Starting phenix.real_space_refine on Thu Jul 2 07:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjh_33227/07_2026/7xjh_33227.cif" } resolution = 3.3 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= 0.011 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 46 5.16 5 C 4962 2.51 5 N 1378 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2047 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.19 Number of scatterers: 7832 At special positions: 0 Unit cell: (96.3829, 120.479, 86.5255, 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 46 16.00 O 1446 8.00 N 1378 7.00 C 4962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " 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: 0.50 Conformation dependent library (CDL) restraints added in 360.8 milliseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 43.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.699A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.662A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 341 Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.888A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.644A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.674A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.513A pdb=" N ALA R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 Processing helix chain 'R' and resid 70 through 90 removed outlier: 3.528A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.784A pdb=" N SER R 124 " --> pdb=" O CYS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.549A pdb=" N MET R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 288 through 318 removed outlier: 3.900A pdb=" N ARG R 292 " --> pdb=" O HIS R 288 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 342 Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 349 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.319A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.725A 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: 6.043A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.053A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.057A 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: 6.684A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.259A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.244A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1200 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: 1.05 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2581 1.34 - 1.46: 1625 1.46 - 1.58: 3719 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7986 Sorted by residual: bond pdb=" CA SER N 21 " pdb=" CB SER N 21 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 6.99e+00 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" C LEU R 306 " pdb=" N PRO R 307 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.19e-02 7.06e+03 1.79e+00 ... (remaining 7981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10580 1.53 - 3.07: 224 3.07 - 4.60: 38 4.60 - 6.13: 13 6.13 - 7.67: 3 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 108.55 113.15 -4.60 1.62e+00 3.81e-01 8.07e+00 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta sigma weight residual 110.28 114.64 -4.36 1.55e+00 4.16e-01 7.90e+00 angle pdb=" CA SER N 21 " pdb=" C SER N 21 " pdb=" O SER N 21 " ideal model delta sigma weight residual 121.16 118.03 3.13 1.13e+00 7.83e-01 7.66e+00 angle pdb=" C LEU N 20 " pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 122.87 118.94 3.93 1.61e+00 3.86e-01 5.95e+00 angle pdb=" C LEU R 89 " pdb=" N VAL R 90 " pdb=" CA VAL R 90 " ideal model delta sigma weight residual 122.63 119.81 2.82 1.19e+00 7.06e-01 5.60e+00 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4298 17.97 - 35.93: 379 35.93 - 53.90: 58 53.90 - 71.87: 9 71.87 - 89.83: 8 Dihedral angle restraints: 4752 sinusoidal: 1776 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -133.54 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 134.21 -41.21 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 4749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 967 0.045 - 0.090: 220 0.090 - 0.134: 67 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.52 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1255 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 215 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO R 216 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 323 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO R 324 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 