Starting phenix.real_space_refine on Wed Mar 4 15:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toe_26030/03_2026/7toe_26030.map" } resolution = 3.0 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= 0.012 sd= 0.163 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 80 5.16 5 C 9632 2.51 5 N 2616 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15100 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3775 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 residue: pdb=" N GLU C 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU C 504 " occ=0.50 residue: pdb=" N GLU D 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D 504 " occ=0.50 Time building chain proxies: 3.53, per 1000 atoms: 0.23 Number of scatterers: 15100 At special positions: 0 Unit cell: (135.29, 95.45, 117.03, 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 80 16.00 O 2772 8.00 N 2616 7.00 C 9632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.13 Conformation dependent library (CDL) restraints added in 546.6 milliseconds 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 43.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.940A pdb=" N LYS A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.554A pdb=" N TYR A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.561A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.638A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.407A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.818A pdb=" N GLU A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.647A pdb=" N ASP A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.689A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.891A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.513A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 4.017A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.550A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.799A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.237A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.743A pdb=" N GLU B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.601A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.993A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.395A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 4.191A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.695A pdb=" N LYS C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.549A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.272A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.662A pdb=" N GLU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 removed outlier: 3.504A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.041A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.450A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.938A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.700A pdb=" N GLU D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.506A pdb=" N LYS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.923A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 4.225A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.626A pdb=" N GLU D 287 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.614A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.880A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 7.968A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.451A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 7.950A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 415 through 421 removed outlier: 6.651A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA B 231 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG B 357 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 235 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY B 359 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 237 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.317A pdb=" N ILE C 33 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR C 139 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 35 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 415 through 421 removed outlier: 6.574A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA C 231 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE C 355 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 233 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG C 357 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 235 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY C 359 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 237 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.274A pdb=" N ILE D 33 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR D 139 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 35 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 415 through 421 removed outlier: 6.620A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1950 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: 2.70 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2647 1.32 - 1.44: 4056 1.44 - 1.57: 8617 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15452 Sorted by residual: bond pdb=" CA PRO A 50 " pdb=" CB PRO A 50 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" CA ILE B 464 " pdb=" C ILE B 464 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.27e-02 6.20e+03 1.38e+01 bond pdb=" CA THR A 51 " pdb=" C THR A 51 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.39e-02 5.18e+03 1.05e+01 bond pdb=" C ILE B 464 " pdb=" O ILE B 464 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.19e-02 7.06e+03 9.19e+00 bond pdb=" CA TRP B 462 " pdb=" CB TRP B 462 " ideal model delta sigma weight residual 1.532 1.489 0.044 1.53e-02 4.27e+03 8.14e+00 ... (remaining 15447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 20285 1.48 - 2.96: 498 2.96 - 4.43: 80 4.43 - 5.91: 26 5.91 - 7.39: 7 Bond angle restraints: 20896 Sorted by residual: angle pdb=" N GLY B 310 " pdb=" CA GLY B 310 " pdb=" C GLY B 310 " ideal model delta sigma weight residual 111.36 118.56 -7.20 1.17e+00 7.31e-01 3.79e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 112.35 104.96 7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta sigma weight residual 119.28 113.94 5.34 1.10e+00 8.26e-01 2.36e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 112.38 107.59 4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N TRP B 462 " pdb=" CA TRP B 462 " pdb=" C TRP B 462 " ideal model delta sigma weight residual 113.41 108.66 4.75 1.22e+00 6.72e-01 1.51e+01 ... (remaining 20891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8445 17.87 - 35.74: 683 35.74 - 53.62: 125 53.62 - 71.49: 38 71.49 - 89.36: 13 Dihedral angle restraints: 9304 sinusoidal: 3868 harmonic: 5436 Sorted by residual: dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N CYS A 158 " pdb=" CA CYS A 158 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA SER D 157 " pdb=" C SER D 157 " pdb=" N CYS D 158 " pdb=" CA CYS D 158 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 259 " pdb=" C VAL A 259 " pdb=" N MET A 260 " pdb=" CA MET A 260 " ideal model delta harmonic sigma weight residual 180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1716 0.046 - 0.093: 383 0.093 - 0.139: 139 0.139 - 0.186: 1 0.186 - 0.232: 1 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA GLN A 119 " pdb=" N GLN A 119 " pdb=" C GLN A 119 " pdb=" CB GLN A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA GLU C 473 " pdb=" N GLU C 473 " pdb=" C GLU C 473 " pdb=" CB GLU C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2237 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 311 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 312 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 49 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 50 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.020 2.00e-02 2.50e+03 1.75e-02 6.13e+00 pdb=" CG TYR B 139 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.005 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1218 2.74 - 3.28: 14964 3.28 - 3.82: 25676 3.82 - 4.36: 32498 4.36 - 4.90: 55183 Nonbonded interactions: 129539 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" OE2 GLU A 170 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" OH TYR A 437 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 139 " pdb=" OH TYR C 437 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 196 " pdb=" NE2 GLN B 449 " model vdw 2.232 3.120 nonbonded pdb=" O LYS B 47 " pdb=" OG1 THR B 51 " model vdw 2.234 3.040 ... (remaining 129534 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.360 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.062 15452 Z= 0.172 Angle : 0.588 7.388 20896 Z= 0.327 Chirality : 0.043 0.232 2240 Planarity : 0.004 0.063 2732 Dihedral : 14.035 89.359 5800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.13 (0.20), residues: 1852 helix: 0.24 (0.20), residues: 704 sheet: -0.60 (0.23), residues: 444 loop : 0.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 439 TYR 0.041 0.002 TYR B 139 PHE 0.021 0.001 PHE C 88 TRP 0.028 0.002 TRP B 225 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00325 (15452) covalent geometry : angle 0.58771 (20896) hydrogen bonds : bond 0.16978 ( 678) hydrogen bonds : angle 7.60923 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 0.604 Fit side-chains REVERT: B 30 ASP cc_start: 0.7179 (t0) cc_final: 0.6711 (OUTLIER) REVERT: B 121 LEU cc_start: 0.8476 (tt) cc_final: 0.8273 (tm) REVERT: B 130 LEU cc_start: 0.8312 (tp) cc_final: 0.8079 (tp) REVERT: B 171 LYS cc_start: 0.7717 (ptmm) cc_final: 0.7397 (pttp) REVERT: B 249 TYR cc_start: 0.7017 (t80) cc_final: 0.6789 (t80) REVERT: B 446 CYS cc_start: 0.7767 (m) cc_final: 0.7461 (m) REVERT: B 497 LYS cc_start: 0.8358 (tptt) cc_final: 0.7998 (tttp) REVERT: D 37 MET cc_start: 0.8817 (mmm) cc_final: 0.8562 (mmt) REVERT: D 140 LEU cc_start: 0.8260 (mp) cc_final: 0.8015 (mt) outliers start: 2 outliers final: 3 residues processed: 292 average time/residue: 