Starting phenix.real_space_refine on Wed Feb 4 17:10:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igz_52862/02_2026/9igz_52862.map" } resolution = 3.5 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= 0.057 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 52 5.16 5 C 7470 2.51 5 N 1992 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11676 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2946 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 360} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2892 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 354} Chain breaks: 5 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 3, 'HIS:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Restraints were copied for chains: B, A Time building chain proxies: 3.30, per 1000 atoms: 0.28 Number of scatterers: 11676 At special positions: 0 Unit cell: (155.196, 107.808, 80.5596, 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 52 16.00 O 2162 8.00 N 1992 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 331 " 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: 0.93 Conformation dependent library (CDL) restraints added in 583.9 milliseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 44.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 75 through 89 Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 214 through 229 Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.676A pdb=" N ILE D 247 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.530A pdb=" N LYS D 281 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 341 through 351 Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.542A pdb=" N ARG C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.710A pdb=" N SER C 108 " --> pdb=" O HIS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 190 through 205 Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.598A pdb=" N ILE C 247 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.868A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.966A pdb=" N ILE C 343 " --> pdb=" O TRP C 339 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 75 through 89 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 164 through 178 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.675A pdb=" N ILE B 247 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.530A pdb=" N LYS B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.543A pdb=" N ARG A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.709A pdb=" N SER A 108 " --> pdb=" O HIS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 214 through 229 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.598A pdb=" N ILE A 247 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.868A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.966A pdb=" N ILE A 343 " --> pdb=" O TRP A 339 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 63 through 70 removed outlier: 6.014A pdb=" N VAL D 27 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS D 67 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 29 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP D 69 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY D 31 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 93 " --> pdb=" O GLN D 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE D 94 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 182 through 185 removed outlier: 6.153A pdb=" N PHE D 156 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 155 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP D 212 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 157 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE D 262 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL D 259 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET D 374 " --> pdb=" O TYR D 389 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR D 389 " --> pdb=" O MET D 374 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 376 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 353 through 356 Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 70 removed outlier: 6.294A pdb=" N VAL C 27 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N HIS C 67 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE C 29 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP C 69 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY C 31 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N ALA C 93 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN C 28 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N PHE C 95 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY C 30 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 94 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 117 " --> pdb=" O LEU C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 180 through 185 removed outlier: 7.456A pdb=" N CYS C 153 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL C 210 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 155 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP C 212 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 157 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE C 262 