192 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO R 193 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.022 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1016 2.75 - 3.29: 7524 3.29 - 3.83: 13177 3.83 - 4.36: 15228 4.36 - 4.90: 27153 Nonbonded interactions: 64098 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.228 3.040 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.252 3.120 ... (remaining 64093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.700 Find NCS groups from input model: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7990 Z= 0.142 Angle : 0.586 7.667 10866 Z= 0.316 Chirality : 0.042 0.224 1258 Planarity : 0.004 0.045 1390 Dihedral : 14.013 89.834 2814 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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 are not related in a simple way. whole: 0.45 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 377 sheet: -0.72 (0.33), residues: 212 loop : -1.14 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 19 TYR 0.011 0.001 TYR B 59 PHE 0.023 0.002 PHE A 222 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 7986) covalent geometry : angle 0.58361 / 0.32 (10858) SS BOND : bond 0.00112 / 0.05 ( 4) SS BOND : angle 1.83083 / 0.93 ( 8) hydrogen bonds : bond 0.09914 / 6.82 ( 425) hydrogen bonds : angle 4.87998 / 3.49 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6774 (mtmt) REVERT: A 32 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mtpt) REVERT: A 34 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7769 (tttt) REVERT: A 213 GLN cc_start: 0.7742 (tt0) cc_final: 0.7514 (tt0) REVERT: A 252 ASP cc_start: 0.7055 (t70) cc_final: 0.6826 (t70) REVERT: A 304 GLU cc_start: 0.7674 (pm20) cc_final: 0.7462 (pm20) REVERT: B 42 ARG cc_start: 0.7577 (tmt170) cc_final: 0.6922 (tpt170) REVERT: B 175 GLN cc_start: 0.7772 (mt0) cc_final: 0.7544 (mt0) REVERT: B 226 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8450 (mt-10) REVERT: N 20 LEU cc_start: 0.8028 (mt) cc_final: 0.7764 (mt) REVERT: N 21 SER cc_start: 0.8305 (m) cc_final: 0.7963 (p) REVERT: N 77 ASN cc_start: 0.6830 (m-40) cc_final: 0.6525 (m-40) REVERT: R 236 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6406 (mtm110) REVERT: R 240 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7003 (ttm170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0823 time to fit residues: 17.5719 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 284 GLN B 220 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116769 restraints weight = 9101.773| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.73 r_work: 0.3099 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7990 Z= 0.199 Angle : 0.609 8.072 10866 Z= 0.318 Chirality : 0.044 0.161 1258 Planarity : 0.005 0.054 1390 Dihedral : 4.469 30.276 1116 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.47 % Allowed : 8.10 % Favored : 90.43 % 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 are not related in a simple way. whole: 0.37 (0.26), residues: 1011 helix: 2.14 (0.26), residues: 381 sheet: -0.61 (0.34), residues: 206 loop : -1.07 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 19 TYR 0.014 0.002 TYR B 59 PHE 0.017 0.002 PHE R 309 TRP 0.012 0.002 TRP B 63 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 7986) covalent geometry : angle 0.60790 / 0.32 (10858) SS BOND : bond 0.00138 / 0.07 ( 4) SS BOND : angle 1.30252 / 0.69 ( 8) hydrogen bonds : bond 0.04806 / 3.27 ( 425) hydrogen bonds : angle 4.63805 / 3.29 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.247 Fit side-chains REVERT: A 32 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7784 (mtpt) REVERT: A 34 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8203 (tttt) REVERT: A 252 ASP cc_start: 0.7608 (t70) cc_final: 0.7331 (t70) REVERT: A 342 SER cc_start: 0.8103 (t) cc_final: 0.7900 (p) REVERT: B 42 ARG cc_start: 0.7639 (tmt170) cc_final: 0.6885 (tpt170) REVERT: B 175 GLN cc_start: 0.8162 (mt0) cc_final: 0.7957 (mt0) REVERT: B 259 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7932 (mm-40) REVERT: N 20 LEU cc_start: 0.8162 (mt) cc_final: 0.7893 (mt) REVERT: N 46 GLU cc_start: 0.8524 (pt0) cc_final: 0.8201 (pt0) REVERT: N 65 LYS cc_start: 0.6675 (ttmm) cc_final: 0.6427 (tptp) REVERT: N 77 ASN cc_start: 0.7043 (m-40) cc_final: 0.6798 (m110) REVERT: R 126 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8424 (mm-30) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.0839 time to fit