0.6156 time to fit residues: 197.8713 Evaluate side-chains 188 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN D 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.165459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121641 restraints weight = 17886.825| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.22 r_work: 0.3327 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15452 Z= 0.165 Angle : 0.597 8.306 20896 Z= 0.310 Chirality : 0.045 0.212 2240 Planarity : 0.005 0.053 2732 Dihedral : 4.582 54.502 2060 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 10.11 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1852 helix: 0.43 (0.20), residues: 692 sheet: -0.61 (0.24), residues: 408 loop : -0.20 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 459 TYR 0.022 0.002 TYR B 139 PHE 0.018 0.001 PHE C 241 TRP 0.015 0.002 TRP B 225 HIS 0.004 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00383 (15452) covalent geometry : angle 0.59728 (20896) hydrogen bonds : bond 0.04212 ( 678) hydrogen bonds : angle 5.89422 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.676 Fit side-chains REVERT: A 152 LYS cc_start: 0.7256 (tmmt) cc_final: 0.7016 (tttt) REVERT: A 405 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8005 (mtp) REVERT: B 30 ASP cc_start: 0.7368 (t0) cc_final: 0.6607 (OUTLIER) REVERT: B 97 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6998 (ttpp) REVERT: B 130 LEU cc_start: 0.8238 (tp) cc_final: 0.7910 (tp) REVERT: B 171 LYS cc_start: 0.7695 (ptmm) cc_final: 0.7389 (pttp) REVERT: B 249 TYR cc_start: 0.7600 (t80) cc_final: 0.7109 (t80) REVERT: B 389 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: B 395 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: B 446 CYS cc_start: 0.8426 (m) cc_final: 0.8117 (m) REVERT: B 497 LYS cc_start: 0.8600 (tptt) cc_final: 0.8219 (tttp) REVERT: C 130 LEU cc_start: 0.8467 (tp) cc_final: 0.8142 (tt) REVERT: C 142 LEU cc_start: 0.8925 (pt) cc_final: 0.8682 (pp) REVERT: C 405 MET cc_start: 0.8461 (mmm) cc_final: 0.7844 (mmt) REVERT: C 475 GLU cc_start: 0.8226 (tm-30) cc_final: 0.8019 (tm-30) REVERT: D 37 MET cc_start: 0.8677 (mmm) cc_final: 0.8144 (mmt) REVERT: D 95 LYS cc_start: 0.7525 (tmmt) cc_final: 0.6879 (tmmt) REVERT: D 99 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: D 135 ASN cc_start: 0.8424 (m-40) cc_final: 0.8034 (m110) REVERT: D 140 LEU cc_start: 0.8067 (mp) cc_final: 0.7769 (mt) outliers start: 24 outliers final: 11 residues processed: 232 average time/residue: 0.5403 time to fit residues: 139.8217 Evaluate side-chains 207 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 493 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 384 GLN A 414 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125676 restraints weight = 17866.381| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.25 r_work: 0.3361 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15452 Z= 0.118 Angle : 0.536 8.239 20896 Z= 0.278 Chirality : 0.043 0.200 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.236 19.054 2056 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 12.44 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1852 helix: 0.69 (0.21), residues: 692 sheet: -0.77 (0.23), residues: 432 loop : -0.16 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 459 TYR 0.019 0.001 TYR A 308 PHE 0.016 0.001 PHE B 102 TRP 0.017 0.001 TRP B 53 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00264 (15452) covalent geometry : angle 0.53573 (20896) hydrogen bonds : bond 0.03558 ( 678) hydrogen bonds : angle 5.41760 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.551 Fit side-chains REVERT: A 152 LYS cc_start: 0.7236 (tmmt) cc_final: 0.7006 (tttt) REVERT: A 159 MET cc_start: 0.7857 (tpp) cc_final: 0.7584 (tpp) REVERT: A 258 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8118 (t70) REVERT: A 405 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: B 63 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: B 97 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7137 (ttpt) REVERT: B 130 LEU cc_start: 0.8181 (tp) cc_final: 0.7894 (tp) REVERT: B 192 ARG cc_start: 0.8099 (ptt-90) cc_final: 0.7848 (ptt90) REVERT: B 249 TYR cc_start: 0.7552 (t80) cc_final: 0.7052 (t80) REVERT: B 395 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: B 446 CYS cc_start: 0.8316 (m) cc_final: 0.8050 (m) REVERT: B 450 MET cc_start: 0.8477 (ttm) cc_final: 0.8251 (ttm) REVERT: B 497 LYS cc_start: 0.8559 (tptt) cc_final: 0.8162 (tttp) REVERT: C 130 LEU cc_start: 0.8314 (tp) cc_final: 0.8097 (tp) REVERT: C 317 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6111 (tt0) REVERT: C 466 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (m) REVERT: C 475 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 37 MET cc_start: 0.8603 (mmm) cc_final: 0.7829 (mmt) REVERT: D 66 PHE cc_start: 0.8023 (m-80) cc_final: 0.7805 (m-80) REVERT: D 95 LYS cc_start: 0.7393 (tmmt) cc_final: 0.6869 (tmmt) REVERT: D 99 