Starting phenix.real_space_refine on Wed May 6 16:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.cif Found real_map, /net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11zs_76231/05_2026/11zs_76231.map" } resolution = 3.28 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 228 5.16 5 C 26820 2.51 5 N 7224 2.21 5 O 7680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s 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: 41952 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "B" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "C" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "D" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "E" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "F" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "G" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "H" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "I" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "J" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "K" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Chain: "L" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3496 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 414} Chain breaks: 2 Time building chain proxies: 9.71, per 1000 atoms: 0.23 Number of scatterers: 41952 At special positions: 0 Unit cell: (158.33, 156.91, 118.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 228 16.00 O 7680 8.00 N 7224 7.00 C 26820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9672 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 14 sheets defined 47.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.583A pdb=" N LEU A 57 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 58 " --> pdb=" O ASN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.655A pdb=" N LEU A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.848A pdb=" N ARG A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 174 through 196 removed outlier: 3.513A pdb=" N THR A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 220 through 241 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 304 removed outlier: 5.178A pdb=" N THR A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.855A pdb=" N TYR A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 318' Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.571A pdb=" N LYS A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.252A pdb=" N LEU A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.652A pdb=" N LEU B 57 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 58 " --> pdb=" O ASN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.665A pdb=" N LEU B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.848A pdb=" N ARG B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 174 through 196 removed outlier: 3.674A pdb=" N THR B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 220 through 241 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 286 through 304 removed outlier: 5.194A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.873A pdb=" N TYR B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 318' Processing helix chain 'B' and resid 360 through 379 Processing helix chain 'B' and resid 402 through 413 Processing helix chain 'B' and resid 413 through 420 removed outlier: 3.563A pdb=" N LYS B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 444 through 450 removed outlier: 4.038A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 54 through 59 removed outlier: 3.603A pdb=" N LEU C 57 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 58 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.667A pdb=" N LEU C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 118 through 134 removed outlier: 3.813A pdb=" N ARG C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 174 through 196 removed outlier: 3.559A pdb=" N THR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 180 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Proline residue: C 183 - end of helix Processing helix chain 'C' and resid 220 through 241 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 286 through 304 removed outlier: 5.181A pdb=" N THR C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.829A pdb=" N TYR C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 318' Processing helix chain 'C' and resid 360 through 379 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.547A pdb=" N LYS C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 441 Processing helix chain 'C' and resid 444 through 450 removed outlier: 4.203A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.536A pdb=" N LEU D 57 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 58 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 removed outlier: 3.652A pdb=" N LEU D 91 " --> pdb=" O LEU D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.847A pdb=" N ARG D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.618A pdb=" N THR D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG D 180 " --> pdb=" O HIS D 176 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Proline residue: D 183 - end of helix Processing helix chain 'D' and resid 220 through 241 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 286 through 300 Processing helix chain 'D' and resid 303 through 308 Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.873A pdb=" N TYR D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG D 316 " --> pdb=" O ASN D 312 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 318 " --> pdb=" O TYR D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 310 through 318' Processing helix chain 'D' and resid 360 through 379 Processing helix chain 'D' and resid 402 through 413 Processing helix chain 'D' and resid 413 through 420 removed outlier: 3.565A pdb=" N LYS D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 442 Processing helix chain 'D' and resid 444 through 450 removed outlier: 4.023A pdb=" N LEU D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.577A pdb=" N LEU E 57 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 58 " --> pdb=" O ASN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 removed outlier: 3.666A pdb=" N LEU E 91 " --> pdb=" O LEU E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 91' Processing helix chain 'E' and resid 118 through 134 removed outlier: 3.840A pdb=" N ARG E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 159 Processing helix chain 'E' and resid 174 through 196 removed outlier: 3.551A pdb=" N THR E 178 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG E 180 " --> pdb=" O HIS E 176 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Proline residue: E 183 - end of helix Processing helix chain 'E' and resid 220 through 241 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 286 through 304 removed outlier: 5.183A pdb=" N THR E 301 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 303 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 308 Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.854A pdb=" N TYR E 314 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 318 " --> pdb=" O TYR E 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 318' Processing helix chain 'E' and resid 360 through 379 Processing helix chain 'E' and resid 402 through 413 Processing helix chain 'E' and resid 413 through 420 removed outlier: 3.560A pdb=" N LYS E 417 " --> pdb=" O SER E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 442 Processing helix chain 'E' and resid 444 through 450 removed outlier: 4.247A pdb=" N LEU E 448 " --> pdb=" O THR E 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 54 through 59 removed outlier: 3.628A pdb=" N LEU F 57 " --> pdb=" O CYS F 54 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 58 " --> pdb=" O ASN F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 91 removed outlier: 3.723A pdb=" N LEU F 91 " --> pdb=" O LEU F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 91' Processing helix chain 'F' and resid 118 through 134 removed outlier: 3.856A pdb=" N ARG F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 159 Processing helix chain 'F' and resid 174 through 196 removed outlier: 3.587A pdb=" N THR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG F 180 " --> pdb=" O HIS F 176 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Proline residue: F 183 - end of helix Processing helix chain 'F' and resid 220 through 241 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 286 through 304 removed outlier: 5.183A pdb=" N THR F 301 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP F 302 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 303 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 308 Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.833A pdb=" N TYR F 314 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS F 315 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG F 316 " --> pdb=" O ASN F 312 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 318 " --> pdb=" O