Starting phenix.real_space_refine on Thu Jul 2 10:19:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyy_60583/07_2026/8zyy_60583.cif" } resolution = 2.83 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= -0.000 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 45 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 32 5.16 5 C 5237 2.51 5 N 1393 2.21 5 O 1546 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8216 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2630 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 27, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 13, 'ARG:plan': 5, 'HIS:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "D" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1648 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "Q" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1613 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2195 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 5, 'ARG:plan': 3, 'GLU:plan': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 5, 'GLN:plan1': 2, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 161 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.20 Number of scatterers: 8216 At special positions: 0 Unit cell: (79.928, 103, 165.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 7 15.00 F 1 9.00 O 1546 8.00 N 1393 7.00 C 5237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 155 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 283.5 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 16 sheets defined 26.9% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.094A pdb=" N ARG B 281 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'Q' and resid 100 through 104 removed outlier: 3.794A pdb=" N PHE Q 104 " --> pdb=" O PRO Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 148 Processing helix chain 'Q' and resid 170 through 174 removed outlier: 3.594A pdb=" N ASN Q 173 " --> pdb=" O LYS Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 205 through 210 Processing helix chain 'R' and resid 59 through 88 Processing helix chain 'R' and resid 100 through 128 removed outlier: 3.755A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.593A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.843A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS R 172 " --> pdb=" O LEU R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 179 removed outlier: 3.819A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU R 179 " --> pdb=" O LYS R 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 173 through 179' Processing helix chain 'R' and resid 181 through 207 removed outlier: 3.627A pdb=" N TRP R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 229 through 267 removed outlier: 5.224A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix removed outlier: 3.611A pdb=" N VAL R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 311 removed outlier: 4.240A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 316 removed outlier: 3.532A pdb=" N TRP R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 326 Processing helix chain 'R' and resid 337 through 366 removed outlier: 3.705A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 380 Processing sheet with id=AA1, first strand: chain 'B' and resid 111 through 114 Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.608A pdb=" N ILE B 167 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR B 143 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LYS B 169 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N VAL B 141 " --> pdb=" O LYS B 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 52 through 64 current: chain 'B' and resid 287 through 289 Processing sheet with id=AA3, first strand: chain 'B' and resid 74 through 84 removed outlier: 6.276A pdb=" N CYS B 58 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 80 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 56 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN B 82 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 54 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN B 84 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 52 " --> pdb=" O GLN B 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 139 through 149 current: chain 'R' and resid 288 through 291 Processing sheet with id=AA4, first strand: chain 'B' and resid 182 through 187 Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 208 removed outlier: 4.006A pdb=" N VAL B 328 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 320 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 350 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N VAL B 318 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 329 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 227 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN B 236 " --> pdb=" O PRO B 251 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA B 238 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 249 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 26 through 30 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 35 removed outlier: 6.180A pdb=" N ARG D 61 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TRP D 70 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.833A pdb=" N TYR D 132 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.592A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 210 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.592A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 210 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 184 removed outlier: 3.518A pdb=" N ASN D 229 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR D 224 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 239 " --> pdb=" O CYS D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 25 through 27 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 34 removed outlier: 6.407A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Q 105 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL Q 54 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR Q 70 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP Q 56 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 31 through 34 removed outlier: 6.407A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA Q 105 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR Q 118 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 135 through 139 removed outlier: 3.525A pdb=" N ALA Q 151 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Q 202 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR Q 194 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 212 through 217 removed outlier: 3.509A pdb=" N LYS Q 228 " --> pdb=" O CYS Q 215 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1284 1.30 - 1.43: 2227 1.43 - 1.56: 4828 1.56 - 1.69: 23 1.69 - 1.81: 42 Bond restraints: 8404 Sorted by residual: bond pdb=" C23 SRW R 501 " pdb=" O2 SRW R 501 " ideal model delta sigma weight residual 1.429 1.189 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C13 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sigma weight residual 1.357 1.492 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C3 SRW R 501 " pdb=" C8 SRW R 501 " ideal model delta sigma weight residual 1.519 1.631 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" OG1 TPO R 407 " pdb=" P TPO R 407 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C1A PIO B 501 " pdb=" O2C PIO B 501 " ideal model delta sigma weight residual 1.332 1.435 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 8399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 11369 2.93 - 5.87: 98 5.87 - 8.80: 18 8.80 - 11.74: 7 11.74 - 14.67: 5 Bond angle restraints: 11497 Sorted by residual: angle pdb=" N PRO B 365 " pdb=" CD PRO B 365 " pdb=" CG PRO B 365 " ideal model delta sigma weight residual 103.20 89.81 13.39 1.50e+00 4.44e-01 7.97e+01 angle pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" CD PRO B 365 " ideal model delta sigma weight residual 112.00 103.13 8.87 1.40e+00 5.10e-01 4.01e+01 angle pdb=" CA PRO B 44 " pdb=" N PRO B 44 " pdb=" CD PRO B 44 " ideal model delta sigma weight residual 112.00 103.75 8.25 1.40e+00 5.10e-01 3.47e+01 angle pdb=" C14 SRW R 501 " pdb=" C24 SRW R 501 " pdb=" C26 SRW R 501 " ideal model delta sigma weight residual 122.08 136.75 -14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" CA PRO B 365 " pdb=" CB PRO B 365 " pdb=" CG PRO B 365 " ideal model delta sigma weight residual 104.50 95.54 8.96 1.90e+00 2.77e-01 2.22e+01 ... (remaining 11492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 4714 27.08 - 54.15: 242 54.15 - 81.23: 29 81.23 - 108.30: 7 108.30 - 135.38: 3 Dihedral angle restraints: 4995 sinusoidal: 1744 harmonic: 3251 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -145.89 59.89 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" C13 SRW R 501 " pdb=" C10 SRW R 501 " pdb=" N1 SRW R 501 " pdb=" C9 SRW R 501 " ideal model delta sinusoidal sigma weight residual 146.69 -77.93 -135.38 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C12 SRW R 501 " pdb=" C11 SRW R 501 " pdb=" N1 SRW R 501 " pdb=" C13 SRW R 501 " ideal model delta sinusoidal sigma weight residual 130.69 -110.34 -118.97 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 4992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1321 0.105 - 0.211: 37 0.211 - 0.316: 0 0.316 - 0.421: 0 0.421 - 0.527: 1 Chirality restraints: 1359 Sorted by residual: chirality pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" C25 SRW R 501 " pdb=" F1 SRW R 501 " both_signs ideal model delta sigma weight residual True 1.45 -1.98 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CG LEU R 199 " pdb=" CB LEU R 199 " pdb=" CD1 LEU R 199 " pdb=" CD2 LEU R 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1 PIO B 501 " pdb=" C2 PIO B 501 " pdb=" C6 PIO B 501 " pdb=" O1 PIO B 501 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1356 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 43 " -0.075 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 44 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 9 " 0.055 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO L 10 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO L 10 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO L 10 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 12 " -0.051 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO B 13 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " -0.043 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 111 2.66 - 3.22: 7429 3.22 - 3.78: 12485 3.78 - 4.34: 16917 4.34 - 4.90: 28644 Nonbonded interactions: 65586 Sorted by model distance: nonbonded pdb=" OD1 ASP B 203 " pdb=" OH TYR B 207 " model vdw 2.095 3.040 nonbonded pdb=" O PHE R 345 " pdb=" OG1 THR R 349 " model vdw 2.142 3.040 nonbonded pdb=" O PRO D 153 " pdb=" OG SER Q 142 " model vdw 2.153 3.040 nonbonded pdb=" OG SER D 191 " pdb=" O THR D 213 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP B 296 " pdb=" OH TYR D 80 " model vdw 2.212 3.040 ... (remaining 65581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.007 0.240 8407 Z= 0.309 Angle : 0.783 14.673 11503 Z= 0.372 Chirality : 0.045 0.527 1359 Planarity : 0.006 0.108 1447 Dihedral : 16.379 135.379 2886 