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: D 135 ASN cc_start: 0.8399 (m-40) cc_final: 0.8109 (m110) outliers start: 36 outliers final: 12 residues processed: 243 average time/residue: 0.6109 time to fit residues: 163.5288 Evaluate side-chains 210 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN C 105 ASN C 155 HIS C 178 GLN D 266 GLN D 451 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121887 restraints weight = 18069.995| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.28 r_work: 0.3302 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15452 Z= 0.212 Angle : 0.605 8.224 20896 Z= 0.309 Chirality : 0.045 0.190 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.411 18.962 2056 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.45 % Allowed : 15.07 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.34 (0.19), residues: 1852 helix: 0.35 (0.20), residues: 720 sheet: -0.85 (0.23), residues: 432 loop : -0.17 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 459 TYR 0.020 0.002 TYR A 308 PHE 0.021 0.002 PHE C 88 TRP 0.014 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00512 (15452) covalent geometry : angle 0.60510 (20896) hydrogen bonds : bond 0.03844 ( 678) hydrogen bonds : angle 5.46964 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.8007 (tpp) cc_final: 0.7776 (tpp) REVERT: A 258 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8095 (t70) REVERT: A 398 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: A 405 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: A 470 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (m-70) REVERT: B 63 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: B 97 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.6982 (ttpp) REVERT: B 130 LEU cc_start: 0.8168 (tp) cc_final: 0.7857 (tp) REVERT: B 249 TYR cc_start: 0.7592 (t80) cc_final: 0.7082 (t80) REVERT: B 389 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: B 395 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7844 (pt0) REVERT: B 446 CYS cc_start: 0.8364 (m) cc_final: 0.8033 (m) REVERT: B 497 LYS cc_start: 0.8536 (tptt) cc_final: 0.8131 (tttp) REVERT: C 89 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8335 (mptt) REVERT: C 130 LEU cc_start: 0.8358 (tp) cc_final: 0.8154 (tp) REVERT: C 166 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7309 (mtp85) REVERT: C 317 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6106 (tt0) REVERT: C 475 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7947 (tm-30) REVERT: D 37 MET cc_start: 0.8561 (mmm) cc_final: 0.7733 (mmt) REVERT: D 66 PHE cc_start: 0.7991 (m-80) cc_final: 0.7754 (m-80) REVERT: D 95 LYS cc_start: 0.7309 (tmmt) cc_final: 0.6828 (tmmt) REVERT: D 99 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: D 135 ASN cc_start: 0.8474 (m-40) cc_final: 0.8182 (m110) outliers start: 40 outliers final: 17 residues processed: 231 average time/residue: 0.5504 time to fit residues: 140.4730 Evaluate side-chains 223 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 159 optimal weight: 0.0030 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 overall best weight: 3.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120967 restraints weight = 17937.250| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.22 r_work: 0.3298 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15452 Z= 0.177 Angle : 0.575 7.494 20896 Z= 0.295 Chirality : 0.044 0.194 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.412 18.678 2056 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.70 % Allowed : 16.67 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1852 helix: 0.40 (0.20), residues: 720 sheet: -0.92 (0.22), residues: 452 loop : -0.04 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 459 TYR 0.019 0.001 TYR A 308 PHE 0.019 0.001 PHE A 253 TRP 0.015 0.002 TRP B 164 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd covalent geometry : bond 0.00424 (15452) covalent geometry : angle 0.57505 (20896) hydrogen bonds : bond 0.03644 ( 678) hydrogen bonds : angle 5.37032 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7996 (tpp) cc_final: 0.7751 (tpp) REVERT: A 258 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8094 (t70) REVERT: A 398 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 405 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: A 470 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7914 (m-70) REVERT: B 63 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: B 130 LEU cc_start: 0.8188 (tp) cc_final: 0.7935 (tp) REVERT: B 249 TYR cc_start: 0.7609 (t80) cc_final: 0.7137 (t80) REVERT: B 258 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: B 389 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: B 395 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7783 (pt0) REVERT: B 446 CYS cc_start: 0.8420 (m) cc_final: 0.8103 (m) REVERT: B 497 LYS cc_start: 0.8591 (tptt) cc_final: 0.8190 (tttp) REVERT: C 89 