TYR F 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 310 through 318' Processing helix chain 'F' and resid 360 through 379 Processing helix chain 'F' and resid 402 through 413 Processing helix chain 'F' and resid 413 through 420 removed outlier: 3.555A pdb=" N LYS F 417 " --> pdb=" O SER F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 442 Processing helix chain 'F' and resid 444 through 450 removed outlier: 4.077A pdb=" N LEU F 448 " --> pdb=" O THR F 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 17 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 54 through 59 removed outlier: 3.579A pdb=" N LEU G 57 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU G 58 " --> pdb=" O ASN G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 91 removed outlier: 3.690A pdb=" N LEU G 91 " --> pdb=" O LEU G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 88 through 91' Processing helix chain 'G' and resid 118 through 134 removed outlier: 3.829A pdb=" N ARG G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 159 Processing helix chain 'G' and resid 174 through 196 removed outlier: 3.545A pdb=" N THR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG G 180 " --> pdb=" O HIS G 176 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) Proline residue: G 183 - end of helix Processing helix chain 'G' and resid 220 through 241 Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 286 through 304 removed outlier: 5.186A pdb=" N THR G 301 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR G 303 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 310 through 318 removed outlier: 3.854A pdb=" N TYR G 314 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS G 315 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN G 318 " --> pdb=" O TYR G 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 310 through 318' Processing helix chain 'G' and resid 360 through 379 Processing helix chain 'G' and resid 402 through 413 Processing helix chain 'G' and resid 413 through 420 removed outlier: 3.576A pdb=" N LYS G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 441 Processing helix chain 'G' and resid 444 through 450 removed outlier: 4.206A pdb=" N LEU G 448 " --> pdb=" O THR G 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 40 through 46 Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.629A pdb=" N LEU H 57 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU H 58 " --> pdb=" O ASN H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 91 removed outlier: 3.684A pdb=" N LEU H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 91' Processing helix chain 'H' and resid 118 through 134 removed outlier: 3.849A pdb=" N ARG H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 159 Processing helix chain 'H' and resid 174 through 196 removed outlier: 3.603A pdb=" N THR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG H 180 " --> pdb=" O HIS H 176 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU H 181 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Proline residue: H 183 - end of helix Processing helix chain 'H' and resid 220 through 241 Processing helix chain 'H' and resid 281 through 285 Processing helix chain 'H' and resid 286 through 300 Processing helix chain 'H' and resid 303 through 308 Processing helix chain 'H' and resid 310 through 318 removed outlier: 3.842A pdb=" N TYR H 314 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 315 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG H 316 " --> pdb=" O ASN H 312 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE H 317 " --> pdb=" O SER H 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN H 318 " --> pdb=" O TYR H 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 310 through 318' Processing helix chain 'H' and resid 360 through 379 Processing helix chain 'H' and resid 402 through 413 Processing helix chain 'H' and resid 413 through 420 removed outlier: 3.563A pdb=" N LYS H 417 " --> pdb=" O SER H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 441 Processing helix chain 'H' and resid 444 through 450 removed outlier: 4.121A pdb=" N LEU H 448 " --> pdb=" O THR H 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 17 Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 54 through 59 removed outlier: 3.581A pdb=" N LEU I 57 " --> pdb=" O CYS I 54 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 58 " --> pdb=" O ASN I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 91 removed outlier: 3.654A pdb=" N LEU I 91 " --> pdb=" O LEU I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 91' Processing helix chain 'I' and resid 118 through 134 removed outlier: 3.843A pdb=" N ARG I 133 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 159 Processing helix chain 'I' and resid 174 through 180 removed outlier: 3.597A pdb=" N THR I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG I 180 " --> pdb=" O HIS I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 196 removed outlier: 3.640A pdb=" N LEU I 185 " --> pdb=" O GLU I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 241 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 286 through 304 removed outlier: 5.191A pdb=" N THR I 301 " --> pdb=" O ILE I 297 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR I 303 " --> pdb=" O TYR I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 308 Processing helix chain 'I' and resid 310 through 318 removed outlier: 3.827A pdb=" N TYR I 314 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS I 315 " --> pdb=" O ILE I 311 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG I 316 " --> pdb=" O ASN I 312 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE I 317 " --> pdb=" O SER I 313 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN I 318 " --> pdb=" O TYR I 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 310 through 318' Processing helix chain 'I' and resid 360 through 379 Processing helix chain 'I' and resid 402 through 413 Processing helix chain 'I' and resid 413 through 420 removed outlier: 3.592A pdb=" N LYS I 417 " --> pdb=" O SER I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 442 Processing helix chain 'I' and resid 444 through 450 removed outlier: 4.126A pdb=" N LEU I 448 " --> pdb=" O THR I 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 17 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 54 through 59 removed outlier: 3.580A pdb=" N LEU J 57 " --> pdb=" O CYS J 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 58 " --> pdb=" O ASN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 91 removed outlier: 3.657A pdb=" N LEU J 91 " --> pdb=" O LEU J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 91' Processing helix chain 'J' and resid 118 through 134 removed outlier: 3.847A pdb=" N ARG J 133 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY J 134 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 159 Processing helix chain 'J' and resid 174 through 196 removed outlier: 3.548A pdb=" N THR J 178 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG J 180 " --> pdb=" O HIS J 176 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU J 181 " --> pdb=" O LEU J 177 " (cutoff:3.500A) Proline residue: J 183 - end of helix Processing helix chain 'J' and resid 220 through 241 Processing helix chain 'J' and resid 281 through 285 Processing helix chain 'J' and resid 286 through 304 removed outlier: 5.191A pdb=" N THR J 301 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP J 302 " --> pdb=" O LYS J 298 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR J 303 " --> pdb=" O TYR J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 308 Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.870A pdb=" N TYR J 314 " --> pdb=" O TYR J 310 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS J 315 " --> pdb=" O ILE J 311 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG J 316 " --> pdb=" O ASN J 312 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE J 317 " --> pdb=" O SER J 313 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN J 318 " --> pdb=" O TYR J 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 310 through 318' Processing helix chain 'J' and resid 360 through 379 Processing helix chain 'J' and resid 402 through 413 Processing helix chain 'J' and resid 413 through 420 removed outlier: 3.567A pdb=" N LYS J 417 " --> pdb=" O SER J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 421 through 441 Processing helix chain 'J' and resid 444 through 450 removed outlier: 4.136A pdb=" N LEU J 448 " --> pdb=" O THR J 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.584A pdb=" N LEU K 57 " --> pdb=" O CYS K 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU K 58 " --> pdb=" O ASN K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 91 removed outlier: 3.651A pdb=" N LEU K 91 " --> pdb=" O LEU K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 91' Processing helix chain 'K' and resid 118 through 134 removed outlier: 