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL C 259 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 388 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU C 378 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYS C 386 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS C 380 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 353 through 356 removed outlier: 3.929A pdb=" N GLN C 362 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 70 removed outlier: 6.012A pdb=" N VAL B 27 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N HIS B 67 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 29 " --> pdb=" O HIS B 67 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP B 69 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY B 31 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 93 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 94 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.153A pdb=" N PHE B 156 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 155 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP B 212 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 157 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 262 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 259 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET B 374 " --> pdb=" O TYR B 389 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 389 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 376 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 353 through 356 Processing sheet with id=AB1, first strand: chain 'A' and resid 63 through 70 removed outlier: 6.295A pdb=" N VAL A 27 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N HIS A 67 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A 29 " --> pdb=" O HIS A 67 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP A 69 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A 31 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N ALA A 93 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLN A 28 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N PHE A 95 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 30 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 117 " --> pdb=" O LEU A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 185 removed outlier: 7.456A pdb=" N CYS A 153 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL A 210 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 155 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP A 212 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 157 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 262 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 259 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 388 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 378 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS A 386 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS A 380 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.929A pdb=" N GLN A 362 " --> pdb=" O VAL A 370 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1650 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: 1.89 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3820 1.34 - 1.46: 2808 1.46 - 1.58: 5228 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 11936 Sorted by residual: bond pdb=" CB PRO C 24 " pdb=" CG PRO C 24 " ideal model delta sigma weight residual 1.492 1.527 -0.035 5.00e-02 4.00e+02 4.93e-01 bond pdb=" CB PRO A 24 " pdb=" CG PRO A 24 " ideal model delta sigma weight residual 1.492 1.526 -0.034 5.00e-02 4.00e+02 4.73e-01 bond pdb=" CB PRO B 24 " pdb=" CG PRO B 24 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.19e-01 bond pdb=" CB PRO D 24 " pdb=" CG PRO D 24 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.06e-01 bond pdb=" N ARG C 324 " pdb=" CA ARG C 324 " ideal model delta sigma weight residual 1.458 1.469 -0.011 1.90e-02 2.77e+03 3.62e-01 ... (remaining 11931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 15578 0.89 - 1.77: 459 1.77 - 2.66: 104 2.66 - 3.54: 30 3.54 - 4.43: 9 Bond angle restraints: 16180 Sorted by residual: angle pdb=" C GLY D 126 " pdb=" N GLU D 127 " pdb=" CA GLU D 127 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.81e+00 angle pdb=" C GLY B 126 " pdb=" N GLU B 127 " pdb=" CA GLU B 127 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" C SER C 323 " pdb=" N ARG C 324 " pdb=" CA ARG C 324 " ideal model delta sigma weight residual 121.70 125.14 -3.44 1.80e+00 3.09e-01 3.65e+00 angle pdb=" C SER A 323 " pdb=" N ARG A 324 " pdb=" CA ARG A 324 " ideal model delta sigma weight residual 121.70 125.14 -3.44 1.80e+00 3.09e-01 3.65e+00 angle pdb=" N ARG C 324 " pdb=" CA ARG C 324 " pdb=" C ARG C 324 " ideal model delta sigma weight residual 111.00 115.43 -4.43 2.80e+00 1.28e-01 2.50e+00 ... (remaining 16175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6427 17.61 - 35.21: 509 35.21 - 52.82: 90 52.82 - 70.42: 14 70.42 - 88.03: 8 Dihedral angle restraints: 7048 sinusoidal: 2746 harmonic: 4302 Sorted by residual: dihedral pdb=" CB GLU A 187 " pdb=" CG GLU A 187 " pdb=" CD GLU A 187 " pdb=" OE1 GLU A 187 " ideal model delta