Starting phenix.real_space_refine on Wed Mar 4 01:54:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jr9_22444/03_2026/7jr9_22444.map" } resolution = 2.95 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= 0.002 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 37 5.16 5 C 6391 2.51 5 N 1706 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 10021 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1970 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1946 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2110 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 22, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 301} Chain breaks: 2 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10021 At special positions: 0 Unit cell: (88.92, 97.47, 164.16, 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 37 16.00 O 1887 8.00 N 1706 7.00 C 6391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 155 " distance=2.02 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: 0.78 Conformation dependent library (CDL) restraints added in 514.8 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 18 sheets defined 23.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.755A pdb=" N HIS A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.531A pdb=" N GLN A 213 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.567A pdb=" N ALA B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.995A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.913A pdb=" N ASN C 214 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 245 removed outlier: 3.647A pdb=" N ARG C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 283 removed outlier: 3.542A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 removed outlier: 4.006A pdb=" N ALA C 315 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 125 through 142 Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.711A pdb=" N VAL D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.631A pdb=" N GLU D 292 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.686A pdb=" N ASP D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 85 removed outlier: 3.536A pdb=" N GLU A 79 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 68 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 81 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR A 66 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 83 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A 64 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A 62 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 48 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR A 66 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 46 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 16.418A pdb=" N TRP A 251 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N THR A 47 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N SER A 253 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 49 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR A 240 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 93 removed outlier: 5.798A pdb=" N ALA B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 71 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 77 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA B 69 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 79 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 67 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 48 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR B 66 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 16.010A pdb=" N TRP B 251 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N THR B 47 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N SER B 253 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP B 49 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR B 240 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 123 Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.458A pdb=" N TYR C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS C 159 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 169 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N ARG C 155 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N TYR C 416 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 157 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 418 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 159 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA C 403 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB2, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 210 removed outlier: 6.515A pdb=" N TYR D 163 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS D 155 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 165 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 149 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 21.775A pdb=" N