3.827A pdb=" N ARG K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 134 " --> pdb=" O LEU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 159 Processing helix chain 'K' and resid 174 through 196 removed outlier: 3.593A pdb=" N THR K 178 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG K 180 " --> pdb=" O HIS K 176 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU K 181 " --> pdb=" O LEU K 177 " (cutoff:3.500A) Proline residue: K 183 - end of helix Processing helix chain 'K' and resid 220 through 241 Processing helix chain 'K' and resid 281 through 285 Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 303 through 308 Processing helix chain 'K' and resid 310 through 318 removed outlier: 3.885A pdb=" N TYR K 314 " --> pdb=" O TYR K 310 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS K 315 " --> pdb=" O ILE K 311 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG K 316 " --> pdb=" O ASN K 312 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE K 317 " --> pdb=" O SER K 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN K 318 " --> pdb=" O TYR K 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 310 through 318' Processing helix chain 'K' and resid 360 through 379 Processing helix chain 'K' and resid 402 through 413 Processing helix chain 'K' and resid 413 through 420 removed outlier: 3.571A pdb=" N LYS K 417 " --> pdb=" O SER K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 441 Processing helix chain 'K' and resid 444 through 450 removed outlier: 4.088A pdb=" N LEU K 448 " --> pdb=" O THR K 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 17 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 54 through 59 removed outlier: 3.590A pdb=" N LEU L 57 " --> pdb=" O CYS L 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU L 58 " --> pdb=" O ASN L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 91 removed outlier: 3.697A pdb=" N LEU L 91 " --> pdb=" O LEU L 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 88 through 91' Processing helix chain 'L' and resid 118 through 134 removed outlier: 3.823A pdb=" N ARG L 133 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 134 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 159 Processing helix chain 'L' and resid 174 through 196 removed outlier: 3.552A pdb=" N THR L 178 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG L 180 " --> pdb=" O HIS L 176 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU L 181 " --> pdb=" O LEU L 177 " (cutoff:3.500A) Proline residue: L 183 - end of helix Processing helix chain 'L' and resid 220 through 241 Processing helix chain 'L' and resid 281 through 285 Processing helix chain 'L' and resid 286 through 304 removed outlier: 5.167A pdb=" N THR L 301 " --> pdb=" O ILE L 297 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP L 302 " --> pdb=" O LYS L 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR L 303 " --> pdb=" O TYR L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 308 Processing helix chain 'L' and resid 310 through 318 removed outlier: 3.844A pdb=" N TYR L 314 " --> pdb=" O TYR L 310 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS L 315 " --> pdb=" O ILE L 311 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG L 316 " --> pdb=" O ASN L 312 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE L 317 " --> pdb=" O SER L 313 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN L 318 " --> pdb=" O TYR L 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 310 through 318' Processing helix chain 'L' and resid 360 through 379 Processing helix chain 'L' and resid 402 through 413 Processing helix chain 'L' and resid 413 through 420 removed outlier: 3.568A pdb=" N LYS L 417 " --> pdb=" O SER L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 441 Processing helix chain 'L' and resid 444 through 450 removed outlier: 4.002A pdb=" N LEU L 448 " --> pdb=" O THR L 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 39 current: chain 'A' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 86 current: chain 'A' and resid 100 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 108 current: chain 'C' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 210 through 215 current: chain 'C' and resid 336 through 341 removed outlier: 3.889A pdb=" N ARG C 339 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 135 through 148 current: chain 'A' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 210 through 215 current: chain 'A' and resid 336 through 341 removed outlier: 3.871A pdb=" N ARG A 339 " --> pdb=" O GLU A 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 351 current: chain 'D' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 33 through 39 current: chain 'D' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 86 current: chain 'D' and resid 100 through 108 Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 33 through 39 current: chain 'B' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 86 current: chain 'B' and resid 100 through 108 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 100 through 108 current: chain 'F' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 210 through 215 current: chain 'F' and resid 336 through 341 removed outlier: 3.872A pdb=" N ARG F 339 " --> pdb=" O GLU F 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 218 through 219 removed outlier: 3.578A pdb=" N ILE B 350 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 339 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LYS B 326 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG B 339 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N MET B 328 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 11.469A pdb=" N CYS B 341 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N SER B 330 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 148 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 143 through 148 current: chain 'B' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 210 through 215 current: chain 'C' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 33 through 39 current: chain 'C' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 86 current: chain 'C' and resid 100 through 108 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 135 through 148 current: chain 'D' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 210 through 215 current: chain 'D' and resid 336 through 341 removed outlier: 3.865A pdb=" N ARG D 339 " --> pdb=" O GLU D 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 349 through 351 current: chain 'E' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 33 through 39 current: chain 'E' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 83 through 86 current: chain 'E' and resid 100 through 108 Processing sheet with id=AA7, first strand: chain 'E' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 135 through 148 current: chain 'E' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 210 through 215 current: chain 'E' and resid 336 through 341 removed outlier: 3.882A pdb=" N ARG E 339 " --> pdb=" O GLU E 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 349 through 351 current: chain 'F' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 33 through 39 current: chain 'F' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 83 through 86 current: chain 'F' and resid 100 through 108 Processing sheet with id=AA8, first strand: chain 'G' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 33 through 39 current: chain 'G' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 83 through 86 current: chain 'G' and resid 100 through 108 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 100 through 108 current: chain 'I' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 210 through 215 current: chain 'I' and resid 336 through 341 removed outlier: 3.867A pdb=" N ARG I 339 " --> pdb=" O GLU I 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 148 current: chain 'G' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 210 through 215 current: chain 'G' and resid 336 through 341 removed outlier: 3.897A pdb=" N ARG G 339 " --> pdb=" O GLU G 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 349 through 351 current: chain 'J' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 33 through 39 current: chain 'J' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 83 through 86 current: chain 'J' and resid 100 through 108 Processing sheet with id=AB1, first strand: chain 'H' and resid 21 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 33 through 39 current: chain 'H' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 83 through 86 current: chain 'H' and resid 100 through 108 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 100 through 108 current: chain 'L' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 210 through 215 current: chain 'L' and resid 336 through 341 removed outlier: 3.877A pdb=" N ARG L 339 " --> pdb=" O GLU L 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 