residues: 14.4333 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114349 restraints weight = 9007.826| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.78 r_work: 0.3077 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7990 Z= 0.200 Angle : 0.598 8.350 10866 Z= 0.313 Chirality : 0.043 0.162 1258 Planarity : 0.005 0.056 1390 Dihedral : 4.523 30.989 1116 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 11.29 % Favored : 86.26 % 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 are not related in a simple way. whole: 0.24 (0.26), residues: 1011 helix: 1.95 (0.26), residues: 388 sheet: -0.55 (0.35), residues: 195 loop : -1.18 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 27 TYR 0.014 0.002 TYR A 381 PHE 0.035 0.002 PHE N 108 TRP 0.014 0.002 TRP B 63 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 7986) covalent geometry : angle 0.59804 / 0.31 (10858) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 0.97623 / 0.53 ( 8) hydrogen bonds : bond 0.04919 / 3.34 ( 425) hydrogen bonds : angle 4.65375 / 3.29 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.169 Fit side-chains REVERT: A 32 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7802 (mtpt) REVERT: A 34 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8189 (tttt) REVERT: A 252 ASP cc_start: 0.7550 (t70) cc_final: 0.7245 (t70) REVERT: A 308 TYR cc_start: 0.7940 (t80) cc_final: 0.7388 (t80) REVERT: A 342 SER cc_start: 0.8066 (t) cc_final: 0.7775 (p) REVERT: B 42 ARG cc_start: 0.7704 (tmt170) cc_final: 0.6909 (tpt170) REVERT: B 175 GLN cc_start: 0.8168 (mt0) cc_final: 0.7957 (mt0) REVERT: B 256 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7246 (mtm110) REVERT: B 259 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7857 (mm-40) REVERT: N 20 LEU cc_start: 0.8128 (mt) cc_final: 0.7882 (mt) REVERT: N 46 GLU cc_start: 0.8581 (pt0) cc_final: 0.8308 (pt0) REVERT: N 65 LYS cc_start: 0.6782 (ttmm) cc_final: 0.6445 (tptp) REVERT: N 77 ASN cc_start: 0.7214 (m-40) cc_final: 0.6931 (m-40) REVERT: R 126 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8440 (mm-30) REVERT: R 211 VAL cc_start: 0.8472 (t) cc_final: 0.8249 (t) outliers start: 20 outliers final: 16 residues processed: 133 average time/residue: 0.0804 time to fit residues: 14.0939 Evaluate side-chains 132 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117946 restraints weight = 9079.173| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.80 r_work: 0.3124 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7990 Z= 0.123 Angle : 0.524 8.968 10866 Z= 0.274 Chirality : 0.041 0.223 1258 Planarity : 0.004 0.051 1390 Dihedral : 4.265 29.226 1116 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.84 % Allowed : 13.87 % Favored : 84.29 % 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 are not related in a simple way. whole: 0.47 (0.27), residues: 1011 helix: 2.21 (0.26), residues: 390 sheet: -0.51 (0.34), residues: 215 loop : -1.11 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 226 TYR 0.014 0.001 TYR A 37 PHE 0.015 0.001 PHE R 308 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7986) covalent geometry : angle 0.52350 / 0.27 (10858) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.90671 / 0.46 ( 8) hydrogen bonds : bond 0.04177 / 2.84 ( 425) hydrogen bonds : angle 4.41812 / 3.13 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.227 Fit side-chains REVERT: A 32 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7781 (mtpt) REVERT: A 230 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 252 ASP cc_start: 0.7503 (t70) cc_final: 0.7184 (t70) REVERT: A 308 TYR cc_start: 0.7899 (t80) cc_final: 0.7171 (t80) REVERT: A 342 SER cc_start: 0.8040 (t) cc_final: 0.7723 (p) REVERT: B 42 ARG cc_start: 0.7604 (tmt170) cc_final: 0.6791 (tpt170) REVERT: B 256 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7238 (mtm110) REVERT: B 259 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7944 (mm-40) REVERT: B 298 ASP cc_start: 0.8284 (t70) cc_final: 0.8057 (t70) REVERT: N 20 LEU cc_start: 0.8098 (mt) cc_final: 0.7828 (mt) REVERT: N 65 LYS cc_start: 0.6807 (ttmm) cc_final: 0.6459 (tptp) REVERT: N 77 ASN cc_start: 0.6989 (m-40) cc_final: 0.6691 (m-40) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 0.0803 time to fit residues: 14.7265 Evaluate side-chains 134 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117097 restraints weight = 8969.835| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.85 r_work: 0.3115 