.56627 (12619) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.67017 ( 6) hydrogen bonds : bond 0.05948 ( 409) hydrogen bonds : angle 4.44834 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7290 (tt0) cc_final: 0.6885 (tm-30) REVERT: B 42 ARG cc_start: 0.7663 (ptm-80) cc_final: 0.7117 (tmt170) REVERT: B 153 ASP cc_start: 0.8134 (t0) cc_final: 0.7862 (t0) REVERT: B 247 ASP cc_start: 0.8331 (t70) cc_final: 0.7748 (t0) REVERT: R 23 ARG cc_start: 0.8131 (mpt-90) cc_final: 0.7892 (mpt180) REVERT: R 69 ASP cc_start: 0.7870 (m-30) cc_final: 0.7598 (m-30) REVERT: R 165 PHE cc_start: 0.8682 (p90) cc_final: 0.8335 (p90) REVERT: S 20 LEU cc_start: 0.7024 (mt) cc_final: 0.6684 (mt) REVERT: S 172 THR cc_start: 0.8101 (m) cc_final: 0.7685 (t) outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 0.0883 time to fit residues: 17.9447 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** B 225 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 = 0.4329 r_free = 0.4329 target = 0.206179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136683 restraints weight = 9217.415| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.72 r_work: 0.3340 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9325 Z= 0.205 Angle : 0.623 7.900 12625 Z= 0.330 Chirality : 0.046 0.165 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.923 83.793 1264 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.83 % Allowed : 16.68 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.50 (0.24), residues: 1136 helix: 1.59 (0.26), residues: 392 sheet: -0.48 (0.33), residues: 253 loop : -1.89 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.016 0.002 TYR S 103 PHE 0.024 0.002 PHE R 165 TRP 0.026 0.002 TRP R 310 HIS 0.005 0.001 HIS R 63 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9322) covalent geometry : angle 0.62300 (12619) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.68504 ( 6) hydrogen bonds : bond 0.07165 ( 409) hydrogen bonds : angle 4.68058 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7013 (mmm) cc_final: 0.6673 (tpt) REVERT: A 209 GLU cc_start: 0.7349 (tt0) cc_final: 0.6929 (tm-30) REVERT: A 333 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8720 (mtp85) REVERT: B 42 ARG cc_start: 0.7681 (ptm-80) cc_final: 0.7211 (tmt170) REVERT: B 153 ASP cc_start: 0.8224 (t0) cc_final: 0.7917 (t0) REVERT: B 247 ASP cc_start: 0.8378 (t70) cc_final: 0.7818 (t0) REVERT: R 23 ARG cc_start: 0.8151 (mpt-90) cc_final: 0.7873 (mpt180) REVERT: R 69 ASP cc_start: 0.7905 (m-30) cc_final: 0.7619 (m-30) REVERT: R 75 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6637 (tt) REVERT: R 161 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7881 (tt) REVERT: R 262 ILE cc_start: 0.8904 (tp) cc_final: 0.8607 (tp) REVERT: S 20 LEU cc_start: 0.7025 (mt) cc_final: 0.6666 (mt) REVERT: S 172 THR cc_start: 0.8180 (m) cc_final: 0.7787 (t) REVERT: S 230 MET cc_start: 0.6397 (tmm) cc_final: 0.6067 (tmm) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.0757 time to fit residues: 17.0734 Evaluate side-chains 153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.209924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137780 restraints weight = 9172.045| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.35 r_work: 0.3398 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9325 Z= 0.125 Angle : 0.547 8.946 12625 Z= 0.286 Chirality : 0.043 0.218 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.736 84.922 1264 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.82 % Allowed : 19.62 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.28 (0.25), residues: 1136 helix: 1.80 (0.26), residues: 394 sheet: -0.41 (0.33), residues: 257 loop : -1.79 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 222 TYR 0.016 0.001 TYR A 37 PHE 0.020 0.001 PHE S 80 TRP 0.029 0.001 TRP R 310 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9322) covalent geometry : angle 0.54663 (12619) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.48126 ( 6) hydrogen bonds : bond 0.05369 ( 409) hydrogen bonds : angle 4.38406 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6920 (mmm) cc_final: 0.6702 (tpt) REVERT: A 209 GLU cc_start: 0.7284 (tt0) cc_final: 0.6917 (tm-30) REVERT: B 42 ARG cc_start: 0.7717 (ptm-80) cc_final: 0.7273 (tmt170) REVERT: B 153 ASP cc_start: 0.8005 (t0) cc_final: 0.7735 (t0) REVERT: B 247 ASP cc_start: 0.8325 (t70) cc_final: 0.7751 (t0) REVERT: R 23 ARG cc_start: 0.8135 (mpt-90) cc_final: 0.7870 (mpt180) REVERT: R 75 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6592 (tt) REVERT: R 161 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7952 (tt) REVERT: R 262 ILE cc_start: 0.8858 (tp) cc_final: 0.8539 (tp) REVERT: S 172 THR cc_start: 0.8113 (m) cc_final: 0.7735 (t) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.0900 time to fit residues: 17.9243 Evaluate side-chains 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.207638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139507 restraints weight = 9205.303| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.29 r_work: 0.3380 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9325 Z= 0.166 Angle : 0.589 9.366 12625 Z= 0.309 Chirality : 0.044 0.211 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.881 87.825 1264 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.22 % Allowed : 19.51 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1136 helix: 1.72 (0.26), residues: 394 sheet: -0.39 (0.33), residues: 258 loop : -1.80 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.017 0.001 TYR A 37 PHE 0.026 0.002 PHE R 165 TRP 0.030 0.002 TRP R 310 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9322) covalent geometry : angle 0.58929 (12619) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.56283 ( 6) hydrogen bonds : bond 0.06225 ( 409) hydrogen bonds : angle 4.51056 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7345 (tt0) cc_final: 0.6928 (tm-30) REVERT: B 42 ARG cc_start: 0.7768 (ptm-80) cc_final: 0.7368 (tmt170) REVERT: B 153 ASP cc_start: 0.8119 (t0) cc_final: 0.7831 (t0) REVERT: B 247 ASP cc_start: 0.8349 (t70) cc_final: 0.7792 (t0) REVERT: B 256 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7867 (mtp180) REVERT: R 23 ARG cc_start: 0.8140 (mpt-90) cc_final: 0.7858 (mpt180) REVERT: R 69 ASP cc_start: 0.7820 (m-30) cc_final: 0.7535 (m-30) REVERT: R 75 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6556 (tt) REVERT: R 161 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7875 (tt) REVERT: R 262 ILE cc_start: 0.8905 (tp) cc_final: 0.8589 (tp) REVERT: S 172 THR cc_start: 0.8165 (m) cc_final: 0.7803 (t) REVERT: Y 21 MET cc_start: 0.6389 (pmm) cc_final: 0.4792 (mtp) outliers start: 22 outliers final: 17 residues processed: 136 average time/residue: 0.0951 time to fit residues: 18.5817 Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 40.0000 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142435 restraints weight = 9215.886| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.07 r_work: 0.3406 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9325 Z= 0.148 Angle : 0.581 9.565 12625 Z= 0.302 Chirality : 0.043 0.191 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.899 88.579 1264 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.33 % Allowed : 20.22 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.30 (0.25), residues: 1136 helix: 1.74 (0.26), residues: 394 sheet: -0.36 (0.33), residues: 258 loop : -1.80 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.017 0.001 TYR A 37 PHE 0.020 0.001 PHE S 80 TRP 0.034 0.002 TRP R 310 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9322) covalent geometry : angle 0.58115 (12619) SS BOND : bond 0.00323 ( 3) SS BOND : angle 0.55503 ( 6) hydrogen bonds : bond 0.05852 ( 409) hydrogen bonds : angle 4.45545 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7507 (tt0) cc_final: 0.7038 (tm-30) REVERT: B 42 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7388 (tmt170) REVERT: B 153 ASP cc_start: 0.8126 (t0) cc_final: 0.7818 (t0) REVERT: B 247 ASP cc_start: 0.8426 (t70) cc_final: 0.7869 (t0) REVERT: B 256 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7859 (mtp180) REVERT: R 23 ARG cc_start: 0.8166 (mpt-90) cc_final: 0.7849 (mpt180) REVERT: R 75 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6668 (tt) REVERT: R 161 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7777 (tt) REVERT: R 262 ILE cc_start: 0.8909 (tp) cc_final: 0.8584 (tp) REVERT: S 172 THR cc_start: 0.8186 (m) cc_final: 0.7823 (t) REVERT: Y 21 MET cc_start: 0.6440 (pmm) cc_final: 0.5056 (mtp) outliers start: 23 outliers final: 19 residues processed: 139 average time/residue: 0.0902 time to fit residues: 18.1190 Evaluate side-chains 147 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.205123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126754 restraints weight = 9296.082| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.83 r_work: 0.3335 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9325 Z= 0.200 Angle : 0.636 10.116 12625 Z= 0.332 Chirality : 0.045 0.194 1403 Planarity : 0.004 0.050 1597 Dihedral : 6.011 89.075 1264 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.43 % Allowed : 20.63 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.50 (0.24), residues: 1136 helix: 1.55 (0.26), residues: 394 sheet: -0.51 (0.32), residues: 260 loop : -1.88 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.016 0.002 TYR A 37 PHE 0.028 0.002 PHE R 165 TRP 0.038 0.002 TRP R 310 HIS 0.005 0.001 HIS R 63 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9322) covalent geometry : angle 0.63623 (12619) SS BOND : bond 0.00404 ( 3) SS BOND : angle 0.65343 ( 6) hydrogen bonds : bond 0.06919 ( 409) hydrogen bonds : angle 4.62796 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7269 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 42 ARG cc_start: 0.7897 (ptm-80) cc_final: 0.7460 (tmt170) REVERT: B 153 ASP cc_start: 0.8287 (t0) cc_final: 0.7968 (t0) REVERT: B 247 ASP cc_start: 0.8354 (t70) cc_final: 0.7794 (t0) REVERT: B 256 ARG cc_start: 0.8182 (mtp180) cc_final: 0.7947 (mtp180) REVERT: R 69 ASP cc_start: 0.7887 (m-30) cc_final: 0.7608 (m-30) REVERT: R 75 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6662 (tt) REVERT: R 161 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7883 (tt) REVERT: R 262 ILE cc_start: 0.8940 (tp) cc_final: 0.8617 (tp) REVERT: S 146 SER cc_start: 0.5652 (m) cc_final: 0.5140 (t) REVERT: S 172 THR cc_start: 0.8180 (m) cc_final: 0.7823 (t) REVERT: Y 21 MET cc_start: 0.6233 (pmm) cc_final: 0.4970 (mtm) outliers start: 24 outliers final: 22 residues processed: 138 average time/residue: 0.0943 time to fit residues: 18.6937 Evaluate side-chains 146 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.210179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132783 restraints weight = 9240.812| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.79 r_work: 0.3389 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9325 Z= 0.121 Angle : 0.573 11.946 12625 Z= 0.294 Chirality : 0.042 0.163 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.881 89.090 1264 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.92 % Allowed : 21.13 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.25), residues: 1136 helix: 1.79 (0.26), residues: 394 sheet: -0.34 (0.33), residues: 255 loop : -1.78 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.018 0.001 TYR A 37 PHE 0.022 0.001 PHE S 80 TRP 0.040 0.002 TRP R 310 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9322) covalent geometry : angle 0.57339 (12619) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.49938 ( 6) hydrogen bonds : bond 0.05196 ( 409) hydrogen bonds : angle 4.34023 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7284 (tt0) cc_final: 0.6888 (tm-30) REVERT: B 42 ARG cc_start: 0.7875 (ptm-80) cc_final: 0.7472 (tmt170) REVERT: B 153 ASP cc_start: 0.7852 (t0) cc_final: 0.7547 (t0) REVERT: B 247 ASP cc_start: 0.8294 (t70) cc_final: 0.7737 (t0) REVERT: R 69 ASP cc_start: 0.7680 (m-30) cc_final: 0.7374 (m-30) REVERT: R 75 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6493 (tt) REVERT: R 161 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7820 (tt) REVERT: R 262 ILE cc_start: 0.8854 (tp) cc_final: 0.8511 (tp) REVERT: S 146 SER cc_start: 0.5514 (m) cc_final: 0.4971 (t) REVERT: Y 21 MET cc_start: 0.6184 (pmm) cc_final: 0.4965 (mtm) outliers start: 19 outliers final: 16 residues processed: 139 average time/residue: 0.0856 time to fit residues: 17.4109 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.208511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146459 restraints weight = 9215.914| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.92 r_work: 0.3390 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9325 Z= 0.144 Angle : 0.593 11.932 12625 Z= 0.304 Chirality : 0.043 0.169 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.869 89.774 1264 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.12 % Allowed : 21.03 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.28 (0.25), residues: 1136 helix: 1.75 (0.26), residues: 395 sheet: -0.31 (0.33), residues: 256 loop : -1.80 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.017 0.001 TYR A 37 PHE 0.026 0.002 PHE R 165 TRP 0.045 0.002 TRP R 310 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9322) covalent geometry : angle 0.59300 (12619) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.55380 ( 6) hydrogen bonds : bond 0.05732 ( 409) hydrogen bonds : angle 4.40349 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2819.35 seconds wall clock time: 48 minutes 58.10 seconds (2938.10 seconds total)