135 through 148 current: chain 'H' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 210 through 215 current: chain 'H' and resid 336 through 341 removed outlier: 3.878A pdb=" N ARG H 339 " --> pdb=" O GLU H 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 349 through 351 current: chain 'I' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 33 through 39 current: chain 'I' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 83 through 86 current: chain 'I' and resid 100 through 108 Processing sheet with id=AB3, first strand: chain 'J' and resid 135 through 148 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 135 through 148 current: chain 'J' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 210 through 215 current: chain 'J' and resid 336 through 341 removed outlier: 3.896A pdb=" N ARG J 339 " --> pdb=" O GLU J 351 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 349 through 351 current: chain 'K' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 33 through 39 current: chain 'K' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 83 through 86 current: chain 'K' and resid 100 through 108 Processing sheet with id=AB4, first strand: chain 'K' and resid 218 through 219 removed outlier: 3.590A pdb=" N ILE K 350 " --> pdb=" O ASN K 264 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG K 339 " --> pdb=" O GLU K 351 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS K 326 " --> pdb=" O ALA K 336 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE K 338 " --> pdb=" O LYS K 326 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET K 328 " --> pdb=" O PHE K 338 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU K 340 " --> pdb=" O MET K 328 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER K 330 " --> pdb=" O LEU K 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 143 through 148 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 143 through 148 current: chain 'K' and resid 210 through 215 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 210 through 215 current: chain 'L' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 33 through 39 current: chain 'L' and resid 83 through 86 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 83 through 86 current: chain 'L' and resid 100 through 108 No H-bonds generated for sheet with id=AB5 1525 hydrogen bonds defined for protein. 4371 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: 8.64 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13682 1.34 - 1.46: 9818 1.46 - 1.58: 19184 1.58 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 43056 Sorted by residual: bond pdb=" N TYR F 173 " pdb=" CA TYR F 173 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.98e-01 bond pdb=" C ARG K 226 " pdb=" O ARG K 226 " ideal model delta sigma weight residual 1.235 1.225 0.011 1.26e-02 6.30e+03 7.10e-01 bond pdb=" CA ARG F 450 " pdb=" CB ARG F 450 " ideal model delta sigma weight residual 1.536 1.570 -0.034 4.10e-02 5.95e+02 6.78e-01 bond pdb=" C ARG I 226 " pdb=" O ARG I 226 " ideal model delta sigma weight residual 1.235 1.225 0.010 1.26e-02 6.30e+03 6.73e-01 bond pdb=" C ARG A 226 " pdb=" O ARG A 226 " ideal model delta sigma weight residual 1.235 1.225 0.010 1.26e-02 6.30e+03 6.64e-01 ... (remaining 43051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 56794 0.98 - 1.96: 1126 1.96 - 2.94: 111 2.94 - 3.93: 192 3.93 - 4.91: 1 Bond angle restraints: 58224 Sorted by residual: angle pdb=" C GLY F 172 " pdb=" N TYR F 173 " pdb=" CA TYR F 173 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.60e+00 angle pdb=" N MET I 64 " pdb=" CA MET I 64 " pdb=" CB MET I 64 " ideal model delta sigma weight residual 113.89 110.21 3.68 1.93e+00 2.68e-01 3.64e+00 angle pdb=" N MET K 64 " pdb=" CA MET K 64 " pdb=" CB MET K 64 " ideal model delta sigma weight residual 113.15 110.26 2.89 1.63e+00 3.76e-01 3.14e+00 angle pdb=" CA PRO K 208 " pdb=" C PRO K 208 " pdb=" O PRO K 208 " ideal model delta sigma weight residual 123.16 120.56 2.60 1.49e+00 4.50e-01 3.04e+00 angle pdb=" CA PRO F 208 " pdb=" C PRO F 208 " pdb=" O PRO F 208 " ideal model delta sigma weight residual 123.16 120.57 2.59 1.49e+00 4.50e-01 3.03e+00 ... (remaining 58219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 24116 14.31 - 28.62: 1067 28.62 - 42.92: 196 42.92 - 57.23: 59 57.23 - 71.54: 14 Dihedral angle restraints: 25452 sinusoidal: 10320 harmonic: 15132 Sorted by residual: dihedral pdb=" CA ARG H 159 " pdb=" CB ARG H 159 " pdb=" CG ARG H 159 " pdb=" CD ARG H 159 " ideal model delta sinusoidal sigma weight residual -60.00 -117.22 57.22 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA GLU I 162 " pdb=" CB GLU I 162 " pdb=" CG GLU I 162 " pdb=" CD GLU I 162 " ideal model delta sinusoidal sigma weight residual -60.00 -116.07 56.07 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB MET D 248 " pdb=" CG MET D 248 " pdb=" SD MET D 248 " pdb=" CE MET D 248 " ideal model delta sinusoidal sigma weight residual 60.00 4.51 55.49 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 25449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3824 0.026 - 0.051: 1338 0.051 - 0.077: 474 0.077 - 0.103: 220 0.103 - 0.128: 192 Chirality restraints: 6048 Sorted by residual: chirality pdb=" CA ILE K 19 " pdb=" N ILE K 19 " pdb=" C ILE K 19 " pdb=" CB ILE K 19 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE D 197 " pdb=" N ILE D 197 " pdb=" C ILE D 197 " pdb=" CB ILE D 197 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE C 197 " pdb=" N ILE C 197 " pdb=" C ILE C 197 " pdb=" CB ILE C 197 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 6045 not shown) Planarity restraints: 7524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 226 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ARG F 226 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG F 226 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS F 227 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 226 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ARG E 226 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG E 226 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS E 227 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 448 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LEU D 448 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU D 448 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR D 449 " 0.011 2.00e-02 2.50e+03 ... (remaining 7521 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 22253 2.98 - 3.46: 43049 3.46 - 3.94: 65738 3.94 - 4.42: 79470 4.42 - 4.90: 130463 Nonbonded interactions: 340973 Sorted by model distance: nonbonded pdb=" O TYR G 283 " pdb=" OG1 THR G 284 " model vdw 2.499 3.040 nonbonded pdb=" O TYR L 283 " pdb=" OG1 THR L 284 " model vdw 2.502 3.040 nonbonded pdb=" O GLU K 162 " pdb=" OE1 GLU K 162 " model vdw 2.503 3.040 nonbonded pdb=" O TYR E 283 " pdb=" OG1 THR E 284 " model vdw 2.503 3.040 nonbonded pdb=" O TYR C 283 " pdb=" OG1 THR C 284 " model vdw 2.504 3.040 ... (remaining 340968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.750 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43056 Z= 0.085 Angle : 0.394 4.906 58224 Z= 0.212 Chirality : 0.038 0.128 6048 Planarity : 0.003 0.038 7524 Dihedral : 8.710 71.541 15780 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.84 % Allowed : 1.42 % Favored : 97.75 % 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: 1.50 (0.13), residues: 5124 helix: 2.68 (0.12), residues: 2040 sheet: -0.23 (0.18), residues: 1020 loop : -0.02 (0.15), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 159 TYR 0.007 0.001 TYR I 173 PHE 0.007 0.001 PHE A 42 TRP 0.009 0.001 TRP D 292 HIS 0.003 0.000 HIS H 227 Details of bonding type rmsd covalent geometry : bond 0.00171 (43056) covalent geometry : angle 0.39384 (58224) hydrogen bonds : bond 0.06021 ( 1525) hydrogen bonds : angle 3.68076 ( 4371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9190 (tpt) cc_final: 0.8910 (tpt) REVERT: B 162 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8364 (tm-30) REVERT: B 455 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8437 (m-10) REVERT: C 162 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8408 (tm-30) REVERT: C 289 MET cc_start: 0.8969 (ttt) cc_final: 0.8593 (ttt) REVERT: C 312 ASN cc_start: 0.9279 (t0) cc_final: 0.8986 (t0) REVERT: D 162 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8352 (tm-30) REVERT: D 455 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8288 (m-10) REVERT: E 64 MET cc_start: 0.4654 (mtm) cc_final: 0.4308 (mtm) REVERT: E 289 MET cc_start: 0.8972 (ttt) cc_final: 0.8615 (ttt) REVERT: E 455 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8568 (m-10) REVERT: F 162 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8480 (tm-30) REVERT: F 455 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: H 162 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8321 (tm-30) REVERT: H 312 ASN cc_start: 0.9342 (t0) cc_final: 0.9042 (t0) REVERT: H 455 