sinusoidal sigma weight residual 0.00 80.27 -80.27 1 3.00e+01 1.11e-03 8.86e+00 dihedral pdb=" CB GLU C 187 " pdb=" CG GLU C 187 " pdb=" CD GLU C 187 " pdb=" OE1 GLU C 187 " ideal model delta sinusoidal sigma weight residual 0.00 80.26 -80.26 1 3.00e+01 1.11e-03 8.86e+00 dihedral pdb=" CA LYS A 380 " pdb=" CB LYS A 380 " pdb=" CG LYS A 380 " pdb=" CD LYS A 380 " ideal model delta sinusoidal sigma weight residual -60.00 -108.19 48.19 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1032 0.026 - 0.052: 484 0.052 - 0.078: 172 0.078 - 0.104: 80 0.104 - 0.130: 36 Chirality restraints: 1804 Sorted by residual: chirality pdb=" CA ILE D 118 " pdb=" N ILE D 118 " pdb=" C ILE D 118 " pdb=" CB ILE D 118 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1801 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 324 " 0.183 9.50e-02 1.11e+02 8.25e-02 5.45e+00 pdb=" NE ARG A 324 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 324 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 324 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 324 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 324 " -0.182 9.50e-02 1.11e+02 8.24e-02 5.41e+00 pdb=" NE ARG C 324 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 324 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 324 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 324 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 65 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO C 66 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " 0.016 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3482 2.82 - 3.34: 11106 3.34 - 3.86: 19836 3.86 - 4.38: 22106 4.38 - 4.90: 38124 Nonbonded interactions: 94654 Sorted by model distance: nonbonded pdb=" O ILE A 34 " pdb=" OG1 THR A 37 " model vdw 2.299 3.040 nonbonded pdb=" O ILE C 34 " pdb=" OG1 THR C 37 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASN D 190 " pdb=" OG SER D 193 " model vdw 2.331 3.040 nonbonded pdb=" OD1 ASN B 190 " pdb=" OG SER B 193 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR B 149 " pdb=" OE2 GLU B 378 " model vdw 2.334 3.040 ... (remaining 94649 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'A' } 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 group one per residue 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.870 Find NCS groups from input model: 0.080 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 0.035 11940 Z= 0.078 Angle : 0.396 4.427 16188 Z= 0.208 Chirality : 0.039 0.130 1804 Planarity : 0.004 0.083 2080 Dihedral : 13.135 88.029 4260 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1448 helix: 2.20 (0.20), residues: 656 sheet: -0.21 (0.33), residues: 256 loop : -0.62 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 324 TYR 0.009 0.001 TYR A 98 PHE 0.010 0.001 PHE B 189 TRP 0.006 0.001 TRP C 279 HIS 0.002 0.001 HIS D 114 Details of bonding type rmsd covalent geometry : bond 0.00185 (11936) covalent geometry : angle 0.39559 (16180) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.50789 ( 8) hydrogen bonds : bond 0.13936 ( 562) hydrogen bonds : angle 5.27945 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: C 231 HIS cc_start: 0.6563 (p-80) cc_final: 0.6102 (p-80) REVERT: C 389 TYR cc_start: 0.6570 (p90) cc_final: 0.6289 (p90) REVERT: A 389 TYR cc_start: 0.6564 (p90) cc_final: 0.6268 (p90) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1083 time to fit residues: 21.7912 Evaluate side-chains 88 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 ASN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.124980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104316 restraints weight = 22655.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107180 restraints weight = 15314.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.110157 restraints weight = 10151.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110447 restraints weight = 7211.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110914 restraints weight = 6931.149| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11940 Z= 0.184 Angle : 0.517 6.506 16188 Z= 0.273 Chirality : 0.043 0.149 1804 Planarity : 0.004 0.055 2080 Dihedral : 3.600 13.437 1600 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.89 % Allowed : 6.52 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.93 (0.23), residues: 1448 helix: 2.12 (0.20), residues: 660 sheet: -0.43 (0.32), residues: 256 loop : -0.74 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 324 TYR 0.021 0.002 TYR A 302 PHE 0.017 0.002 PHE B 189 TRP 0.010 0.001 TRP C 279 HIS 0.005 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00430 (11936) covalent geometry : angle 0.51746 (16180) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.44800 ( 8) hydrogen bonds : bond 0.03579 ( 562) hydrogen bonds : angle 4.45795 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: D 42 THR cc_start: 0.8966 (p) cc_final: 0.8712 (p) REVERT: C 89 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6952 (mpp80) REVERT: C 171 MET cc_start: 0.7626 (mmp) cc_final: 0.7277 (mmp) REVERT: C 389 TYR cc_start: 0.6485 (p90) cc_final: 0.6249 (p90) REVERT: B 42 THR cc_start: 0.8955 (p) cc_final: 0.8713 (p) REVERT: A 89 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7013 (mpp80) REVERT: A 389 TYR cc_start: 0.6470 (p90) cc_final: 0.6231 (p90) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.0921 time to fit residues: 14.6178 Evaluate side-chains 97 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 374 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 83 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 ASN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105891 restraints weight = 22600.