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8364 (mptt) REVERT: C 120 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8036 (ptp90) REVERT: C 130 LEU cc_start: 0.8308 (tp) cc_final: 0.8099 (tp) REVERT: C 166 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: C 466 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8221 (m) REVERT: C 475 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 66 PHE cc_start: 0.7979 (m-80) cc_final: 0.7757 (m-80) REVERT: D 135 ASN cc_start: 0.8457 (m-40) cc_final: 0.8166 (m110) outliers start: 44 outliers final: 20 residues processed: 237 average time/residue: 0.5831 time to fit residues: 153.1146 Evaluate side-chains 225 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 131 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 451 HIS D 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119520 restraints weight = 17950.713| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.18 r_work: 0.3267 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15452 Z= 0.247 Angle : 0.635 8.695 20896 Z= 0.323 Chirality : 0.046 0.208 2240 Planarity : 0.005 0.053 2732 Dihedral : 4.587 18.920 2056 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 2.70 % Allowed : 18.01 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.19), residues: 1852 helix: 0.27 (0.19), residues: 732 sheet: -1.01 (0.22), residues: 452 loop : -0.12 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 459 TYR 0.016 0.002 TYR A 308 PHE 0.024 0.002 PHE C 102 TRP 0.014 0.002 TRP B 164 HIS 0.005 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00597 (15452) covalent geometry : angle 0.63477 (20896) hydrogen bonds : bond 0.03996 ( 678) hydrogen bonds : angle 5.50728 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8131 (tpp) cc_final: 0.7860 (tpp) REVERT: A 258 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8164 (t70) REVERT: B 130 LEU cc_start: 0.8207 (tp) cc_final: 0.7904 (tp) REVERT: B 249 TYR cc_start: 0.7613 (t80) cc_final: 0.7160 (t80) REVERT: B 258 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: B 389 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 446 CYS cc_start: 0.8438 (m) cc_final: 0.8072 (m) REVERT: B 497 LYS cc_start: 0.8614 (tptt) cc_final: 0.8232 (tttp) REVERT: C 89 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8398 (mptt) REVERT: C 120 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7452 (ptp90) REVERT: C 166 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7442 (mpp80) REVERT: C 329 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.7268 (Cg_endo) REVERT: C 356 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8759 (mt) REVERT: C 466 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 475 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7864 (tm-30) REVERT: D 66 PHE cc_start: 0.8001 (m-80) cc_final: 0.7466 (m-80) REVERT: D 135 ASN cc_start: 0.8525 (m-40) cc_final: 0.8232 (m110) outliers start: 44 outliers final: 17 residues processed: 233 average time/residue: 0.5883 time to fit residues: 152.0690 Evaluate side-chains 216 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN D 266 GLN D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124909 restraints weight = 17590.313| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.13 r_work: 0.3345 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15452 Z= 0.112 Angle : 0.543 7.746 20896 Z= 0.280 Chirality : 0.043 0.181 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.302 17.680 2056 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 2.02 % Allowed : 19.18 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.13 (0.20), residues: 1852 helix: 0.75 (0.21), residues: 688 sheet: -0.92 (0.23), residues: 452 loop : -0.12 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 459 TYR 0.021 0.001 TYR A 308 PHE 0.024 0.001 PHE C 56 TRP 0.019 0.002 TRP B 164 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00258 (15452) covalent geometry : angle 0.54342 (20896) hydrogen bonds : bond 0.03185 ( 678) hydrogen bonds : angle 5.15944 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: A 470 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7859 (m-70) REVERT: B 63 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 88 PHE cc_start: 0.8135 (m-80) cc_final: 0.7301 (m-80) REVERT: B 130 LEU cc_start: 0.8133 (tp) cc_final: 0.7922 (tp) REVERT: B 192 ARG cc_start: 0.8090 (ptt-90) cc_final: 0.7887 (ptt90) REVERT: B 249 TYR cc_start: 0.7566 (t80) cc_final: 0.7113 (t80) REVERT: B 258 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: B 395 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: B 446 CYS cc_start: 0.8381 (m) cc_final: 0.8082 (m) REVERT: B 497 LYS cc_start: 0.8483 (tptt) cc_final: 0.8099 (tttp) REVERT: C 89 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8409 (mptt) REVERT: C 120 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7331 (ptp90) REVERT: C 130 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7943 (tt) REVERT: C 166 