Starting phenix.real_space_refine on Tue May 5 13:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3z_65613/05_2026/9w3z_65613.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 9890 2.51 5 N 2384 2.21 5 O 2504 1.98 5 H 14568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29422 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 5098 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 8, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5323 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2120 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "D" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2170 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "E" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 5098 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 8, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5323 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2120 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "H" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2170 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Time building chain proxies: 5.16, per 1000 atoms: 0.18 Number of scatterers: 29422 At special positions: 0 Unit cell: (144.72, 196.176, 106.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 2504 8.00 N 2384 7.00 C 9890 6.00 H 14568 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 142 " 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: 2.32 Conformation dependent library (CDL) restraints added in 858.4 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 66.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 84 through 101 removed outlier: 3.770A pdb=" N ALA A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 130 through 154 removed outlier: 3.596A pdb=" N CYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASP A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 168 through 196 removed outlier: 3.572A pdb=" N GLN A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.610A pdb=" N HIS A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 239 Processing helix chain 'A' and resid 248 through 269 removed outlier: 3.623A pdb=" N LEU A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 298 removed outlier: 4.063A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.837A pdb=" N ALA A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 323 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 385 removed outlier: 4.378A pdb=" N ILE A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 84 through 100 removed outlier: 3.662A pdb=" N VAL C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 130 through 154 removed outlier: 3.819A pdb=" N CYS C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.731A pdb=" N ILE C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 187 removed outlier: 4.026A pdb=" N LYS C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.831A pdb=" N MET C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 240 removed outlier: 3.640A pdb=" N GLN C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.039A pdb=" N PHE C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 277 - end of helix Processing helix chain 'C' and resid 302 through 336 removed outlier: 3.893A pdb=" N SER C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 removed outlier: 4.461A pdb=" N ILE C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 387 removed outlier: 3.797A pdb=" N ARG C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 47 removed outlier: 3.592A pdb=" N PHE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.652A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.528A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 47 removed outlier: 3.597A pdb=" N LEU D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.879A pdb=" N TYR D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 84 through 101 removed outlier: 3.767A pdb=" N ALA E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 130 through 154 removed outlier: 3.590A pdb=" N CYS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 145 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET E 151 " --> pdb=" O ARG E 147 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL E 153 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 168 through 196 removed outlier: 3.572A pdb=" N GLN E 176 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL E 185 " --> pdb=" O PHE E 181 " (cutoff:3.500A) Proline residue: E 188 - end of helix removed outlier: 3.608A pdb=" N HIS E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 239 Processing helix chain 'E' and resid 248 through 269 removed outlier: 3.534A pdb=" N LEU E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 removed outlier: 3.565A pdb=" N GLY E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Proline residue: E 277 - end of helix Processing helix chain 'E' and resid 302 through 332 removed outlier: 3.843A pdb=" N ALA E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU E 323 " --> pdb=" O HIS E 319 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 385 removed outlier: 4.394A pdb=" N ILE E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU E 364 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 367 " --> pdb=" O ALA E 363 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 84 through 100 removed