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109486 restraints weight = 16619.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111457 restraints weight = 10213.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112072 restraints weight = 7451.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.112711 restraints weight = 7154.758| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11940 Z= 0.104 Angle : 0.435 8.014 16188 Z= 0.229 Chirality : 0.040 0.138 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.394 14.131 1600 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.48 % Allowed : 8.62 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1448 helix: 2.27 (0.20), residues: 662 sheet: -0.50 (0.32), residues: 256 loop : -0.61 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.011 0.001 TYR C 302 PHE 0.013 0.001 PHE D 312 TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00240 (11936) covalent geometry : angle 0.43486 (16180) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.49068 ( 8) hydrogen bonds : bond 0.03050 ( 562) hydrogen bonds : angle 4.14694 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: C 171 MET cc_start: 0.7580 (mmp) cc_final: 0.7274 (mmp) REVERT: C 231 HIS cc_start: 0.6561 (p-80) cc_final: 0.6298 (p-80) REVERT: C 389 TYR cc_start: 0.6478 (p90) cc_final: 0.6245 (p90) REVERT: A 171 MET cc_start: 0.7426 (mmp) cc_final: 0.7100 (mmp) REVERT: A 389 TYR cc_start: 0.6491 (p90) cc_final: 0.6247 (p90) outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.0663 time to fit residues: 11.6467 Evaluate side-chains 94 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 HIS ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104828 restraints weight = 22743.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108318 restraints weight = 13500.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.110775 restraints weight = 9506.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112486 restraints weight = 7420.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.113608 restraints weight = 6194.345| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.115 Angle : 0.446 8.572 16188 Z= 0.232 Chirality : 0.040 0.138 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.364 14.021 1600 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.81 % Allowed : 10.87 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1448 helix: 2.28 (0.20), residues: 660 sheet: -0.60 (0.32), residues: 256 loop : -0.62 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.013 0.001 TYR A 302 PHE 0.012 0.001 PHE D 312 TRP 0.009 0.001 TRP C 279 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00271 (11936) covalent geometry : angle 0.44595 (16180) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.45385 ( 8) hydrogen bonds : bond 0.02865 ( 562) hydrogen bonds : angle 4.10277 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: C 171 MET cc_start: 0.7495 (mmp) cc_final: 0.7164 (mmp) REVERT: C 231 HIS cc_start: 0.6523 (p-80) cc_final: 0.6315 (p-80) REVERT: C 389 TYR cc_start: 0.6461 (p90) cc_final: 0.6248 (p90) REVERT: B 308 MET cc_start: 0.8206 (mtt) cc_final: 0.7875 (mtt) REVERT: A 171 MET cc_start: 0.7560 (mmp) cc_final: 0.7199 (mmp) REVERT: A 389 TYR cc_start: 0.6444 (p90) cc_final: 0.6228 (p90) outliers start: 10 outliers final: 4 residues processed: 109 average time/residue: 0.0701 time to fit residues: 12.8885 Evaluate side-chains 100 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.125286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104729 restraints weight = 22675.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107327 restraints weight = 15470.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108608 restraints weight = 10710.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110338 restraints weight = 8873.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111279 restraints weight = 7807.276| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.148 Angle : 0.486 10.004 16188 Z= 0.251 Chirality : 0.041 0.136 1804 Planarity : 0.003 0.032 2080 Dihedral : 3.485 16.602 1600 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 11.03 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.95 (0.23), residues: 1448 helix: 2.21 (0.20), residues: 660 sheet: -0.61 (0.32), residues: 252 loop : -0.73 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.016 0.002 TYR A 302 PHE 0.015 0.001 PHE D 312 TRP 0.009 0.001 TRP A 279 HIS 0.004 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00348 (11936) covalent geometry : angle 0.48650 (16180) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.44829 ( 