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7990 Z= 0.123 Angle : 0.522 8.868 10866 Z= 0.272 Chirality : 0.041 0.169 1258 Planarity : 0.004 0.049 1390 Dihedral : 4.169 28.516 1116 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.82 % Allowed : 14.36 % Favored : 82.82 % 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 are not related in a simple way. whole: 0.57 (0.27), residues: 1011 helix: 2.31 (0.26), residues: 390 sheet: -0.43 (0.34), residues: 213 loop : -1.10 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.014 0.001 TYR A 37 PHE 0.015 0.001 PHE R 308 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7986) covalent geometry : angle 0.52191 / 0.27 (10858) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.89146 / 0.46 ( 8) hydrogen bonds : bond 0.04119 / 2.80 ( 425) hydrogen bonds : angle 4.34617 / 3.08 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.244 Fit side-chains REVERT: A 32 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7796 (mtpt) REVERT: A 230 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 252 ASP cc_start: 0.7531 (t70) cc_final: 0.7210 (t70) REVERT: A 342 SER cc_start: 0.7983 (t) cc_final: 0.7709 (p) REVERT: B 42 ARG cc_start: 0.7645 (tmt170) cc_final: 0.6801 (tpt170) REVERT: B 256 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7219 (mtm110) REVERT: B 259 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8122 (mm-40) REVERT: N 20 LEU cc_start: 0.8127 (mt) cc_final: 0.7835 (mt) REVERT: N 65 LYS cc_start: 0.6791 (ttmm) cc_final: 0.6464 (tptp) REVERT: N 77 ASN cc_start: 0.6957 (m-40) cc_final: 0.6676 (m-40) REVERT: N 108 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7820 (t80) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.0799 time to fit residues: 15.2901 Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118939 restraints weight = 8939.131| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.80 r_work: 0.3140 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7990 Z= 0.110 Angle : 0.515 8.935 10866 Z= 0.266 Chirality : 0.041 0.351 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.067 27.906 1116 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.82 % Allowed : 14.85 % Favored : 82.33 % 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 are not related in a simple way. whole: 0.67 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 390 sheet: -0.42 (0.34), residues: 214 loop : -1.06 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 7986) covalent geometry : angle 0.51437 / 0.27 (10858) SS BOND : bond 0.00074 / 0.04 ( 4) SS BOND : angle 0.82691 / 0.42 ( 8) hydrogen bonds : bond 0.03898 / 2.65 ( 425) hydrogen bonds : angle 4.25232 / 3.01 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.301 Fit side-chains REVERT: A 32 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7798 (mtpt) REVERT: A 221 MET cc_start: 0.8436 (ttm) cc_final: 0.8218 (ttp) REVERT: A 252 ASP cc_start: 0.7580 (t70) cc_final: 0.7183 (t70) REVERT: A 329 TYR cc_start: 0.8656 (m-80) cc_final: 0.8311 (m-80) REVERT: A 342 SER cc_start: 0.7918 (t) cc_final: 0.7644 (p) REVERT: B 42 ARG cc_start: 0.7683 (tmt170) cc_final: 0.6871 (tpt170) REVERT: B 137 ARG cc_start: 0.8141 (mmt180) cc_final: 0.7934 (tpt170) REVERT: B 256 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7162 (mtm110) REVERT: B 259 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7946 (mm-40) REVERT: N 20 LEU cc_start: 0.8168 (mt) cc_final: 0.7832 (mt) REVERT: N 61 THR cc_start: 0.9048 (t) cc_final: 0.8739 (p) REVERT: N 65 LYS cc_start: 0.6791 (ttmm) cc_final: 0.6476 (tptp) REVERT: N 77 ASN cc_start: 0.6872 (m-40) cc_final: 0.6609 (m-40) REVERT: N 108 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7645 (t80) REVERT: R 68 LEU cc_start: 0.7555 (mt) cc_final: 0.7285 (mt) REVERT: R 345 ILE cc_start: 0.8445 (mt) cc_final: 0.8222 (mt) outliers start: 23 outliers final: 17 residues processed: 144 average time/residue: 0.1021 time to fit residues: 19.6022 Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116472 restraints weight = 8960.092| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.85 r_work: 0.3103 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7990 Z= 0.143 Angle : 0.544 8.689 10866 Z= 0.281 Chirality : 0.042 0.365 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.181 29.210 1116 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.82 % Allowed : 15.09 % Favored : 82.09 % 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 are not related in a simple