outlier: 3.662A pdb=" N VAL G 94 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 130 through 154 removed outlier: 3.823A pdb=" N CYS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.723A pdb=" N ILE G 160 " --> pdb=" O ARG G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 187 removed outlier: 4.029A pdb=" N LYS G 171 " --> pdb=" O LYS G 167 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG G 172 " --> pdb=" O HIS G 168 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 181 " --> pdb=" O MET G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'G' and resid 203 through 209 removed outlier: 3.839A pdb=" N MET G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR G 208 " --> pdb=" O THR G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 240 removed outlier: 3.640A pdb=" N GLN G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 269 removed outlier: 4.040A pdb=" N PHE G 254 " --> pdb=" O ASN G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 Proline residue: G 277 - end of helix Processing helix chain 'G' and resid 302 through 336 removed outlier: 3.893A pdb=" N SER G 306 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS G 319 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN G 322 " --> pdb=" O ARG G 318 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE G 333 " --> pdb=" O VAL G 329 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 364 removed outlier: 4.460A pdb=" N ILE G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU G 364 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 387 removed outlier: 3.797A pdb=" N ARG G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG G 385 " --> pdb=" O ARG G 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 47 removed outlier: 3.590A pdb=" N PHE F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE F 29 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.654A pdb=" N TYR F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.522A pdb=" N VAL F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 47 removed outlier: 3.598A pdb=" N LEU H 23 " --> pdb=" O LYS H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 76 through 91 removed outlier: 3.878A pdb=" N TYR H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 140 Processing sheet with id=AA1, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 59 removed outlier: 4.159A pdb=" N ALA B 69 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B 125 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 104 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 130 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 100 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 99 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 61 removed outlier: 7.186A pdb=" N VAL D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 101 through 105 removed outlier: 3.653A pdb=" N ILE D 104 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 126 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 126 through 127 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 59 removed outlier: 4.148A pdb=" N ALA F 69 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR F 125 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 104 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 130 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER F 100 " --> pdb=" O GLY F 130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 99 " --> pdb=" O MET F 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 61 removed outlier: 7.190A pdb=" N VAL H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 101 through 105 removed outlier: 3.651A pdb=" N ILE H 104 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 126 " --> pdb=" O ILE H 104 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2472 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: 6.57 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14548 1.03 - 1.23: 26 1.23 - 1.42: 6856 1.42 - 1.61: 8352 1.61 - 1.81: 116 Bond restraints: 29898 Sorted by residual: bond pdb=" N LYS F 19 " pdb=" CA LYS F 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LYS B 19 " pdb=" CA LYS B 19 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" N ILE E 71 " pdb=" CA ILE E 71 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.57e+00 bond pdb=" N ILE A 71 " pdb=" CA ILE A 71 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.57e+00 ... (remaining 29893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 52023 1.41 - 2.83: 1628 2.83 - 4.24: 116 4.24 - 5.66: 13 5.66 - 7.07: 2 Bond angle restraints: 53782 Sorted by residual: angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.96 107.86 5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" N VAL E 185 " pdb=" CA VAL E 185 " pdb=" C VAL E 185 " ideal model delta sigma weight residual 112.96 107.88 5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" N PHE G 220 " pdb=" CA PHE G 220 " pdb=" CB PHE G 220 " ideal model delta sigma weight residual 110.20 105.96 4.24 1.49e+00 4.50e-01 8.12e+00 angle pdb=" N PHE C 220 " pdb=" CA PHE C 220 " pdb=" CB PHE C 220 " ideal model delta sigma weight residual 110.20 105.96 4.24 1.49e+00 4.50e-01 8.10e+00 angle pdb=" C PHE C 181 " pdb=" N TYR C 182 " pdb=" CA TYR C 182 " ideal model delta sigma weight residual 120.31 116.66 3.65 1.52e+00 4.33e-01 5.77e+00 ... (remaining 53777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 12783 17.22 - 34.43: 1116 34.43 - 51.65: 248 51.65 - 68.86: 75 68.86 - 86.08: 20 Dihedral angle restraints: 14242 sinusoidal: 7210 harmonic: 7032 Sorted by residual: dihedral pdb=" CA ASN F 108 " pdb=" C ASN F 108 " pdb=" N VAL F 109 " pdb=" CA VAL F 109 " ideal model delta harmonic sigma weight residual 180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASN B 108 " pdb=" C ASN B 108 " pdb=" N VAL B 109 " pdb=" CA VAL B 109 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASP F 107 " pdb=" C ASP F 107 " pdb=" N ASN F 108 " pdb=" CA ASN F 108 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 14239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1346 0.028 - 0.056: 564 0.056 - 0.084: 261 0.084 - 0.112: 74 0.112 - 0.140: 29 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA VAL H 126 " pdb=" N VAL H 126 " pdb=" C VAL H 126 " pdb=" CB VAL H 126 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL D 126 " pdb=" N VAL D 126 " pdb=" C VAL D 126 " pdb=" CB VAL D 126 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2271 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 220 " -0.022 2.00e-02 2.50e+03 1.32e-02 5.23e+00 pdb=" CG PHE G 220 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE G 220 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE G 220 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE G 220 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 220 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 220 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE G 220 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE G 220 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE G 220 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE G 220 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE G 220 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 317 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C LEU C 317 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU C 317 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG C 318 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 317 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C LEU G 317 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU G 317 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG G 318 " 0.013 2.00e-02 2.50e+03 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1180 2.16 - 2.77: 56178 2.77 - 3.38: 83423 3.38 - 3.99: 102639 3.99 - 4.60: 161329 Nonbonded interactions: 404749 Sorted by model distance: nonbonded pdb=" OE2 GLU F 58 " pdb=" HE1 TRP F 68 " model vdw 1.547 2.450 nonbonded pdb=" OE2 GLU B 58 " pdb=" HE1 TRP B 68 " model vdw 1.549 2.450 nonbonded pdb=" O LEU A 252 " pdb=" HD1 HIS A 256 " model vdw 1.577 2.450 nonbonded pdb=" O LEU E 252 " pdb=" HD1 HIS E 256 " model vdw 1.590 2.450 nonbonded pdb=" O THR F 89 " pdb="HH11 ARG H 78 " model vdw 1.593 2.450 ... (remaining 404744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 71 through 155 or (resid 156 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 157 through 160 or (re \ sid 161 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 162 or resid 166 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 242 through 290 \ or (resid 291 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 292 through 372 or (resid 373 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 374 through 383 or (r \ esid 384 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 385)) selection = chain 'E' selection = (chain 'G' and (resid 71 through 155 or (resid 156 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 157 through 160 or (re \ sid 161 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 162 or resid 166 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 242 through 290 \ or (resid 291 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 292 through 372 or (resid 373 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 374 through 383 or (r \ esid 384 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 385)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 19 through 150) selection = chain 'F' selection = (chain 'H' and resid 19 through 150) } 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: 10.700 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: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.030 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.004 0.036 15338 Z= 0.175 Angle : 0.592 7.073 20870 Z= 0.349 Chirality : 0.040 0.140 2274 Planarity : 0.005 0.050 2562 Dihedral : 14.077 86.081 5340 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -1.80 (0.20), residues: 1780 helix: -0.18 (0.16), residues: 1034 sheet: -2.82 (0.49), residues: 118 loop : -2.52 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 156 TYR 0.027 0.002 TYR E 279 PHE 0.038 0.002 PHE G 220 TRP 0.018 0.001 TRP C 200 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00368 (15330) covalent geometry : angle 0.59240 (20854) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.66761 ( 16) hydrogen bonds : bond 0.12470 ( 838) hydrogen bonds : angle 5.85777 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2042 time to fit residues: 70.8900 Evaluate side-chains 181 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.181280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150651 