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.92 % Allowed : 23.26 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 1085 helix: 1.22 (0.33), residues: 254 sheet: 0.02 (0.28), residues: 342 loop : -1.29 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 166 TYR 0.010 0.001 TYR R 354 PHE 0.025 0.001 PHE D 125 TRP 0.014 0.001 TRP R 316 HIS 0.002 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.31 ( 8404) covalent geometry : angle 0.78333 / 0.37 (11497) SS BOND : bond 0.00221 / 0.10 ( 3) SS BOND : angle 0.35247 / 0.19 ( 6) hydrogen bonds : bond 0.19189 / 13.10 ( 385) hydrogen bonds : angle 8.23122 / 5.65 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.240 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 126 average time/residue: 0.2584 time to fit residues: 36.0360 Evaluate side-chains 125 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 44 CYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 411 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.212686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149650 restraints weight = 10316.299| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.15 r_work: 0.3656 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 8407 Z= 0.301 Angle : 0.741 7.726 11503 Z= 0.383 Chirality : 0.048 0.232 1359 Planarity : 0.006 0.070 1447 Dihedral : 12.833 137.767 1268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.09 % Allowed : 20.10 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 1085 helix: 0.98 (0.32), residues: 250 sheet: -0.02 (0.28), residues: 339 loop : -1.51 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 322 TYR 0.020 0.002 TYR D 127 PHE 0.052 0.003 PHE D 125 TRP 0.020 0.003 TRP D 126 HIS 0.005 0.002 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.30 ( 8404) covalent geometry : angle 0.74067 / 0.38 (11497) SS BOND : bond 0.00446 / 0.21 ( 3) SS BOND : angle 0.66931 / 0.42 ( 6) hydrogen bonds : bond 0.04629 / 3.20 ( 385) hydrogen bonds : angle 6.00597 / 4.13 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: D 194 HIS cc_start: 0.4413 (OUTLIER) cc_final: 0.3622 (m170) REVERT: D 199 VAL cc_start: 0.8229 (p) cc_final: 0.8006 (t) REVERT: Q 45 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7101 (mmm-85) REVERT: R 243 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7223 (mmp) REVERT: R 249 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.5994 (tmm) outliers start: 50 outliers final: 29 residues processed: 143 average time/residue: 0.2732 time to fit residues: 43.0366 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 44 CYS Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 309 VAL Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 411 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 106 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.215175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154562 restraints weight = 10299.396| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.26 r_work: 0.3689 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8407 Z= 0.173 Angle : 0.619 7.050 11503 Z= 0.316 Chirality : 0.044 0.213 1359 Planarity : 0.005 0.064 1447 Dihedral : 12.528 138.214 1260 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.72 % Allowed : 21.32 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1085 helix: 0.97 (0.32), residues: 262 sheet: 0.14 (0.28), residues: 336 loop : -1.35 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 9 TYR 0.014 0.002 TYR R 319 PHE 0.038 0.002 PHE D 125 TRP 0.009 0.002 TRP R 316 HIS 0.003 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8404) covalent geometry : angle 0.61877 / 0.32 (11497) SS BOND : bond 0.00246 / 0.12 ( 3) SS BOND : angle 0.68712 / 0.42 ( 6) hydrogen bonds : bond 0.03937 / 2.72 ( 385) hydrogen bonds : angle 5.51959 / 3.81 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: B 294 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6552 (p90) REVERT: D 194 HIS cc_start: 0.4301 (OUTLIER) cc_final: 0.3547 (m170) REVERT: D 199 VAL cc_start: 0.8211 (p) cc_final: 0.8010 (t) REVERT: R 243 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7160 (mmp) REVERT: R 291 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: R 345 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6435 (t80) outliers start: 47 outliers final: 19 residues processed: 148 average time/residue: 0.2795 time to fit residues: 45.9375 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 44 CYS Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 309 VAL Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 54 optimal weight: 0.0030 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN R 98 GLN ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.214616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156312 restraints weight = 10573.518| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.25 r_work: 0.3646 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8407 Z= 0.256 Angle : 0.686 8.147 11503 Z= 0.352 Chirality : 0.047 0.233 1359 Planarity : 0.006 0.063 1447 Dihedral : 12.449 138.210 1257 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.33 % Allowed : 22.29 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.26), residues: 1085 helix: 0.91 (0.32), residues: 254 sheet: 0.05 (0.28), residues: 343 loop : -1.38 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 39 TYR 0.019 0.002 TYR R 167 PHE 0.049 0.002 PHE D 125 TRP 0.015 0.002 TRP D 126 HIS 0.006 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 ( 8404) covalent geometry : angle 0.68561 / 0.35 (11497) SS BOND : bond 0.00340 / 0.16 ( 3) SS BOND : angle 0.67298 / 0.42 ( 6) hydrogen bonds : bond 0.04110 / 2.86 ( 385) hydrogen