PHE D 400 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N THR D 149 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 14.927A pdb=" N SER D 402 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ARG D 151 " --> pdb=" O SER D 402 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N TYR D 404 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 153 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY D 406 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS D 155 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266 Processing sheet with id=AB5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AB7, first strand: chain 'G' and resid -3 through -1 removed outlier: 3.560A pdb=" N UNK G -3 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 29 " --> pdb=" O UNK G -3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1173 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: 1.59 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3191 1.34 - 1.45: 1777 1.45 - 1.57: 5256 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 10280 Sorted by residual: bond pdb=" C ALA D 294 " pdb=" N LEU D 295 " ideal model delta sigma weight residual 1.332 1.289 0.042 1.92e-02 2.71e+03 4.89e+00 bond pdb=" CA GLY D 121 " pdb=" C GLY D 121 " ideal model delta sigma weight residual 1.514 1.489 0.025 1.41e-02 5.03e+03 3.25e+00 bond pdb=" CG LEU D 134 " pdb=" CD1 LEU D 134 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB ARG C 396 " pdb=" CG ARG C 396 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 bond pdb=" C THR E 111 " pdb=" N TYR E 112 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.86e-02 2.89e+03 2.36e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13125 1.54 - 3.07: 719 3.07 - 4.61: 115 4.61 - 6.14: 18 6.14 - 7.68: 8 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C THR E 111 " pdb=" N TYR E 112 " pdb=" CA TYR E 112 " ideal model delta sigma weight residual 121.48 128.38 -6.90 2.04e+00 2.40e-01 1.14e+01 angle pdb=" C VAL B 157 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 121.58 115.41 6.17 1.95e+00 2.63e-01 1.00e+01 angle pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " pdb=" CG TYR A 78 " ideal model delta sigma weight residual 113.90 119.52 -5.62 1.80e+00 3.09e-01 9.74e+00 angle pdb=" C GLY C 372 " pdb=" N GLU C 373 " pdb=" CA GLU C 373 " ideal model delta sigma weight residual 122.40 126.92 -4.52 1.45e+00 4.76e-01 9.73e+00 angle pdb=" C THR B 164 " pdb=" N SER B 165 " pdb=" CA SER B 165 " ideal model delta sigma weight residual 122.82 127.22 -4.40 1.42e+00 4.96e-01 9.60e+00 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 5821 14.84 - 29.68: 186 29.68 - 44.52: 24 44.52 - 59.35: 1 59.35 - 74.19: 5 Dihedral angle restraints: 6037 sinusoidal: 2309 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TYR C 260 " pdb=" C TYR C 260 " pdb=" N PRO C 261 " pdb=" CA PRO C 261 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR D 168 " pdb=" C THR D 168 " pdb=" N THR D 169 " pdb=" CA THR D 169 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 92 " pdb=" C SER A 92 " pdb=" N ASP A 93 " pdb=" CA ASP A 93 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1073 0.052 - 0.105: 355 0.105 - 0.157: 63 0.157 - 0.210: 9 0.210 - 0.262: 3 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB VAL E 71 " pdb=" CA VAL E 71 " pdb=" CG1 VAL E 71 " pdb=" CG2 VAL E 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL E 88 " pdb=" CA VAL E 88 " pdb=" CG1 VAL E 88 " pdb=" CG2 VAL E 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE B 8 " pdb=" CA ILE B 8 " pdb=" CG1 ILE B 8 " pdb=" CG2 ILE B 8 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1500 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 184 " -0.022 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR E 184 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR E 184 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 184 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 184 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 184 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 168 " -0.010 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE E 168 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 168 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE E 168 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 168 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE E 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 168 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " -0.018 2.00e-02 2.50e+03 1.79e-02 6.42e+00 pdb=" CG TYR B 78 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1999 2.77 - 3.30: 8334 3.30 - 3.83: 16447 3.83 - 4.37: 19983 4.37 - 4.90: 34353 Nonbonded interactions: 81116 Sorted by model distance: nonbonded pdb=" OG SER C 383 " pdb=" OE1 GLN C 391 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 234 " pdb=" O PHE A 237 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 255 " pdb=" O ASP A 258 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR D 230 " pdb=" OE1 GLU D 247 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 250 " pdb=" OE1 GLU C 267 " model vdw 2.313 3.040 ... (remaining 81111 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 124 or resid 142 through 269)) selection = chain 'B' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.008 0.057 10281 Z= 0.339 Angle : 0.818 7.675 13987 Z= 0.460 Chirality : 0.054 0.262 1503 Planarity : 0.008 0.055 1828 Dihedral : 8.260 74.192 3664 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.53 (0.20), residues: 1274 helix: -2.33 (0.23), residues: 266 sheet: -1.43 (0.26), residues: 310 loop : -1.46 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 252 TYR 0.048 0.004 TYR E 184 PHE 0.040 0.004 PHE E 168 TRP 0.032 0.003 TRP E 156 HIS 0.006 0.002 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00795 (10280) covalent geometry : angle 0.81525 (13985) SS BOND : bond 0.01287 ( 1) SS BOND : angle 5.66267 ( 2) hydrogen bonds : bond 0.15977 ( 368) hydrogen bonds : angle 7.10334 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 HIS cc_start: 0.7901 (p-80) cc_final: 0.7218 (t-170) REVERT: E 87 MET cc_start: 0.7786 (tpt) cc_final: 0.6797 (tpt) REVERT: E 119 GLN cc_start: 0.7860 (mt0) cc_final: 0.7575 (mt0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.7915 time to fit residues: 146.8689 Evaluate side-chains 73 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 80 GLN C 238 GLN C 374 GLN C 391 GLN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.069454 restraints weight = 17229.797| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.17 r_work: 0.2743 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10281 Z= 0.125 Angle : 0.528 8.047 13987 Z= 0.277 Chirality : 0.040 0.142 1503 Planarity : 0.005 0.040 1828 Dihedral : 4.408 17.224 1422 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.76 % Allowed : 8.61 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.22), residues: 1274 helix: -0.61 (0.29), residues: 276 sheet: -0.94 (0.28), residues: 294 loop : -0.77 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.018 0.002 TYR B 255 PHE 0.011 0.001 PHE A 267 TRP 0.013 0.001 TRP D 415 HIS 0.003 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00280 (10280) covalent geometry : angle 0.52802 (13985) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.96920 ( 2) hydrogen bonds : bond 0.03976 ( 368) hydrogen bonds : angle 4.98065 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8034 (mm-40) REVERT: A 173 ILE cc_start: 0.9061 (tp) cc_final: 0.8681 (pt) REVERT: C 303 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7525 (pm20) REVERT: C 325 HIS cc_start: 0.8268 (p-80) cc_final: 0.7011 (t-170) REVERT: C 366 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: D 191 GLU cc_start: 0.8052 (tt0) cc_final: 0.7841 (tt0) REVERT: E 87 MET cc_start: 0.8270 (tpt) cc_final: 0.7582 (tpt) REVERT: E 197 LYS cc_start: 0.9016 (mttt) cc_final: 0.8591 (mppt) outliers start: 18 outliers final: 4 residues processed: 92 average time/residue: 0.7865 time to fit residues: 76.6425 Evaluate side-chains 75 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 200 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.063763 restraints weight = 17402.444| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.23 r_work: 0.2623 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10281 Z= 0.214 Angle : 0.565 6.532 13987 Z= 0.294 Chirality : 0.042 0.161 1503 Planarity : 0.005 0.033 1828 Dihedral : 4.446 18.975 1422 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 9.59 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.77 (0.22), residues: 1274 helix: -0.00 (0.31), residues: 277 sheet: -0.75 (0.29), residues: 269 loop : -0.54 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 142 TYR 0.029 0.002 TYR D 198 PHE 0.012 0.002 PHE A 186 TRP 0.014 0.001 TRP E 99 HIS 0.003 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00504 (10280) covalent geometry : angle 0.56508 (13985) SS BOND : bond 0.01005 ( 1) SS BOND : angle 1.88436 ( 2) hydrogen bonds : bond 0.04711 ( 368) hydrogen bonds : angle 4.89304 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: C 325 HIS cc_start: 0.8299 (p-80) cc_final: 0.6903 (t-170) REVERT: C 366 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 160 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8717 (mt0) REVERT: D 191 GLU cc_start: 0.8135 (tt0) cc_final: 0.7858 (tt0) REVERT: E 49 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7927 (tm-30) outliers start: 20 outliers final: 7 residues processed: 80 average time/residue: 0.8408 time to fit residues: 71.0453 Evaluate side-chains 74 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 160 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.066525 