restraints weight = 64469.764| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.10 r_work: 0.3710 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15338 Z= 0.161 Angle : 0.575 8.420 20870 Z= 0.318 Chirality : 0.039 0.126 2274 Planarity : 0.005 0.048 2562 Dihedral : 5.373 26.184 1998 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.89 % Allowed : 8.01 % Favored : 91.11 % 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: -1.33 (0.20), residues: 1780 helix: 0.05 (0.16), residues: 1046 sheet: -2.00 (0.51), residues: 118 loop : -2.21 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.021 0.002 TYR C 182 PHE 0.030 0.002 PHE G 220 TRP 0.011 0.001 TRP C 200 HIS 0.010 0.001 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00355 (15330) covalent geometry : angle 0.57453 (20854) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.55305 ( 16) hydrogen bonds : bond 0.05247 ( 838) hydrogen bonds : angle 4.99104 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 TYR cc_start: 0.5817 (t80) cc_final: 0.5608 (t80) REVERT: C 200 TRP cc_start: 0.7883 (t-100) cc_final: 0.7542 (t-100) REVERT: C 279 TYR cc_start: 0.7539 (m-80) cc_final: 0.7233 (m-80) REVERT: E 279 TYR cc_start: 0.5860 (t80) cc_final: 0.5651 (t80) REVERT: G 200 TRP cc_start: 0.7877 (t-100) cc_final: 0.7530 (t-100) REVERT: G 279 TYR cc_start: 0.7610 (m-80) cc_final: 0.7292 (m-80) outliers start: 14 outliers final: 10 residues processed: 212 average time/residue: 0.2083 time to fit residues: 71.2278 Evaluate side-chains 203 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 176 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149499 restraints weight = 64521.886| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.17 r_work: 0.3694 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15338 Z= 0.184 Angle : 0.565 8.871 20870 Z= 0.313 Chirality : 0.039 0.126 2274 Planarity : 0.004 0.045 2562 Dihedral : 5.258 26.431 1998 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.33 % Allowed : 10.67 % Favored : 87.99 % 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: -1.18 (0.20), residues: 1780 helix: 0.20 (0.16), residues: 1046 sheet: -1.90 (0.51), residues: 118 loop : -2.21 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 78 TYR 0.019 0.002 TYR E 279 PHE 0.026 0.002 PHE C 220 TRP 0.008 0.001 TRP B 68 HIS 0.009 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00415 (15330) covalent geometry : angle 0.56495 (20854) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.48852 ( 16) hydrogen bonds : bond 0.05139 ( 838) hydrogen bonds : angle 4.81702 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 TRP cc_start: 0.7869 (t-100) cc_final: 0.7482 (t-100) REVERT: G 279 TYR cc_start: 0.7696 (m-80) cc_final: 0.7220 (m-80) REVERT: F 97 GLU cc_start: 0.7048 (pm20) cc_final: 0.6834 (pm20) outliers start: 21 outliers final: 19 residues processed: 209 average time/residue: 0.2176 time to fit residues: 73.8886 Evaluate side-chains 206 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4230 r_free = 0.4230 target = 0.181899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151155 restraints weight = 63949.696| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.14 r_work: 0.3723 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15338 Z= 0.137 Angle : 0.537 8.788 20870 Z= 0.295 Chirality : 0.038 0.122 2274 Planarity : 0.004 0.043 2562 Dihedral : 5.063 24.756 1998 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.21 % Allowed : 11.69 % Favored : 87.10 % 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: -0.92 (0.21), residues: 1780 helix: 0.43 (0.16), residues: 1048 sheet: -1.70 (0.52), residues: 118 loop : -2.17 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 78 TYR 0.018 0.001 TYR G 182 PHE 0.020 0.001 PHE C 220 TRP 0.007 0.001 TRP G 231 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00300 (15330) covalent geometry : angle 0.53664 (20854) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.50588 ( 16) hydrogen bonds : bond 0.04724 ( 838) hydrogen bonds : angle 4.62038 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TRP cc_start: 0.7791 (t-100) cc_final: 0.7459 (t-100) REVERT: C 279 TYR cc_start: 0.7488 (m-80) cc_final: 0.7219 (m-80) REVERT: B 128 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6643 (m-10) REVERT: G 200 TRP cc_start: 0.7788 (t-100) cc_final: 0.7443 (t-100) REVERT: G 279 TYR cc_start: 0.7375 (m-80) cc_final: 0.7114 (m-80) outliers start: 19 outliers final: 15 residues processed: 211 average time/residue: 0.2197 time to fit residues: 74.5814 Evaluate side-chains 202 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 137 optimal weight: 0.0050 chunk 120 optimal weight: 8.9990 chunk 131 optimal weight: 0.0980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4239 r_free = 0.4239 target = 0.182708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152528 restraints weight = 64383.900| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.19 r_work: 0.3730 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15338 Z= 0.128 Angle : 0.519 8.823 20870 Z= 0.284 Chirality : 0.038 0.122 2274 Planarity : 0.004 0.043 2562 Dihedral : 4.880 23.459 1998 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.65 % Allowed : 12.71 % Favored : 85.64 % 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: -0.73 (0.21), residues: 1780 helix: 0.62 (0.16), residues: 1062 sheet: -1.66 (0.51), residues: 118 loop : -2.23 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 381 TYR 0.022 0.001 TYR F 128 PHE 0.018 0.001 PHE C 220 TRP 0.007 0.001 TRP C 231 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00279 (15330) covalent geometry : angle 0.51872 (20854) SS BOND : bond 0.00136 ( 8) SS BOND : angle 0.50048 ( 16) hydrogen bonds : bond 0.04466 ( 838) hydrogen bonds : angle 4.48114 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8520 (tt0) cc_final: 0.8061 (mt-10) REVERT: C 200 TRP cc_start: 0.7869 (t-100) cc_final: 0.7586 (t-100) REVERT: C 279 TYR cc_start: 0.7533 (m-80) cc_final: 0.7296 (m-80) REVERT: B 128 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: G 200 TRP cc_start: 0.7864 (t-100) cc_final: 0.7565 (t-100) REVERT: G 279 TYR cc_start: 0.7458 (m-80) cc_final: 0.7228 (m-80) outliers start: 26 outliers final: 22 residues processed: 216 average time/residue: 0.2256 time to fit residues: 78.0888 Evaluate side-chains 210 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 126 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.0370 chunk 145 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 160 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4246 r_free = 0.4246 target = 0.183486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153373 restraints weight = 63998.869| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.31 r_work: 0.3744 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15338 Z= 0.117 Angle : 0.505 8.820 20870 Z= 0.275 Chirality : 0.037 0.122 2274 Planarity : 0.004 0.041 2562 Dihedral : 4.726 22.389 1998 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.59 % Allowed : 13.09 % Favored : 85.32 % 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: -0.54 (0.21), residues: 1780 helix: 0.79 (0.16), residues: 1062 sheet: -1.67 (0.50), residues: 124 loop : -2.18 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 381 TYR 0.017 0.001 TYR C 182 PHE 0.028 0.001 PHE E 310 TRP 0.007 0.001 TRP G 231 HIS 0.004 0.001 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00258 (15330) covalent geometry : angle 0.50530 (20854) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.42393 ( 16) hydrogen bonds : bond 0.04259 ( 838) hydrogen bonds : angle 4.37220 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.8505 (tt0) cc_final: 0.8086 (mt-10) REVERT: C 200 TRP cc_start: 0.7797 (t-100) cc_final: 0.7469 (t-100) REVERT: C 279 TYR cc_start: 0.7530 (m-80) cc_final: 0.7310 (m-80) REVERT: B 128 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: G 200 TRP cc_start: 0.7798 (t-100) cc_final: 0.7465 (t-100) REVERT: G 279 TYR cc_start: 0.7445 (m-80) cc_final: 0.7240 (m-80) REVERT: F 76 ASP cc_start: 0.7343 (p0) cc_final: 0.7104 (p0) outliers start: 25 outliers final: 22 residues processed: 217 average time/residue: 0.2386 time to fit residues: 81.4649 Evaluate side-chains 219 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4231 r_free = 0.4231 target = 0.181980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150963 restraints weight = 64083.210| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.20 r_work: 0.3717 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15338 Z= 0.140 Angle : 0.515 8.661 20870 Z= 0.281 Chirality : 0.038 0.125 2274 Planarity : 0.004 0.040 2562 Dihedral : 4.711 22.941 1998 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.91 % Allowed : 13.34 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1780 helix: 0.83 (0.16), residues: 1060 sheet: -1.69 (0.50), residues: 124 loop : -2.14 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 381 TYR 0.016 0.001 TYR C 182 PHE 0.019 0.001 PHE E 310 TRP 0.007 0.001 TRP F 68 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00313 (15330) covalent geometry : angle 0.51515 (20854) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.44063 ( 16) hydrogen bonds : bond 0.04306 ( 838) hydrogen bonds : angle 4.36692 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TRP cc_start: 0.7843 (t-100) cc_final: 0.7496 (t-100) REVERT: B 128 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6789 (m-10) REVERT: G 200 TRP cc_start: 0.7828 (t-100) cc_final: 0.7473 (t-100) REVERT: F 76 ASP cc_start: 0.7376 (p0) cc_final: 0.7114 (p0) outliers start: 30 outliers final: 25 residues processed: 221 average time/residue: 0.2416 time to fit residues: 83.8356 Evaluate side-chains 215 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4233 r_free = 0.4233 target = 0.182306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151538 restraints weight = 63979.090| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.14 r_work: 0.3727 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15338 Z= 0.133 Angle : 0.509 8.691 20870 Z= 0.277 Chirality : 0.038 0.125 2274 Planarity : 0.004 0.040 2562 Dihedral : 4.688 22.611 1998 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.91 % Allowed : 13.41 % Favored : 84.69 % 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: -0.44 (0.21), residues: 1780 helix: 0.87 (0.16), residues: 1060 sheet: -1.62 (0.50), residues: 124 loop : -2.11 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.014 0.001 TYR C 182 PHE 0.015 0.001 PHE C 220 TRP 0.007 0.001 TRP F 68 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00297 (15330) covalent geometry : angle 0.50900 (20854) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.39455 ( 16) hydrogen bonds : bond 0.04238 ( 838) hydrogen bonds : angle 4.35650 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TRP cc_start: 0.7820 (t-100) cc_final: 0.7476 (t-100) REVERT: B 128 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6727 (m-10) REVERT: E 279 TYR cc_start: 0.6369 (t80) cc_final: 0.6110 (t80) REVERT: G 200 TRP cc_start: 0.7830 (t-100) cc_final: 0.7482 (t-100) outliers start: 30 outliers final: 29 residues processed: 214 average time/residue: 0.2145 time to fit residues: 73.7071 Evaluate side-chains 224 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4230 r_free = 0.4230 target = 0.182034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151799 restraints weight = 64057.369| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.18 r_work: 0.3720 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15338 Z= 0.138 Angle : 0.514 8.631 20870 Z= 0.280 Chirality : 0.038 0.128 2274 Planarity : 0.004 0.039 2562 Dihedral : 4.662 22.627 1998 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.03 % Allowed : 13.53 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1780 helix: 0.87 (0.16), residues: 1060 sheet: -1.58 (0.50), residues: 124 loop : -2.11 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 381 TYR 0.015 0.001 TYR C 182 PHE 0.015 0.001 PHE F 101 TRP 0.006 0.001 TRP F 68 HIS 0.004 0.001 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00310 (15330) covalent geometry : angle 0.51375 (20854) SS BOND : bond 0.00175 ( 8) SS BOND : angle 0.41712 ( 16) hydrogen bonds : bond 0.04229 ( 838) hydrogen bonds : angle 4.33530 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TRP cc_start: 0.7805 (t-100) cc_final: 0.7431 (t-100) REVERT: B 128 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6759 (m-10) REVERT: E 279 TYR cc_start: 0.6342 (t80) cc_final: 0.6025 (t80) REVERT: G 200 TRP cc_start: 0.7827 (t-100) cc_final: 0.7469 (t-100) outliers start: 32 outliers final: 29 residues processed: 216 average time/residue: 0.2241 time to fit residues: 77.9186 Evaluate side-chains 221 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4232 r_free = 0.4232 target = 0.182261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152009 restraints weight = 64207.871| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.12 r_work: 0.3739 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15338 Z= 0.137 Angle : 0.511 8.633 20870 Z= 0.278 Chirality : 0.038 0.121 2274 Planarity : 0.004 0.039 2562 Dihedral : 4.633 22.582 1998 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.03 % Allowed : 14.17 % Favored : 83.80 % 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: -0.41 (0.21), residues: 1780 helix: 0.90 (0.16), residues: 1060 sheet: -1.66 (0.50), residues: 126 loop : -2.09 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 147 TYR 0.014 0.001 TYR C 182 PHE 0.015 0.001 PHE F 101 TRP 0.006 0.001 TRP B 68 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00307 (15330) covalent geometry : angle 0.51119 (20854) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.36426 ( 16) hydrogen bonds : bond 0.04211 ( 838) hydrogen bonds : angle 4.31174 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Residue ILE 71 is missing expected H atoms. Skipping. Residue SER 74 is missing expected H atoms. Skipping. Residue ILE 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue TYR 80 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 TRP cc_start: 0.7810 (t-100) cc_final: 0.7450 (t-100) REVERT: B 128 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: E 279 TYR cc_start: 0.6211 (t80) cc_final: 0.5930 (t80) REVERT: G 200 TRP cc_start: 0.7802 (t-100) cc_final: 0.7440 (t-100) REVERT: F 128 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6650 (m-10) outliers start: 32 outliers final: 28 residues processed: 211 average time/residue: 0.2261 time to fit residues: 76.3892 Evaluate side-chains 222 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain D residue 102 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 132 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4237 r_free = 0.4237 target = 0.182826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152341 restraints weight = 64082.979| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.22 r_work: 0.3748 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15338 Z= 0.127 Angle : 0.504 8.666 20870 Z= 0.274 Chirality : 0.037 0.122 2274 Planarity : 0.004 0.039 2562 Dihedral : 4.548 22.733 1998 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.97 % Allowed : 14.61 % Favored : 83.42 % 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 (0.21), residues: 1780 helix: 0.96 (0.17), residues: 1062 sheet: -1.63 (0.50), residues: 126 loop : -2.08 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.015 0.001 TYR C 182 PHE 0.014 0.001 PHE C 220 TRP 0.006 0.001 TRP G 231 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00282 (15330) covalent geometry : angle 0.50383 (20854) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.40780 ( 16) hydrogen bonds : bond 0.04098 ( 838) hydrogen bonds : angle 4.26600 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7603.64 seconds wall clock time: 129 minutes 40.10 seconds (7780.10 seconds total)