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7383 (mtp85) REVERT: C 317 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: C 448 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8360 (m) REVERT: C 466 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8206 (m) REVERT: C 475 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7862 (tm-30) REVERT: D 66 PHE cc_start: 0.7978 (m-80) cc_final: 0.7401 (m-80) REVERT: D 99 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7551 (mm-30) outliers start: 33 outliers final: 8 residues processed: 243 average time/residue: 0.5543 time to fit residues: 149.1915 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 317 GLU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 150 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 130 optimal weight: 0.0020 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 overall best weight: 2.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123515 restraints weight = 17938.033| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.19 r_work: 0.3321 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15452 Z= 0.136 Angle : 0.558 8.678 20896 Z= 0.283 Chirality : 0.043 0.182 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.287 18.840 2056 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 2.08 % Allowed : 20.04 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.12 (0.20), residues: 1852 helix: 0.81 (0.20), residues: 684 sheet: -0.92 (0.23), residues: 452 loop : -0.16 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 72 TYR 0.021 0.001 TYR A 308 PHE 0.024 0.001 PHE C 56 TRP 0.019 0.002 TRP B 53 HIS 0.005 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00324 (15452) covalent geometry : angle 0.55830 (20896) hydrogen bonds : bond 0.03291 ( 678) hydrogen bonds : angle 5.14467 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: A 411 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6594 (mtt) REVERT: B 63 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: B 88 PHE cc_start: 0.8165 (m-80) cc_final: 0.7284 (m-80) REVERT: B 130 LEU cc_start: 0.8156 (tp) cc_final: 0.7952 (tp) REVERT: B 192 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7924 (ptt90) REVERT: B 249 TYR cc_start: 0.7564 (t80) cc_final: 0.7115 (t80) REVERT: B 258 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: B 395 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: B 446 CYS cc_start: 0.8360 (m) cc_final: 0.8069 (m) REVERT: B 497 LYS cc_start: 0.8522 (tptt) cc_final: 0.8130 (tttp) REVERT: C 89 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8394 (mptt) REVERT: C 120 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8050 (ptp90) REVERT: C 130 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8013 (tt) REVERT: C 166 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7268 (mtp85) REVERT: C 356 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 466 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (m) REVERT: C 475 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7899 (tm-30) REVERT: D 66 PHE cc_start: 0.7925 (m-80) cc_final: 0.7366 (m-80) REVERT: D 99 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7627 (mm-30) outliers start: 34 outliers final: 14 residues processed: 231 average time/residue: 0.5914 time to fit residues: 150.8779 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 0.0980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.164349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124669 restraints weight = 17733.393| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.13 r_work: 0.3354 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15452 Z= 0.113 Angle : 0.544 10.205 20896 Z= 0.277 Chirality : 0.042 0.182 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.199 19.367 2056 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.02 % Allowed : 20.22 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.20), residues: 1852 helix: 0.91 (0.21), residues: 684 sheet: -0.95 (0.22), residues: 472 loop : -0.08 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 175 TYR 0.020 0.001 TYR A 308 PHE 0.031 0.001 PHE C 56 TRP 0.023 0.002 TRP B 53 HIS 0.007 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00261 (15452) covalent geometry : angle 0.54414 (20896) hydrogen bonds : bond 0.03101 ( 678) hydrogen bonds : angle 5.05159 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: A 411 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6630 (mtt) REVERT: A 470 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7826 (m-70) REVERT: B 63 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: B 88 PHE cc_start: 0.8113 (m-80) cc_final: 0.7280 (m-80) REVERT: B 130 LEU cc_start: 0.8118 (tp) cc_final: 0.7897 (tp) REVERT: B 170 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: B 192 ARG cc_start: 0.8096 (ptt-90) cc_final: 0.7894 (ptt90) REVERT: B 249 TYR cc_start: 0.7544 (t80) cc_final: 0.7081 (t80) REVERT: B 319 THR cc_start: 0.9099 (t) cc_final: 0.8770 (p) REVERT: B 