restraints weight = 17319.149| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.23 r_work: 0.2688 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10281 Z= 0.113 Angle : 0.480 6.985 13987 Z= 0.248 Chirality : 0.039 0.138 1503 Planarity : 0.004 0.033 1828 Dihedral : 4.018 16.674 1422 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.37 % Allowed : 10.57 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.27 (0.23), residues: 1274 helix: 0.49 (0.32), residues: 277 sheet: -0.30 (0.29), residues: 287 loop : -0.31 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.015 0.001 TYR D 198 PHE 0.009 0.001 PHE A 267 TRP 0.011 0.001 TRP E 99 HIS 0.002 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00255 (10280) covalent geometry : angle 0.47995 (13985) SS BOND : bond 0.00541 ( 1) SS BOND : angle 1.34728 ( 2) hydrogen bonds : bond 0.03570 ( 368) hydrogen bonds : angle 4.49446 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 303 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: C 325 HIS cc_start: 0.8302 (p-80) cc_final: 0.6885 (t-170) REVERT: C 366 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: D 191 GLU cc_start: 0.8050 (tt0) cc_final: 0.7772 (tt0) REVERT: E 47 LYS cc_start: 0.8637 (mttt) cc_final: 0.8379 (mmtm) REVERT: E 57 ARG cc_start: 0.7369 (mtm180) cc_final: 0.7012 (mtm-85) REVERT: E 197 LYS cc_start: 0.9019 (mttt) cc_final: 0.8574 (mppt) outliers start: 14 outliers final: 4 residues processed: 84 average time/residue: 0.7873 time to fit residues: 70.2238 Evaluate side-chains 73 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 104 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.066481 restraints weight = 17269.222| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.24 r_work: 0.2683 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10281 Z= 0.111 Angle : 0.475 6.326 13987 Z= 0.245 Chirality : 0.039 0.142 1503 Planarity : 0.004 0.033 1828 Dihedral : 3.889 17.625 1422 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.47 % Allowed : 11.06 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.02 (0.23), residues: 1274 helix: 0.78 (0.32), residues: 272 sheet: -0.12 (0.29), residues: 287 loop : -0.13 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.013 0.001 TYR D 198 PHE 0.008 0.001 PHE B 242 TRP 0.010 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00255 (10280) covalent geometry : angle 0.47484 (13985) SS BOND : bond 0.00570 ( 1) SS BOND : angle 1.37878 ( 2) hydrogen bonds : bond 0.03566 ( 368) hydrogen bonds : angle 4.40341 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.445 Fit side-chains REVERT: A 95 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7946 (mm-40) REVERT: B 213 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: C 325 HIS cc_start: 0.8291 (p-80) cc_final: 0.6839 (t-170) REVERT: C 366 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 47 LYS cc_start: 0.8649 (mttt) cc_final: 0.8387 (mmtm) REVERT: E 57 ARG cc_start: 0.7341 (mtm180) cc_final: 0.6897 (mtm-85) REVERT: E 197 LYS cc_start: 0.9008 (mttt) cc_final: 0.8589 (mppt) outliers start: 15 outliers final: 5 residues processed: 80 average time/residue: 0.7752 time to fit residues: 65.6343 Evaluate side-chains 72 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3205 r_free = 0.3205 target = 0.088608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.065741 restraints weight = 17303.209| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.22 r_work: 0.2664 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10281 Z= 0.129 Angle : 0.488 6.903 13987 Z= 0.251 Chirality : 0.040 0.146 1503 Planarity : 0.004 0.032 1828 Dihedral : 3.901 17.267 1422 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.66 % Allowed : 11.25 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.19 (0.23), residues: 1274 helix: 0.89 (0.32), residues: 271 sheet: 0.02 (0.30), residues: 272 loop : -0.03 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 44 TYR 0.013 0.001 TYR D 198 PHE 0.009 0.001 PHE B 242 TRP 0.010 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00300 (10280) covalent geometry : angle 0.48732 (13985) SS BOND : bond 0.00599 ( 1) SS BOND : angle 1.41806 ( 2) hydrogen bonds : bond 0.03703 ( 368) hydrogen bonds : angle 4.42207 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.426 Fit side-chains REVERT: A 90 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8298 (ptm-80) REVERT: A 213 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8587 (mp10) REVERT: B 213 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8677 (mp10) REVERT: C 325 HIS cc_start: 0.8334 (p-80) cc_final: 0.6887 (t-170) REVERT: C 366 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: E 47 LYS cc_start: 0.8700 (mttt) cc_final: 0.8327 (mmtm) REVERT: E 57 ARG cc_start: 0.7273 (mtm180) cc_final: 0.6984 (mtm-85) REVERT: E 78 ASN