8) hydrogen bonds : bond 0.02969 ( 562) hydrogen bonds : angle 4.17702 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.518 Fit side-chains REVERT: D 308 MET cc_start: 0.8040 (mtt) cc_final: 0.7785 (mtt) REVERT: C 171 MET cc_start: 0.7585 (mmp) cc_final: 0.7173 (mmp) REVERT: C 389 TYR cc_start: 0.6508 (p90) cc_final: 0.6273 (p90) REVERT: B 308 MET cc_start: 0.8079 (mtt) cc_final: 0.7803 (mtt) REVERT: A 171 MET cc_start: 0.7675 (mmp) cc_final: 0.7238 (mmp) REVERT: A 231 HIS cc_start: 0.6651 (p-80) cc_final: 0.6399 (p-80) REVERT: A 389 TYR cc_start: 0.6500 (p90) cc_final: 0.6260 (p90) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.0704 time to fit residues: 13.6617 Evaluate side-chains 104 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 100 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.0070 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105284 restraints weight = 22671.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108845 restraints weight = 16558.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110671 restraints weight = 10252.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111790 restraints weight = 7518.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.112363 restraints weight = 6970.443| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.117 Angle : 0.468 10.512 16188 Z= 0.239 Chirality : 0.041 0.191 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.439 16.456 1600 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.13 % Allowed : 12.00 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.98 (0.23), residues: 1448 helix: 2.23 (0.20), residues: 660 sheet: -0.59 (0.32), residues: 252 loop : -0.71 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.012 0.001 TYR C 302 PHE 0.016 0.001 PHE B 312 TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00277 (11936) covalent geometry : angle 0.46777 (16180) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.45199 ( 8) hydrogen bonds : bond 0.02837 ( 562) hydrogen bonds : angle 4.08845 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.301 Fit side-chains REVERT: D 308 MET cc_start: 0.8057 (mtt) cc_final: 0.7736 (mtt) REVERT: C 171 MET cc_start: 0.7630 (mmp) cc_final: 0.7216 (mmp) REVERT: C 389 TYR cc_start: 0.6506 (p90) cc_final: 0.6235 (p90) REVERT: A 171 MET cc_start: 0.7756 (mmp) cc_final: 0.7354 (mmp) REVERT: A 389 TYR cc_start: 0.6490 (p90) cc_final: 0.6222 (p90) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.0643 time to fit residues: 12.0018 Evaluate side-chains 100 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 77 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105920 restraints weight = 22597.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109520 restraints weight = 16431.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.111244 restraints weight = 10273.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112446 restraints weight = 7579.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112913 restraints weight = 7003.440| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11940 Z= 0.103 Angle : 0.459 11.141 16188 Z= 0.236 Chirality : 0.040 0.134 1804 Planarity : 0.003 0.030 2080 Dihedral : 3.372 16.073 1600 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.21 % Allowed : 12.88 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1448 helix: 2.27 (0.20), residues: 660 sheet: -0.55 (0.32), residues: 252 loop : -0.71 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.011 0.001 TYR D 98 PHE 0.014 0.001 PHE B 312 TRP 0.009 0.001 TRP C 279 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00246 (11936) covalent geometry : angle 0.45868 (16180) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.42881 ( 8) hydrogen bonds : bond 0.02728 ( 562) hydrogen bonds : angle 4.00578 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.322 Fit side-chains REVERT: C 171 MET cc_start: 0.7604 (mmp) cc_final: 0.7192 (mmp) REVERT: C 389 TYR cc_start: 0.6489 (p90) cc_final: 0.6257 (p90) REVERT: A 171 MET cc_start: 0.7731 (mmp) cc_final: 0.7297 (mmp) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.0639 time to fit residues: 11.9417 Evaluate side-chains 104 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 145 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104967 restraints weight = 22673.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108564 restraints weight = 16157.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110402 restraints weight = 10209.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110990 restraints weight = 7500.