bonds : angle 5.52765 / 3.84 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6751 (ttpp) REVERT: B 294 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6693 (p90) REVERT: D 194 HIS cc_start: 0.4262 (OUTLIER) cc_final: 0.3559 (m170) REVERT: R 210 GLN cc_start: 0.5817 (mp10) cc_final: 0.5556 (mm110) REVERT: R 291 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: R 345 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.6431 (t80) outliers start: 52 outliers final: 28 residues processed: 148 average time/residue: 0.3053 time to fit residues: 49.8205 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 44 CYS Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.218199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165212 restraints weight = 10512.852| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.01 r_work: 0.3712 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8407 Z= 0.139 Angle : 0.600 7.076 11503 Z= 0.304 Chirality : 0.043 0.204 1359 Planarity : 0.005 0.060 1447 Dihedral : 12.046 138.723 1257 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.26 % Allowed : 23.51 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1085 helix: 1.08 (0.32), residues: 262 sheet: 0.21 (0.28), residues: 334 loop : -1.26 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 322 TYR 0.014 0.001 TYR Q 112 PHE 0.031 0.002 PHE D 125 TRP 0.007 0.001 TRP R 316 HIS 0.002 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8404) covalent geometry : angle 0.59948 / 0.30 (11497) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 0.65246 / 0.39 ( 6) hydrogen bonds : bond 0.03510 / 2.43 ( 385) hydrogen bonds : angle 5.18925 / 3.60 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.302 Fit side-chains REVERT: B 105 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6735 (ttpp) REVERT: D 194 HIS cc_start: 0.4393 (OUTLIER) cc_final: 0.3615 (m170) REVERT: R 141 CYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6897 (t) REVERT: R 291 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: R 345 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6409 (t80) outliers start: 35 outliers final: 17 residues processed: 141 average time/residue: 0.3006 time to fit residues: 46.6308 Evaluate side-chains 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 40.0000 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.212987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149903 restraints weight = 10277.476| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.12 r_work: 0.3655 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 8407 Z= 0.270 Angle : 0.701 8.489 11503 Z= 0.358 Chirality : 0.047 0.238 1359 Planarity : 0.006 0.062 1447 Dihedral : 11.996 137.729 1256 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.60 % Allowed : 23.51 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 1085 helix: 0.96 (0.33), residues: 254 sheet: 0.09 (0.28), residues: 341 loop : -1.37 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 322 TYR 0.019 0.002 TYR D 127 PHE 0.051 0.003 PHE D 125 TRP 0.015 0.002 TRP D 126 HIS 0.006 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 ( 8404) covalent geometry : angle 0.70069 / 0.36 (11497) SS BOND : bond 0.00347 / 0.16 ( 3) SS BOND : angle 0.65473 / 0.41 ( 6) hydrogen bonds : bond 0.04058 / 2.83 ( 385) hydrogen bonds : angle 5.38852 / 3.75 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6782 (ttpp) REVERT: B 294 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6625 (p90) REVERT: D 194 HIS cc_start: 0.4303 (OUTLIER) cc_final: 0.3539 (m170) REVERT: R 291 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: R 345 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6464 (t80) outliers start: 46 outliers final: 24 residues processed: 143 average time/residue: 0.2907 time to fit residues: 45.9823 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.0050 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.216093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154062 restraints weight = 10410.717| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.14 r_work: 0.3711 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8407 Z= 0.146 Angle : 0.615 10.304 11503 Z= 0.310 Chirality : 0.043 0.211 1359 Planarity : 0.005 0.060 1447 Dihedral : 11.681 138.125 1255 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.53 % Allowed : 25.70 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1085 helix: 1.12 (0.32), residues: 262 sheet: 0.27 (0.28), residues: 334 loop : -1.30 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 322 TYR 0.015 0.001 TYR Q 112 PHE 0.036 0.002 PHE Q 160 TRP 0.008 0.001 TRP D 126 HIS 0.002 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8404) covalent geometry : angle 0.61510 / 0.31 (11497) SS BOND : bond 0.00212 / 0.10 ( 3) SS BOND : angle 0.59721 / 0.36 ( 6) hydrogen bonds : bond 0.03511 / 2.45 ( 385) hydrogen bonds : angle 5.11744 / 3.56 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6738 (ttpp) REVERT: D 194 HIS cc_start: 0.4282 (OUTLIER) cc_final: 0.3495 (m170) REVERT: R 291 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: R 345 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6428 (t80) outliers start: 29 outliers final: 18 residues processed: 131 average time/residue: 0.3012 time to fit residues: 43.5721 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157994 restraints weight = 10450.801| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.28 r_work: 0.3685 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8407 Z= 0.183 Angle : 0.639 11.771 11503 Z= 0.322 Chirality : 0.044 0.223 1359 Planarity : 0.005 0.060 1447 Dihedral : 11.630 