way. whole: 0.62 (0.27), residues: 1011 helix: 2.34 (0.26), residues: 390 sheet: -0.39 (0.34), residues: 205 loop : -1.05 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.013 0.001 TYR A 37 PHE 0.016 0.001 PHE R 308 TRP 0.011 0.001 TRP B 99 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7986) covalent geometry : angle 0.54360 / 0.28 (10858) SS BOND : bond 0.00107 / 0.05 ( 4) SS BOND : angle 0.92183 / 0.47 ( 8) hydrogen bonds : bond 0.04231 / 2.88 ( 425) hydrogen bonds : angle 4.32726 / 3.06 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.321 Fit side-chains REVERT: A 32 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7821 (mtpt) REVERT: A 221 MET cc_start: 0.8468 (ttm) cc_final: 0.8266 (ttp) REVERT: A 252 ASP cc_start: 0.7615 (t70) cc_final: 0.7133 (t0) REVERT: A 329 TYR cc_start: 0.8781 (m-80) cc_final: 0.8425 (m-80) REVERT: A 342 SER cc_start: 0.7845 (t) cc_final: 0.7557 (p) REVERT: B 42 ARG cc_start: 0.7680 (tmt170) cc_final: 0.6828 (tpt170) REVERT: B 256 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7158 (mtm110) REVERT: B 259 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7905 (mm-40) REVERT: N 20 LEU cc_start: 0.8151 (mt) cc_final: 0.7837 (mt) REVERT: N 65 LYS cc_start: 0.6847 (ttmm) cc_final: 0.6518 (tptp) REVERT: N 77 ASN cc_start: 0.6943 (m-40) cc_final: 0.6683 (m-40) REVERT: N 108 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7957 (t80) REVERT: R 345 ILE cc_start: 0.8455 (mt) cc_final: 0.8241 (mt) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.1021 time to fit residues: 18.9650 Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118992 restraints weight = 9045.659| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.89 r_work: 0.3132 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7990 Z= 0.112 Angle : 0.516 9.011 10866 Z= 0.268 Chirality : 0.042 0.363 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.064 27.708 1116 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.33 % Allowed : 15.58 % Favored : 82.09 % 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 are not related in a simple way. whole: 0.69 (0.27), residues: 1011 helix: 2.40 (0.26), residues: 390 sheet: -0.41 (0.34), residues: 213 loop : -0.99 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.015 0.001 PHE A 212 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7986) covalent geometry : angle 0.51577 / 0.27 (10858) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.81347 / 0.42 ( 8) hydrogen bonds : bond 0.03910 / 2.66 ( 425) hydrogen bonds : angle 4.21839 / 2.99 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.297 Fit side-chains REVERT: A 32 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7760 (mtpt) REVERT: A 252 ASP cc_start: 0.7533 (t70) cc_final: 0.7044 (t0) REVERT: A 308 TYR cc_start: 0.7879 (t80) cc_final: 0.7362 (t80) REVERT: A 329 TYR cc_start: 0.8649 (m-80) cc_final: 0.8318 (m-80) REVERT: A 342 SER cc_start: 0.7751 (t) cc_final: 0.7448 (p) REVERT: B 42 ARG cc_start: 0.7648 (tmt170) cc_final: 0.6827 (tpt170) REVERT: B 137 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7953 (tpt170) REVERT: B 256 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7159 (mtm110) REVERT: B 259 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7980 (mm-40) REVERT: N 20 LEU cc_start: 0.8138 (mt) cc_final: 0.7825 (mt) REVERT: N 60 TYR cc_start: 0.8708 (m-80) cc_final: 0.8438 (m-80) REVERT: N 65 LYS cc_start: 0.6786 (ttmm) cc_final: 0.6489 (tptp) REVERT: N 77 ASN cc_start: 0.6875 (m-40) cc_final: 0.6613 (m-40) REVERT: N 108 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7860 (t80) outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 0.1037 time to fit residues: 19.5175 Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119752 restraints weight = 8960.361| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.81 r_work: 0.3148 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7990 Z= 0.111 Angle : 0.527 9.003 10866 Z= 0.274 Chirality : 0.042 0.387 1258 Planarity : 0.004 0.045 1390 Dihedral : 4.013 27.468 1116 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.21 % Allowed : 15.83 % Favored : 81.96 % 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 are not related in a simple way. whole: 0.70 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 391 sheet: -0.30 (0.34), residues: 211 loop : -1.09 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7986) covalent geometry : angle 0.52689 / 0.27 (10858) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 