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8506 (m-10) REVERT: I 162 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8107 (tm-30) REVERT: I 164 GLU cc_start: 0.8994 (tt0) cc_final: 0.8780 (tt0) REVERT: I 289 MET cc_start: 0.8758 (ttt) cc_final: 0.8468 (ttt) REVERT: I 455 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: J 162 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8376 (tm-30) REVERT: K 162 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8306 (tm-30) REVERT: K 455 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8573 (m-10) REVERT: L 162 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8410 (mm-30) REVERT: L 289 MET cc_start: 0.8982 (ttt) cc_final: 0.8682 (ttt) outliers start: 36 outliers final: 28 residues processed: 291 average time/residue: 0.2216 time to fit residues: 114.1592 Evaluate side-chains 235 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN D 312 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN F 296 GLN F 427 HIS ** G 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS H 296 GLN I 296 GLN J 296 GLN J 312 ASN ** K 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 ASN ** L 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 312 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060877 restraints weight = 118905.143| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.85 r_work: 0.2735 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 43056 Z= 0.083 Angle : 0.411 7.084 58224 Z= 0.219 Chirality : 0.039 0.142 6048 Planarity : 0.003 0.039 7524 Dihedral : 4.657 50.880 5866 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.44 % Allowed : 2.88 % Favored : 95.68 % 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: 1.60 (0.13), residues: 5124 helix: 2.62 (0.12), residues: 2112 sheet: 0.02 (0.18), residues: 1020 loop : -0.01 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 450 TYR 0.009 0.001 TYR E 303 PHE 0.011 0.001 PHE B 386 TRP 0.010 0.001 TRP B 292 HIS 0.004 0.000 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00180 (43056) covalent geometry : angle 0.41138 (58224) hydrogen bonds : bond 0.03646 ( 1525) hydrogen bonds : angle 3.43357 ( 4371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9241 (tpt) cc_final: 0.9029 (tpt) REVERT: A 289 MET cc_start: 0.9033 (ttt) cc_final: 0.8116 (tpp) REVERT: A 455 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: B 236 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8014 (mp0) REVERT: B 455 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: C 162 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 289 MET cc_start: 0.9014 (ttt) cc_final: 0.8561 (ttt) REVERT: D 162 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8607 (tm-30) REVERT: D 248 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8545 (mtp) REVERT: D 289 MET cc_start: 0.9102 (ttt) cc_final: 0.8249 (tpp) REVERT: D 455 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: E 162 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8686 (tm-30) REVERT: E 289 MET cc_start: 0.9052 (ttt) cc_final: 0.8564 (ttt) REVERT: E 455 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: F 455 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: H 162 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8543 (tm-30) REVERT: H 312 ASN cc_start: 0.9345 (t0) cc_final: 0.9111 (t0) REVERT: H 455 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8003 (m-10) REVERT: I 162 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8299 (tm-30) REVERT: I 236 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: I 289 MET cc_start: 0.8982 (ttt) cc_final: 0.8546 (ttt) REVERT: I 455 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: J 162 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8629 (tm-30) REVERT: J 455 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: K 162 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8477 (tm-30) REVERT: K 248 MET cc_start: 0.8799 (mtp) cc_final: 0.8581 (mtp) REVERT: K 455 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: L 158 LYS cc_start: 0.9721 (ttmm) cc_final: 0.9352 (ttpt) REVERT: L 162 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8526 (tm-30) REVERT: L 289 MET cc_start: 0.9085 (ttt) cc_final: 0.8620 (ttt) outliers start: 62 outliers final: 43 residues processed: 263 average time/residue: 0.2182 time to fit residues: 100.8359 Evaluate side-chains 251 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 236 GLU Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 362 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 427 HIS ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 HIS ** I 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053988 restraints weight = 120612.175| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.68 r_work: 0.2555 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 43056 Z= 0.266 Angle : 0.535 8.441 58224 Z= 0.285 Chirality : 0.043 0.168 6048 Planarity : 0.004 0.039 7524 Dihedral : 5.056 53.645 5860 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.51 % Allowed : 4.76 % Favored : 93.73 % 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: 1.35 (0.12), residues: 5124 helix: 2.23 (0.11), residues: 2124 sheet: 0.19 (0.18), residues: 960 loop : -0.12 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 159 TYR 0.013 0.002 TYR C 314 PHE 0.013 0.001 PHE A 386 TRP 0.015 0.001 TRP B 292 HIS 0.005 0.001 HIS G 161 Details of bonding type rmsd covalent geometry : bond 0.00613 (43056) covalent geometry : angle 0.53479 (58224) hydrogen bonds : bond 0.05716 ( 1525) hydrogen bonds : angle 4.18186 ( 4371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9396 (tpt) cc_final: 0.9156 (tpt) REVERT: A 289 MET cc_start: 0.9285 (ttt) cc_final: 0.8607 (ttt) REVERT: A 455 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: B 108 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8907 (pp) REVERT: B 289 MET cc_start: 0.9340 (ttt) cc_final: 0.8521 (ttt) REVERT: B 455 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: C 162 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8784 (tm-30) REVERT: C 289 MET cc_start: 0.9217 (ttt) cc_final: 0.8614 (ttt) REVERT: D 108 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8989 (pp) REVERT: D 162 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8818 (tm-30) REVERT: D 455 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: E 162 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8798 (tm-30) REVERT: E 289 MET cc_start: 0.9221 (ttt) cc_final: 0.8810 (ttt) REVERT: E 328 MET cc_start: 0.8504 (pmm) cc_final: 0.8237 (pmm) REVERT: F 455 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: G 289 MET cc_start: 0.9319 (ttt) cc_final: 0.8774 (ttt) REVERT: H 162 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8591 (tm-30) REVERT: H 289 MET cc_start: 0.9359 (ttt) cc_final: 0.8659 (ttt) REVERT: H 455 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: I 162 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8645 (tm-30) REVERT: I 289 MET cc_start: 0.9218 (ttt) cc_final: 0.8703 (ttt) REVERT: I 455 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: J 162 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8720 (tm-30) REVERT: J 455 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: K 162 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8724 (tm-30) REVERT: K 455 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: L 162 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8575 (tm-30) REVERT: L 289 MET cc_start: 0.9220 (ttt) cc_final: 0.8815 (ttt) outliers start: 65 outliers final: 49 residues processed: 259 average time/residue: 0.2222 time to fit residues: 100.7046 Evaluate side-chains 253 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 497 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 437 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 427 optimal weight: 2.9990 chunk 484 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054791 restraints weight = 119170.885| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.66 r_work: 0.2583 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 43056 Z= 0.164 Angle : 0.442 6.090 58224 Z= 0.237 Chirality : 0.040 0.178 6048 Planarity : 0.003 0.041 7524 Dihedral : 4.980 55.210 5860 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.53 % Allowed : 6.31 % Favored : 92.15 % 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: 1.49 (0.12), residues: 5124 helix: 2.35 (0.11), residues: 2136 sheet: 0.16 (0.18), residues: 1020 loop : -0.01 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 159 TYR 0.011 0.001 TYR C 314 PHE 0.010 0.001 PHE L 415 TRP 0.016 0.001 TRP A 292 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00376 (43056) covalent geometry : angle 0.44192 (58224) hydrogen bonds : bond 0.04558 ( 1525) hydrogen bonds : angle 3.90296 ( 4371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.9010 (tpp) cc_final: 0.8759 (mtt) REVERT: A 455 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.7969 (m-10) REVERT: B 108 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8902 (pp) REVERT: B 455 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: C 162 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 163 MET cc_start: 0.9394 (tpp) cc_final: 0.9118 (mmm) REVERT: C 289 MET cc_start: 0.9206 (ttt) cc_final: 0.8611 (ttt) REVERT: D 162 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8838 (tm-30) REVERT: D 455 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.7759 (m-10) REVERT: E 162 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8893 (tm-30) REVERT: E 289 MET cc_start: 0.9147 (ttt) cc_final: 0.8646 (ttt) REVERT: F 455 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: G 289 MET cc_start: 0.9284 (ttt) cc_final: 0.8983 (ttt) REVERT: H 455 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: I 162 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8662 (tm-30) REVERT: I 163 MET cc_start: 0.9340 (mmm) cc_final: 0.8975 (mmm) REVERT: I 289 MET cc_start: 0.9186 (ttt) cc_final: 0.8652 (ttt) REVERT: I 455 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7623 (m-10) REVERT: J 162 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8800 (tm-30) REVERT: J 455 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8045 (m-10) REVERT: K 162 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8781 (tm-30) REVERT: K 455 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: L 289 MET cc_start: 0.9151 (ttt) cc_final: 0.8677 (ttt) outliers start: 66 outliers final: 49 residues processed: 255 average time/residue: 0.2220 time to fit residues: 99.2952 Evaluate side-chains 243 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 173 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 415 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 331 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.055178 restraints weight = 119336.171| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.68 r_work: 0.2596 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43056 Z= 0.129 Angle : 0.428 8.991 58224 Z= 0.229 Chirality : 0.040 0.186 6048 Planarity : 0.003 0.041 7524 Dihedral : 4.917 55.913 5860 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.53 % Allowed : 7.06 % Favored : 91.41 % 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: 1.54 (0.12), residues: 5124 helix: 2.38 (0.11), residues: 2136 sheet: 0.22 (0.18), residues: 1020 loop : 0.01 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 159 TYR 0.010 0.001 TYR G 314 PHE 0.012 0.001 PHE D 386 TRP 0.014 0.001 TRP H 292 HIS 0.010 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00292 (43056) covalent geometry : angle 0.42817 (58224) hydrogen bonds : bond 0.04278 ( 1525) hydrogen bonds : angle 3.79447 ( 4371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 1.528 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 29 MET cc_start: 0.9006 (tpp) cc_final: 0.8725 (mtt) REVERT: A 455 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8019 (m-10) REVERT: B 163 MET cc_start: 0.9273 (mmm) cc_final: 0.9061 (mmm) REVERT: B 164 GLU cc_start: 0.8825 (tt0) cc_final: 0.8557 (tt0) REVERT: B 455 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: C 162 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8903 (tm-30) REVERT: C 163 MET cc_start: 0.9393 (tpp) cc_final: 0.9146 (mmm) REVERT: C 289 MET cc_start: 0.9190 (ttt) cc_final: 0.8667 (ttt) REVERT: C 455 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: D 162 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8893 (tm-30) REVERT: D 163 MET cc_start: 0.9275 (tpp) cc_final: 0.9005 (mmm) REVERT: D 455 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8016 (m-10) REVERT: E 289 MET cc_start: 0.9152 (ttt) cc_final: 0.8613 (ttt) REVERT: E 455 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8034 (m-10) REVERT: F 455 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: G 161 HIS cc_start: 0.8498 (t-170) cc_final: 0.7972 (t-170) REVERT: G 162 GLU cc_start: 0.8258 (mp0) cc_final: 0.7835 (mp0) REVERT: G 289 MET cc_start: 0.9281 (ttt) cc_final: 0.8967 (ttt) REVERT: G 455 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: H 455 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: I 162 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8754 (tm-30) REVERT: I 289 MET cc_start: 0.9172 (ttt) cc_final: 0.8591 (ttt) REVERT: I 455 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: J 162 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8893 (tm-30) REVERT: J 455 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: K 162 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8828 (tm-30) REVERT: K 455 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: L 289 MET cc_start: 0.9166 (ttt) cc_final: 0.8631 (ttt) REVERT: L 455 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8054 (m-10) outliers start: 66 outliers final: 51 residues processed: 249 average time/residue: 0.2269 time to fit residues: 99.2758 Evaluate side-chains 249 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 358 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN D 312 ASN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 GLN ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.054068 restraints weight = 120284.276| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.66 r_work: 0.2562 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 43056 Z= 0.184 Angle : 0.465 10.732 58224 Z= 0.248 Chirality : 0.041 0.179 6048 Planarity : 0.003 0.041 7524 Dihedral : 5.046 56.839 5860 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.76 % Allowed : 7.36 % Favored : 90.88 % 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: 1.46 (0.12), residues: 5124 helix: 2.39 (0.11), residues: 2124 sheet: 0.22 (0.18), residues: 1020 loop : -0.15 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 159 TYR 0.011 0.001 TYR A 428 PHE 0.011 0.001 PHE G 386 TRP 0.015 0.001 TRP A 292 HIS 0.009 0.001 HIS L 161 Details of bonding type rmsd covalent geometry : bond 0.00420 (43056) covalent geometry : angle 0.46548 (58224) hydrogen bonds : bond 0.04846 ( 1525) hydrogen bonds : angle 3.95445 ( 4371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 191 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.9015 (tpp) cc_final: 0.8755 (mtt) REVERT: A 455 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.7952 (m-10) REVERT: B 163 MET cc_start: 0.9330 (mmm) cc_final: 0.9113 (mmm) REVERT: B 164 GLU cc_start: 0.8823 (tt0) cc_final: 0.8553 (tt0) REVERT: B 248 MET cc_start: 0.9154 (mtp) cc_final: 0.8863 (mtp) REVERT: B 455 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: C 162 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8927 (tm-30) REVERT: C 163 MET cc_start: 0.9438 (tpp) cc_final: 0.9091 (mmm) REVERT: C 289 MET cc_start: 0.9163 (ttt) cc_final: 0.8601 (ttt) REVERT: C 455 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: D 162 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8953 (tm-30) REVERT: D 164 GLU cc_start: 0.9030 (tt0) cc_final: 0.8771 (tt0) REVERT: D 455 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: E 289 MET cc_start: 0.9197 (ttt) cc_final: 0.8620 (ttt) REVERT: E 328 MET cc_start: 0.8426 (pmm) cc_final: 0.8185 (pmm) REVERT: F 455 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: G 161 HIS cc_start: 0.8489 (t-170) cc_final: 0.8113 (t-170) REVERT: G 162 GLU cc_start: 0.8274 (mp0) cc_final: 0.7991 (mp0) REVERT: H 455 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: I 162 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8854 (tm-30) REVERT: I 289 MET cc_start: 0.9197 (ttt) cc_final: 0.8658 (ttt) REVERT: I 455 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7960 (m-10) REVERT: J 162 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8912 (tm-30) REVERT: J 455 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: K 162 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8900 (tm-30) REVERT: K 164 GLU cc_start: 0.9038 (tt0) cc_final: 0.8819 (tt0) REVERT: K 455 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: L 289 MET cc_start: 0.9194 (ttt) cc_final: 0.8622 (ttt) REVERT: L 455 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.8035 (m-10) outliers start: 76 outliers final: 58 residues processed: 249 average time/residue: 0.2255 time to fit residues: 98.2464 Evaluate side-chains 257 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 64 MET Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 298 optimal weight: 3.9990 chunk 403 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 419 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 GLN ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 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 = 0.3145 r_free = 0.3145 target = 0.069902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.053804 restraints weight = 120790.076| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.65 r_work: 0.2555 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43056 Z= 0.194 Angle : 0.473 10.045 58224 Z= 0.252 Chirality : 0.041 0.170 6048 