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111590 restraints weight = 7248.650| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.125 Angle : 0.471 11.576 16188 Z= 0.241 Chirality : 0.040 0.136 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.418 16.372 1600 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.21 % Allowed : 13.12 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.97 (0.23), residues: 1448 helix: 2.22 (0.20), residues: 660 sheet: -0.59 (0.32), residues: 252 loop : -0.73 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.013 0.001 TYR A 302 PHE 0.014 0.001 PHE B 312 TRP 0.010 0.001 TRP A 279 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00299 (11936) covalent geometry : angle 0.47117 (16180) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.42543 ( 8) hydrogen bonds : bond 0.02771 ( 562) hydrogen bonds : angle 4.04024 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.457 Fit side-chains REVERT: C 171 MET cc_start: 0.7630 (mmp) cc_final: 0.7198 (mmp) REVERT: C 389 TYR cc_start: 0.6468 (p90) cc_final: 0.6267 (p90) REVERT: A 171 MET cc_start: 0.7749 (mmp) cc_final: 0.7335 (mmp) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.0623 time to fit residues: 11.4793 Evaluate side-chains 106 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106179 restraints weight = 22485.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109882 restraints weight = 16033.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111501 restraints weight = 10268.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.112289 restraints weight = 7561.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112955 restraints weight = 7145.793| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11940 Z= 0.100 Angle : 0.463 12.068 16188 Z= 0.236 Chirality : 0.040 0.141 1804 Planarity : 0.003 0.030 2080 Dihedral : 3.347 15.729 1600 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 13.45 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1448 helix: 2.26 (0.20), residues: 660 sheet: -0.51 (0.33), residues: 252 loop : -0.71 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 89 TYR 0.011 0.001 TYR A 87 PHE 0.012 0.001 PHE B 312 TRP 0.010 0.001 TRP C 279 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00240 (11936) covalent geometry : angle 0.46307 (16180) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.41501 ( 8) hydrogen bonds : bond 0.02697 ( 562) hydrogen bonds : angle 3.95649 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.575 Fit side-chains REVERT: C 171 MET cc_start: 0.7668 (mmp) cc_final: 0.7283 (mmp) REVERT: A 171 MET cc_start: 0.7709 (mmp) cc_final: 0.7305 (mmp) outliers start: 15 outliers final: 14 residues processed: 113 average time/residue: 0.0800 time to fit residues: 15.3034 Evaluate side-chains 111 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 389 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105379 restraints weight = 22578.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108920 restraints weight = 15989.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.110737 restraints weight = 10041.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111470 restraints weight = 7382.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111923 restraints weight = 7060.322| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.125 Angle : 0.492 12.540 16188 Z= 0.250 Chirality : 0.041 0.249 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.407 15.948 1600 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.21 % Allowed : 13.85 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.97 (0.23), residues: 1448 helix: 2.22 (0.20), residues: 660 sheet: -0.59 (0.33), residues: 252 loop : -0.72 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.012 0.001 TYR A 302 PHE 0.012 0.001 PHE B 312 TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00298 (11936) covalent geometry : angle 0.49211 (16180) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.42474 ( 8) hydrogen bonds : bond 0.02791 ( 562) hydrogen bonds : angle 4.00733 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.387 Fit side-chains REVERT: A 171 MET cc_start: 0.7824 (mmp) cc_final: 0.7384 (mmp) outliers start: 15 outliers final: 14 residues processed: 112 average time/residue: 0.0759 time to fit residues: 14.2792 Evaluate side-chains 108 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 389 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104997 restraints weight = 22771.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.107626 restraints weight = 16231.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110511 restraints weight = 10588.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110822 restraints weight = 7670.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111346 restraints weight = 7296.945| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11940 Z= 0.130 Angle : 0.512 12.733 16188 Z= 0.259 Chirality : 0.042 0.260 1804 Planarity : 0.003 0.031 2080 Dihedral : 3.454 16.240 1600 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.21 % Allowed : 14.09 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.92 (0.23), residues: 1448 helix: 2.16 (0.20), residues: 660 sheet: -0.61 (0.33), residues: 252 loop : -0.72 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.013 0.001 TYR A 302 PHE 0.012 0.001 PHE B 312 TRP 0.009 0.001 TRP A 279 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00310 (11936) covalent geometry : angle 0.51156 (16180) SS BOND : bond 0.00058 ( 4) SS BOND : angle 0.42409 ( 8) hydrogen bonds : bond 0.02847 ( 562) hydrogen bonds : angle 4.04135 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1584.81 seconds wall clock time: 28 minutes 19.36 seconds (1699.36 seconds total)