395 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: B 446 CYS cc_start: 0.8267 (m) cc_final: 0.8013 (m) REVERT: B 497 LYS cc_start: 0.8484 (tptt) cc_final: 0.7760 (mptt) REVERT: C 89 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8371 (mptt) REVERT: C 120 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7912 (ptp90) REVERT: C 130 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7871 (tt) REVERT: C 166 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7416 (mtp85) REVERT: C 356 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8721 (mt) REVERT: C 448 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 466 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8204 (m) REVERT: D 66 PHE cc_start: 0.7937 (m-80) cc_final: 0.7299 (m-80) outliers start: 33 outliers final: 15 residues processed: 229 average time/residue: 0.6221 time to fit residues: 156.8894 Evaluate side-chains 221 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 46 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 0.0050 chunk 117 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN C 133 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.161853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122054 restraints weight = 17929.496| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.01 r_work: 0.3323 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15452 Z= 0.159 Angle : 0.581 11.904 20896 Z= 0.293 Chirality : 0.043 0.195 2240 Planarity : 0.004 0.063 2732 Dihedral : 4.295 21.089 2056 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.84 % Allowed : 20.71 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.12 (0.20), residues: 1852 helix: 0.78 (0.20), residues: 688 sheet: -0.97 (0.22), residues: 472 loop : -0.07 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 175 TYR 0.019 0.002 TYR A 308 PHE 0.026 0.001 PHE C 56 TRP 0.027 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00384 (15452) covalent geometry : angle 0.58104 (20896) hydrogen bonds : bond 0.03347 ( 678) hydrogen bonds : angle 5.11808 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3704 Ramachandran restraints generated. 1852 Oldfield, 0 Emsley, 1852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: A 258 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: A 411 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6619 (mtt) REVERT: B 63 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: B 88 PHE cc_start: 0.8087 (m-80) cc_final: 0.7398 (m-80) REVERT: B 130 LEU cc_start: 0.8144 (tp) cc_final: 0.7940 (tp) REVERT: B 192 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7923 (ptt90) REVERT: B 249 TYR cc_start: 0.7562 (t80) cc_final: 0.7089 (t80) REVERT: B 258 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: B 446 CYS cc_start: 0.8346 (m) cc_final: 0.8067 (m) REVERT: B 497 LYS cc_start: 0.8546 (tptt) cc_final: 0.7806 (mptt) REVERT: C 43 LEU cc_start: 0.8177 (tm) cc_final: 0.7945 (tp) REVERT: C 80 ILE cc_start: 0.8507 (mm) cc_final: 0.8292 (mp) REVERT: C 88 PHE cc_start: 0.7542 (m-80) cc_final: 0.7302 (m-80) REVERT: C 89 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8366 (mptt) REVERT: C 120 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8082 (ptp90) REVERT: C 130 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8005 (tt) REVERT: C 166 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7273 (mtp85) REVERT: C 356 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8766 (mt) REVERT: C 448 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8378 (m) REVERT: C 466 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8224 (m) REVERT: D 66 PHE cc_start: 0.7936 (m-80) cc_final: 0.7298 (m-80) REVERT: D 99 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7750 (mm-30) outliers start: 30 outliers final: 16 residues processed: 219 average time/residue: 0.5768 time to fit residues: 139.8693 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.161620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120489 restraints weight = 17929.291| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.20 r_work: 0.3279 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15452 Z= 0.213 Angle : 0.629 11.524 20896 Z= 0.318 Chirality : 0.045 0.223 2240 Planarity : 0.005 0.065 2732 Dihedral : 4.538 20.501 2056 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.90 % Allowed : 20.83 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.31 (0.20), residues: 1852 helix: 0.54 (0.20), residues: 700 sheet: -0.97 (0.22), residues: 452 loop : -0.21 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 175 TYR 0.018 0.002 TYR A 308 PHE 0.026 0.002 PHE C 56 TRP 0.034 0.002 TRP B 53 HIS 0.005 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00515 (15452) covalent geometry : angle 0.62895 (20896) hydrogen bonds : bond 0.03747 ( 678) hydrogen bonds : angle 5.32655 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5837.12 seconds wall clock time: 100 minutes 2.28 seconds (6002.28 seconds total)