137.222 1255 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.14 % Allowed : 25.46 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.26), residues: 1085 helix: 1.12 (0.33), residues: 256 sheet: 0.27 (0.28), residues: 336 loop : -1.28 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 322 TYR 0.019 0.002 TYR R 167 PHE 0.039 0.002 PHE D 125 TRP 0.008 0.001 TRP D 126 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 8404) covalent geometry : angle 0.63889 / 0.32 (11497) SS BOND : bond 0.00266 / 0.13 ( 3) SS BOND : angle 0.60050 / 0.37 ( 6) hydrogen bonds : bond 0.03632 / 2.54 ( 385) hydrogen bonds : angle 5.10199 / 3.55 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6774 (ttpp) REVERT: B 294 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6512 (p90) REVERT: D 194 HIS cc_start: 0.4153 (OUTLIER) cc_final: 0.3395 (m170) REVERT: R 291 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: R 345 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6483 (t80) outliers start: 34 outliers final: 21 residues processed: 138 average time/residue: 0.3267 time to fit residues: 49.8458 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.216299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158168 restraints weight = 10279.017| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.35 r_work: 0.3688 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8407 Z= 0.151 Angle : 0.627 13.027 11503 Z= 0.314 Chirality : 0.044 0.213 1359 Planarity : 0.005 0.060 1447 Dihedral : 11.548 137.294 1255 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.41 % Allowed : 26.55 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1085 helix: 1.14 (0.32), residues: 262 sheet: 0.33 (0.28), residues: 334 loop : -1.22 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 322 TYR 0.015 0.001 TYR Q 112 PHE 0.033 0.002 PHE Q 160 TRP 0.008 0.001 TRP D 126 HIS 0.002 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8404) covalent geometry : angle 0.62668 / 0.31 (11497) SS BOND : bond 0.00235 / 0.11 ( 3) SS BOND : angle 0.58088 / 0.35 ( 6) hydrogen bonds : bond 0.03483 / 2.43 ( 385) hydrogen bonds : angle 5.00242 / 3.48 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 105 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6805 (ttpp) REVERT: D 194 HIS cc_start: 0.4285 (OUTLIER) cc_final: 0.3476 (m170) REVERT: D 199 VAL cc_start: 0.8184 (p) cc_final: 0.7984 (t) REVERT: R 291 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: R 345 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6492 (t80) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.2937 time to fit residues: 44.0216 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 45 optimal weight: 0.0870 chunk 2 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.215696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155275 restraints weight = 10277.791| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.18 r_work: 0.3692 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8407 Z= 0.169 Angle : 0.639 13.520 11503 Z= 0.320 Chirality : 0.044 0.215 1359 Planarity : 0.005 0.060 1447 Dihedral : 11.535 137.196 1255 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.29 % Allowed : 26.92 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1085 helix: 1.13 (0.32), residues: 262 sheet: 0.32 (0.28), residues: 336 loop : -1.23 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 322 TYR 0.021 0.002 TYR R 167 PHE 0.035 0.002 PHE D 125 TRP 0.009 0.001 TRP D 126 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 8404) covalent geometry : angle 0.63860 / 0.32 (11497) SS BOND : bond 0.00262 / 0.12 ( 3) SS BOND : angle 0.55761 / 0.35 ( 6) hydrogen bonds : bond 0.03529 / 2.46 ( 385) hydrogen bonds : angle 5.00931 / 3.49 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: D 194 HIS cc_start: 0.4029 (OUTLIER) cc_final: 0.3277 (m170) REVERT: R 291 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: R 345 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.6520 (t80) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.2869 time to fit residues: 42.1726 Evaluate side-chains 128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 126 TRP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 128 LYS Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 291 GLU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0770 chunk 85 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 84 optimal weight: 0.0040 chunk 96 optimal weight: 3.9990 overall best weight: 0.2950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN Q 27 GLN R 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158597 restraints weight = 10439.951| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.08 r_work: 0.3766 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8407 Z= 0.116 Angle : 0.601 13.599 11503 Z= 0.298 Chirality : 0.043 0.186 1359 Planarity : 0.005 0.059 1447 Dihedral : 11.315 137.191 1253 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.07 % Allowed : 27.89 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1085 helix: 1.40 (0.33), residues: 258 sheet: 0.49 (0.28), residues: 334 loop : -1.18 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 322 TYR 0.014 0.001 TYR R 319 PHE 0.033 0.001 PHE Q 160 TRP 0.010 0.001 TRP D 126 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8404) covalent geometry : angle 0.60100 / 0.30 (11497) SS BOND : bond 0.00208 / 0.10 ( 3) SS BOND : angle 0.55233 / 0.32 ( 6) hydrogen bonds : bond 0.03204 / 2.22 ( 385) hydrogen bonds : angle 4.77956 / 3.32 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.56 seconds wall clock time: 53 minutes 8.64 seconds (3188.64 seconds total)