0.80309 / 0.41 ( 8) hydrogen bonds : bond 0.03908 / 2.65 ( 425) hydrogen bonds : angle 4.23939 / 3.03 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.309 Fit side-chains REVERT: A 32 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7788 (mtpt) REVERT: A 213 GLN cc_start: 0.8404 (tt0) cc_final: 0.8098 (tt0) REVERT: A 252 ASP cc_start: 0.7492 (t70) cc_final: 0.7013 (t0) REVERT: A 329 TYR cc_start: 0.8640 (m-80) cc_final: 0.8305 (m-80) REVERT: A 342 SER cc_start: 0.7721 (t) cc_final: 0.7423 (p) REVERT: B 42 ARG cc_start: 0.7686 (tmt170) cc_final: 0.6844 (tpt170) REVERT: B 137 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7953 (tpt170) REVERT: B 256 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7103 (mtm110) REVERT: B 259 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7997 (mm-40) REVERT: N 20 LEU cc_start: 0.8135 (mt) cc_final: 0.7819 (mt) REVERT: N 65 LYS cc_start: 0.6772 (ttmm) cc_final: 0.6446 (tptp) REVERT: N 77 ASN cc_start: 0.6844 (m-40) cc_final: 0.6590 (m-40) REVERT: N 108 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7845 (t80) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 0.1043 time to fit residues: 19.1648 Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.0570 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121253 restraints weight = 8928.542| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.84 r_work: 0.3164 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7990 Z= 0.108 Angle : 0.524 8.992 10866 Z= 0.271 Chirality : 0.042 0.419 1258 Planarity : 0.004 0.045 1390 Dihedral : 3.936 26.900 1116 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 16.07 % Favored : 81.84 % 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 are not related in a simple way. whole: 0.75 (0.27), residues: 1011 helix: 2.50 (0.26), residues: 391 sheet: -0.32 (0.34), residues: 214 loop : -1.06 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.009 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7986) covalent geometry : angle 0.52363 / 0.27 (10858) SS BOND : bond 0.00068 / 0.03 ( 4) SS BOND : angle 0.75836 / 0.39 ( 8) hydrogen bonds : bond 0.03818 / 2.58 ( 425) hydrogen bonds : angle 4.16922 / 2.97 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.297 Fit side-chains REVERT: A 32 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7742 (mtpt) REVERT: A 213 GLN cc_start: 0.8411 (tt0) cc_final: 0.8109 (tt0) REVERT: A 252 ASP cc_start: 0.7517 (t70) cc_final: 0.6971 (t0) REVERT: A 329 TYR cc_start: 0.8583 (m-80) cc_final: 0.8250 (m-80) REVERT: A 342 SER cc_start: 0.7666 (t) cc_final: 0.7367 (p) REVERT: B 42 ARG cc_start: 0.7668 (tmt170) cc_final: 0.6855 (tpt170) REVERT: B 256 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7069 (mtm110) REVERT: B 259 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7990 (mm-40) REVERT: N 20 LEU cc_start: 0.8095 (mt) cc_final: 0.7769 (mt) REVERT: N 60 TYR cc_start: 0.8634 (m-80) cc_final: 0.8381 (m-80) REVERT: N 65 LYS cc_start: 0.6692 (ttmm) cc_final: 0.6366 (tptp) REVERT: N 77 ASN cc_start: 0.6695 (m-40) cc_final: 0.6447 (m-40) REVERT: N 108 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7816 (t80) outliers start: 17 outliers final: 16 residues processed: 143 average time/residue: 0.1014 time to fit residues: 19.3592 Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 40.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116997 restraints weight = 8990.537| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.88 r_work: 0.3109 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7990 Z= 0.147 Angle : 0.558 8.645 10866 Z= 0.290 Chirality : 0.043 0.426 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.113 27.929 1116 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.09 % Allowed : 16.07 % Favored : 81.84 % 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 are not related in a simple way. whole: 0.65 (0.27), residues: 1011 helix: 2.27 (0.26), residues: 396 sheet: -0.29 (0.34), residues: 215 loop : -1.05 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.013 0.002 TYR A 37 PHE 0.016 0.002 PHE R 308 TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7986) covalent geometry : angle 0.55772 / 0.29 (10858) SS BOND : bond 0.00093 / 0.05 ( 4) SS BOND : angle 0.86917 / 0.45 ( 8) hydrogen bonds : bond 0.04255 / 2.88 ( 425) hydrogen bonds : angle 4.32413 / 3.07 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.13 seconds wall clock time: 34 minutes 17.27 seconds (2057.27 seconds total)