cc_start: 0.8863 (t0) cc_final: 0.8611 (t0) REVERT: E 197 LYS cc_start: 0.9039 (mttt) cc_final: 0.8624 (mppt) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 0.8217 time to fit residues: 67.0539 Evaluate side-chains 79 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 0.1980 chunk 120 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3227 r_free = 0.3227 target = 0.089910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067157 restraints weight = 17187.947| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.22 r_work: 0.2702 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10281 Z= 0.101 Angle : 0.470 7.605 13987 Z= 0.241 Chirality : 0.039 0.139 1503 Planarity : 0.003 0.033 1828 Dihedral : 3.756 17.024 1422 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 11.06 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.23), residues: 1274 helix: 1.02 (0.33), residues: 272 sheet: 0.07 (0.30), residues: 275 loop : 0.08 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.011 0.001 TYR B 255 PHE 0.008 0.001 PHE A 267 TRP 0.009 0.001 TRP E 99 HIS 0.002 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00229 (10280) covalent geometry : angle 0.46942 (13985) SS BOND : bond 0.00496 ( 1) SS BOND : angle 1.36257 ( 2) hydrogen bonds : bond 0.03343 ( 368) hydrogen bonds : angle 4.30635 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.409 Fit side-chains REVERT: A 90 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8240 (ptm-80) REVERT: A 95 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7868 (mm-40) REVERT: A 145 PHE cc_start: 0.8185 (m-80) cc_final: 0.7897 (m-80) REVERT: A 213 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: B 213 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8705 (mp10) REVERT: C 325 HIS cc_start: 0.8321 (p-80) cc_final: 0.6890 (t-170) REVERT: C 366 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 47 LYS cc_start: 0.8676 (mttt) cc_final: 0.8297 (mmtm) REVERT: E 57 ARG cc_start: 0.7219 (mtm180) cc_final: 0.6832 (mtm-85) REVERT: E 78 ASN cc_start: 0.8860 (t0) cc_final: 0.8641 (t0) REVERT: E 197 LYS cc_start: 0.9000 (mttt) cc_final: 0.8588 (mppt) outliers start: 16 outliers final: 8 residues processed: 84 average time/residue: 0.7405 time to fit residues: 66.1817 Evaluate side-chains 79 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.0020 chunk 83 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3242 r_free = 0.3242 target = 0.090793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.068146 restraints weight = 16946.714| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.21 r_work: 0.2722 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10281 Z= 0.090 Angle : 0.463 7.669 13987 Z= 0.237 Chirality : 0.039 0.137 1503 Planarity : 0.003 0.033 1828 Dihedral : 3.638 16.379 1422 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.37 % Allowed : 11.64 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.24), residues: 1274 helix: 1.13 (0.33), residues: 272 sheet: 0.12 (0.31), residues: 275 loop : 0.19 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.020 0.001 TYR E 72 PHE 0.008 0.001 PHE A 267 TRP 0.009 0.001 TRP E 99 HIS 0.002 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00204 (10280) covalent geometry : angle 0.46322 (13985) SS BOND : bond 0.00388 ( 1) SS BOND : angle 1.36637 ( 2) hydrogen bonds : bond 0.03154 ( 368) hydrogen bonds : angle 4.22441 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.383 Fit side-chains REVERT: A 90 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8252 (ptm-80) REVERT: A 145 PHE cc_start: 0.8128 (m-80) cc_final: 0.7816 (m-80) REVERT: A 213 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: B 213 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8706 (mp10) REVERT: C 325 HIS cc_start: 0.8324 (p-80) cc_final: 0.6831 (t-170) REVERT: C 366 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 47 LYS cc_start: 0.8683 (mttt) cc_final: 0.8299 (mmtm) REVERT: E 53 GLU cc_start: 0.8638 (tt0) cc_final: 0.8242 (mm-30) REVERT: E 57 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6837 (mtm-85) REVERT: E 197 LYS cc_start: 0.8994 (mttt) cc_final: 0.8598 (mppt) outliers start: 14 outliers final: 4 residues processed: 78 average time/residue: 0.7720 time to fit residues: 63.7383 Evaluate side-chains 75 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3257 r_free = 0.3257 target = 0.091712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069196 restraints weight = 17118.397| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.22 r_work: 0.2740 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10281 Z= 0.087 Angle : 0.461 7.999 13987 Z= 0.238 Chirality : 0.038 0.135 1503 Planarity : 0.003 0.033 1828 Dihedral : 3.552 16.033 1422 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.98 % Allowed : 12.52 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.50 (0.23), residues: 1274 helix: 1.20 (0.33), residues: 272 sheet: 0.17 (0.31), residues: 272 loop : 0.17 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 44 TYR 0.017 0.001 TYR E 72 PHE 0.008 0.001 PHE A 267 TRP 0.009 0.001 TRP E 99 HIS 0.002 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00195 (10280) covalent geometry : angle 0.46060 (13985) SS BOND : bond 0.00376 ( 1) SS BOND : angle 1.34621 ( 2) hydrogen bonds : bond 0.03013 ( 368) hydrogen bonds : angle 4.13500 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.374 Fit side-chains REVERT: A 90 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8260 (ptm-80) REVERT: A 95 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 143 LEU cc_start: 0.8587 (mt) cc_final: 0.8246 (mt) REVERT: A 145 PHE cc_start: 0.8125 (m-80) cc_final: 0.7877 (m-80) REVERT: A 213 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8526 (mp10) REVERT: B 213 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8699 (mp10) REVERT: C 325 HIS cc_start: 0.8294 (p-80) cc_final: 0.6813 (t-170) REVERT: C 366 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: E 53 GLU cc_start: 0.8546 (tt0) cc_final: 0.8221 (mm-30) REVERT: E 57 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7032 (mtm-85) REVERT: E 78 ASN cc_start: 0.8226 (t0) cc_final: 0.7945 (p0) REVERT: E 197 LYS cc_start: 0.8997 (mttt) cc_final: 0.8600 (mppt) outliers start: 10 outliers final: 4 residues processed: 76 average time/residue: 0.7435 time to fit residues: 59.8963 Evaluate side-chains 74 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 72 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3227 r_free = 0.3227 target = 0.089899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.067192 restraints weight = 17044.000| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.20 r_work: 0.2701 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10281 Z= 0.112 Angle : 0.480 8.046 13987 Z= 0.247 Chirality : 0.039 0.143 1503 Planarity : 0.004 0.073 1828 Dihedral : 3.672 16.717 1422 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.78 % Allowed : 12.82 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.24), residues: 1274 helix: 1.15 (0.33), residues: 272 sheet: 0.26 (0.31), residues: 271 loop : 0.18 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 44 TYR 0.018 0.001 TYR E 72 PHE 0.008 0.001 PHE B 242 TRP 0.009 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00260 (10280) covalent geometry : angle 0.47961 (13985) SS BOND : bond 0.00480 ( 1) SS BOND : angle 1.40074 ( 2) hydrogen bonds : bond 0.03407 ( 368) hydrogen bonds : angle 4.23617 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.303 Fit side-chains REVERT: A 90 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8334 (ptm-80) REVERT: A 95 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7792 (mm-40) REVERT: A 143 LEU cc_start: 0.8587 (mt) cc_final: 0.8255 (mt) REVERT: A 145 PHE cc_start: 0.8239 (m-80) cc_final: 0.7898 (m-80) REVERT: A 213 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: B 213 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8696 (mp10) REVERT: C 325 HIS cc_start: 0.8325 (p-80) cc_final: 0.6894 (t-170) REVERT: C 366 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: E 53 GLU cc_start: 0.8481 (tt0) cc_final: 0.8162 (mm-30) REVERT: E 57 ARG cc_start: 0.7542 (mtm180) cc_final: 0.7085 (mtm-85) REVERT: E 78 ASN cc_start: 0.8257 (t0) cc_final: 0.7829 (p0) REVERT: E 197 LYS cc_start: 0.9008 (mttt) cc_final: 0.8613 (mppt) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.7976 time to fit residues: 60.9129 Evaluate side-chains 71 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** 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 = 0.3202 r_free = 0.3202 target = 0.088387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065521 restraints weight = 17227.461| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.22 r_work: 0.2664 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10281 Z= 0.142 Angle : 0.503 7.458 13987 Z= 0.259 Chirality : 0.040 0.148 1503 Planarity : 0.004 0.066 1828 Dihedral : 3.831 17.350 1422 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.88 % Allowed : 12.62 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.49 (0.24), residues: 1274 helix: 1.05 (0.33), residues: 272 sheet: 0.28 (0.31), residues: 272 loop : 0.17 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 44 TYR 0.018 0.001 TYR E 72 PHE 0.009 0.001 PHE B 242 TRP 0.009 0.001 TRP E 99 HIS 0.002 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00334 (10280) covalent geometry : angle 0.50296 (13985) SS BOND : bond 0.00562 ( 1) SS BOND : angle 1.44366 ( 2) hydrogen bonds : bond 0.03768 ( 368) hydrogen bonds : angle 4.36318 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.17 seconds wall clock time: 56 minutes 46.28 seconds (3406.28 seconds total)