Planarity : 0.003 0.042 7524 Dihedral : 5.121 57.825 5860 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.79 % Allowed : 7.50 % Favored : 90.71 % 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: 1.44 (0.12), residues: 5124 helix: 2.37 (0.11), residues: 2124 sheet: 0.18 (0.18), residues: 1020 loop : -0.14 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.010 0.001 TYR G 314 PHE 0.010 0.001 PHE C 415 TRP 0.015 0.001 TRP A 292 HIS 0.010 0.001 HIS L 161 Details of bonding type rmsd covalent geometry : bond 0.00442 (43056) covalent geometry : angle 0.47269 (58224) hydrogen bonds : bond 0.04841 ( 1525) hydrogen bonds : angle 3.98092 ( 4371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 186 time to evaluate : 1.697 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: A 29 MET cc_start: 0.9012 (tpp) cc_final: 0.8736 (mtt) REVERT: A 164 GLU cc_start: 0.8863 (tt0) cc_final: 0.8653 (tt0) REVERT: A 455 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: B 163 MET cc_start: 0.9306 (mmm) cc_final: 0.8885 (mmm) REVERT: B 164 GLU cc_start: 0.8861 (tt0) cc_final: 0.8646 (tt0) REVERT: B 248 MET cc_start: 0.9193 (mtp) cc_final: 0.8932 (mtp) REVERT: B 455 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7796 (m-10) REVERT: C 162 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8984 (tm-30) REVERT: C 163 MET cc_start: 0.9444 (tpp) cc_final: 0.9126 (mmm) REVERT: C 289 MET cc_start: 0.9219 (ttt) cc_final: 0.8644 (ttt) REVERT: C 455 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7987 (m-10) REVERT: D 162 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8972 (tm-30) REVERT: D 164 GLU cc_start: 0.9036 (tt0) cc_final: 0.8780 (tt0) REVERT: D 455 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: E 289 MET cc_start: 0.9194 (ttt) cc_final: 0.8664 (ttt) REVERT: F 64 MET cc_start: 0.6652 (ptp) cc_final: 0.6245 (ptp) REVERT: F 162 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8817 (pp20) REVERT: F 455 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7962 (m-10) REVERT: G 289 MET cc_start: 0.9297 (ttt) cc_final: 0.8621 (tpp) REVERT: H 163 MET cc_start: 0.9281 (mmm) cc_final: 0.8886 (mmm) REVERT: H 455 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: I 162 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8940 (tm-30) REVERT: I 289 MET cc_start: 0.9193 (ttt) cc_final: 0.8620 (ttt) REVERT: I 455 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: J 162 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8959 (tm-30) REVERT: J 455 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: K 162 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8931 (tm-30) REVERT: K 164 GLU cc_start: 0.9040 (tt0) cc_final: 0.8823 (tt0) REVERT: K 455 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7785 (m-10) REVERT: L 163 MET cc_start: 0.9313 (mmm) cc_final: 0.8899 (mmm) REVERT: L 289 MET cc_start: 0.9184 (ttt) cc_final: 0.8610 (ttt) REVERT: L 455 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.7978 (m-10) outliers start: 77 outliers final: 59 residues processed: 245 average time/residue: 0.2273 time to fit residues: 98.1072 Evaluate side-chains 253 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 64 MET Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 59 optimal weight: 0.7980 chunk 382 optimal weight: 7.9990 chunk 490 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 433 optimal weight: 3.9990 chunk 410 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.055680 restraints weight = 120022.459| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.72 r_work: 0.2600 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43056 Z= 0.099 Angle : 0.419 11.916 58224 Z= 0.223 Chirality : 0.039 0.169 6048 Planarity : 0.003 0.044 7524 Dihedral : 4.930 58.386 5860 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.72 % Allowed : 7.71 % Favored : 90.58 % 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: 1.61 (0.12), residues: 5124 helix: 2.46 (0.11), residues: 2136 sheet: 0.28 (0.19), residues: 1020 loop : 0.00 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 159 TYR 0.010 0.001 TYR J 303 PHE 0.011 0.001 PHE G 386 TRP 0.015 0.001 TRP C 292 HIS 0.003 0.001 HIS L 161 Details of bonding type rmsd covalent geometry : bond 0.00217 (43056) covalent geometry : angle 0.41853 (58224) hydrogen bonds : bond 0.03869 ( 1525) hydrogen bonds : angle 3.70679 ( 4371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 1.636 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: A 29 MET cc_start: 0.9012 (tpp) cc_final: 0.8656 (mtt) REVERT: A 164 GLU cc_start: 0.8873 (tt0) cc_final: 0.8603 (tt0) REVERT: A 455 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: B 163 MET cc_start: 0.9296 (mmm) cc_final: 0.8985 (mmm) REVERT: B 164 GLU cc_start: 0.8848 (tt0) cc_final: 0.8512 (tt0) REVERT: B 248 MET cc_start: 0.9126 (mtp) cc_final: 0.8849 (mtp) REVERT: B 455 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7986 (m-10) REVERT: C 162 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9070 (tm-30) REVERT: C 163 MET cc_start: 0.9416 (tpp) cc_final: 0.9181 (mmm) REVERT: C 289 MET cc_start: 0.9135 (ttt) cc_final: 0.8546 (ttt) REVERT: C 455 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: D 162 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8986 (tm-30) REVERT: D 163 MET cc_start: 0.9282 (tpp) cc_final: 0.8906 (mmm) REVERT: D 164 GLU cc_start: 0.9016 (tt0) cc_final: 0.8771 (tt0) REVERT: D 455 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: E 163 MET cc_start: 0.9412 (mmm) cc_final: 0.8988 (mmm) REVERT: E 289 MET cc_start: 0.9129 (ttt) cc_final: 0.8619 (ttt) REVERT: E 455 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: F 64 MET cc_start: 0.6514 (ptp) cc_final: 0.6035 (ptp) REVERT: F 455 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: G 455 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: H 455 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8073 (m-10) REVERT: I 162 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8975 (tm-30) REVERT: I 164 GLU cc_start: 0.9087 (tt0) cc_final: 0.8867 (tt0) REVERT: I 289 MET cc_start: 0.9151 (ttt) cc_final: 0.8627 (ttt) REVERT: I 455 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7972 (m-10) REVERT: J 162 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9055 (tm-30) REVERT: J 455 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7968 (m-10) REVERT: K 162 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8963 (tm-30) REVERT: K 164 GLU cc_start: 0.9054 (tt0) cc_final: 0.8816 (tt0) REVERT: K 248 MET cc_start: 0.9122 (mtp) cc_final: 0.8867 (mtp) REVERT: K 455 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: L 236 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8117 (mp0) REVERT: L 289 MET cc_start: 0.9122 (ttt) cc_final: 0.8575 (ttt) REVERT: L 455 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8057 (m-10) outliers start: 74 outliers final: 59 residues processed: 239 average time/residue: 0.2301 time to fit residues: 96.3703 Evaluate side-chains 251 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 64 MET Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 91 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 476 optimal weight: 4.9990 chunk 451 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 343 optimal weight: 7.9990 chunk 485 optimal weight: 2.9990 chunk 437 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.054506 restraints weight = 119648.495| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.65 r_work: 0.2580 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 43056 Z= 0.149 Angle : 0.451 12.737 58224 Z= 0.238 Chirality : 0.040 0.201 6048 Planarity : 0.003 0.043 7524 Dihedral : 4.989 58.884 5860 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.74 % Allowed : 7.87 % Favored : 90.39 % 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: 1.61 (0.12), residues: 5124 helix: 2.51 (0.11), residues: 2136 sheet: 0.29 (0.19), residues: 1020 loop : -0.07 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 159 TYR 0.010 0.001 TYR K 428 PHE 0.010 0.001 PHE L 415 TRP 0.014 0.001 TRP I 292 HIS 0.003 0.001 HIS H 427 Details of bonding type rmsd covalent geometry : bond 0.00339 (43056) covalent geometry : angle 0.45084 (58224) hydrogen bonds : bond 0.04373 ( 1525) hydrogen bonds : angle 3.80437 ( 4371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 1.546 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: symmetry clash REVERT: A 29 MET cc_start: 0.9022 (tpp) cc_final: 0.8714 (mtt) REVERT: A 164 GLU cc_start: 0.8863 (tt0) cc_final: 0.8636 (tt0) REVERT: A 455 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8027 (m-10) REVERT: B 163 MET cc_start: 0.9270 (mmm) cc_final: 0.8877 (mmm) REVERT: B 164 GLU cc_start: 0.8897 (tt0) cc_final: 0.8603 (tt0) REVERT: B 248 MET cc_start: 0.9194 (mtp) cc_final: 0.8969 (mtp) REVERT: B 455 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7931 (m-10) REVERT: C 162 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9056 (tm-30) REVERT: C 163 MET cc_start: 0.9428 (tpp) cc_final: 0.9128 (mmm) REVERT: C 289 MET cc_start: 0.9176 (ttt) cc_final: 0.8622 (ttt) REVERT: C 455 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8025 (m-10) REVERT: D 162 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9011 (tm-30) REVERT: D 164 GLU cc_start: 0.9038 (tt0) cc_final: 0.8744 (tt0) REVERT: D 455 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: E 163 MET cc_start: 0.9349 (mmm) cc_final: 0.8953 (mmm) REVERT: E 289 MET cc_start: 0.9167 (ttt) cc_final: 0.8655 (ttt) REVERT: E 455 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: F 64 MET cc_start: 0.6589 (ptp) cc_final: 0.6183 (ptp) REVERT: F 455 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: G 289 MET cc_start: 0.9272 (ttt) cc_final: 0.8588 (tpp) REVERT: G 455 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: H 163 MET cc_start: 0.9279 (mmm) cc_final: 0.8975 (mmm) REVERT: H 455 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: I 162 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9033 (tm-30) REVERT: I 164 GLU cc_start: 0.9094 (tt0) cc_final: 0.8849 (tt0) REVERT: I 289 MET cc_start: 0.9119 (ttt) cc_final: 0.8657 (ttt) REVERT: I 455 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: J 162 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9004 (tm-30) REVERT: J 455 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: K 162 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8994 (tm-30) REVERT: K 163 MET cc_start: 0.9338 (mmm) cc_final: 0.9044 (mmm) REVERT: K 248 MET cc_start: 0.9163 (mtp) cc_final: 0.8908 (mtp) REVERT: K 455 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: L 236 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8139 (mp0) REVERT: L 289 MET cc_start: 0.9162 (ttt) cc_final: 0.8653 (ttt) REVERT: L 455 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8034 (m-10) outliers start: 75 outliers final: 59 residues processed: 241 average time/residue: 0.2255 time to fit residues: 95.3692 Evaluate side-chains 252 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 64 MET Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 205 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 512 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 507 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.053802 restraints weight = 120658.163| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.65 r_work: 0.2556 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 43056 Z= 0.186 Angle : 0.480 13.523 58224 Z= 0.252 Chirality : 0.040 0.213 6048 Planarity : 0.003 0.041 7524 Dihedral : 5.126 59.483 5860 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.74 % Allowed : 8.03 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.12), residues: 5124 helix: 2.43 (0.11), residues: 2124 sheet: 0.25 (0.19), residues: 1020 loop : -0.09 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 159 TYR 0.011 0.001 TYR D 428 PHE 0.010 0.001 PHE L 415 TRP 0.014 0.001 TRP I 292 HIS 0.003 0.001 HIS E 427 Details of bonding type rmsd covalent geometry : bond 0.00423 (43056) covalent geometry : angle 0.47973 (58224) hydrogen bonds : bond 0.04783 ( 1525) hydrogen bonds : angle 3.93203 ( 4371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10248 Ramachandran restraints generated. 5124 Oldfield, 0 Emsley, 5124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 180 time to evaluate : 1.620 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: A 29 MET cc_start: 0.9013 (tpp) cc_final: 0.8736 (mtt) REVERT: A 289 MET cc_start: 0.9285 (ttt) cc_final: 0.8620 (tpp) REVERT: A 455 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: B 162 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8926 (pp20) REVERT: B 163 MET cc_start: 0.9314 (mmm) cc_final: 0.9033 (mmm) REVERT: B 164 GLU cc_start: 0.8904 (tt0) cc_final: 0.8491 (tt0) REVERT: B 248 MET cc_start: 0.9225 (mtp) cc_final: 0.9006 (mtp) REVERT: B 455 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: C 162 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9060 (tm-30) REVERT: C 289 MET cc_start: 0.9193 (ttt) cc_final: 0.8629 (ttt) REVERT: C 455 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: D 162 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8993 (tm-30) REVERT: D 164 GLU cc_start: 0.9022 (tt0) cc_final: 0.8748 (tt0) REVERT: D 248 MET cc_start: 0.9111 (mtp) cc_final: 0.8860 (mtp) REVERT: D 289 MET cc_start: 0.9332 (ttt) cc_final: 0.8737 (ttt) REVERT: D 455 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: E 162 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8763 (pp20) REVERT: E 163 MET cc_start: 0.9368 (mmm) cc_final: 0.8981 (mmm) REVERT: E 289 MET cc_start: 0.9183 (ttt) cc_final: 0.8617 (ttt) REVERT: E 455 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: F 64 MET cc_start: 0.6600 (ptp) cc_final: 0.6194 (ptp) REVERT: F 164 GLU cc_start: 0.8843 (tt0) cc_final: 0.8558 (tt0) REVERT: F 455 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: G 289 MET cc_start: 0.9299 (ttt) cc_final: 0.8629 (tpp) REVERT: G 455 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.7991 (m-10) REVERT: H 163 MET cc_start: 0.9304 (mmm) cc_final: 0.9023 (mmm) REVERT: H 455 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: I 164 GLU cc_start: 0.9074 (tt0) cc_final: 0.8833 (tt0) REVERT: I 289 MET cc_start: 0.9098 (ttt) cc_final: 0.8701 (ttt) REVERT: I 455 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: J 162 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8973 (tm-30) REVERT: J 289 MET cc_start: 0.9289 (ttt) cc_final: 0.8614 (tpp) REVERT: J 455 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: K 162 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8983 (tm-30) REVERT: K 163 MET cc_start: 0.9343 (mmm) cc_final: 0.9066 (mmm) REVERT: K 248 MET cc_start: 0.9188 (mtp) cc_final: 0.8944 (mtp) REVERT: K 289 MET cc_start: 0.9322 (ttt) cc_final: 0.8717 (ttt) REVERT: K 455 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: L 236 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8178 (mp0) REVERT: L 289 MET cc_start: 0.9181 (ttt) cc_final: 0.8612 (ttt) REVERT: L 455 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8000 (m-10) outliers start: 75 outliers final: 60 residues processed: 239 average time/residue: 0.2339 time to fit residues: 98.0957 Evaluate side-chains 251 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 455 TYR Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 415 PHE Chi-restraints excluded: chain D residue 455 TYR Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 223 MET Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 415 PHE Chi-restraints excluded: chain E residue 455 TYR Chi-restraints excluded: chain F residue 25 CYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 415 PHE Chi-restraints excluded: chain F residue 455 TYR Chi-restraints excluded: chain G residue 25 CYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 251 TYR Chi-restraints excluded: chain G residue 415 PHE Chi-restraints excluded: chain G residue 455 TYR Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 415 PHE Chi-restraints excluded: chain H residue 455 TYR Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 251 TYR Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 455 TYR Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 64 MET Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 251 TYR Chi-restraints excluded: chain J residue 415 PHE Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 64 MET Chi-restraints excluded: chain K residue 251 TYR Chi-restraints excluded: chain K residue 415 PHE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 25 CYS Chi-restraints excluded: chain L residue 64 MET Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 223 MET Chi-restraints excluded: chain L residue 251 TYR Chi-restraints excluded: chain L residue 415 PHE Chi-restraints excluded: chain L residue 455 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 83 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 432 optimal weight: 8.9990 chunk 442 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 511 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.054098 restraints weight = 120666.770| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.66 r_work: 0.2569 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43056 Z= 0.158 Angle : 0.471 13.339 58224 Z= 0.248 Chirality : 0.040 0.194 6048 Planarity : 0.003 0.042 7524 Dihedral : 5.103 59.886 5860 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.72 % Allowed : 8.01 % Favored : 90.27 % 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: 1.56 (0.12), residues: 5124 helix: 2.45 (0.11), residues: 2136 sheet: 0.25 (0.19), residues: 1020 loop : -0.07 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 159 TYR 0.010 0.001 TYR D 428 PHE 0.009 0.001 PHE D 415 TRP 0.014 0.001 TRP C 292 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00360 (43056) covalent geometry : angle 0.47126 (58224) hydrogen bonds : bond 0.04473 ( 1525) hydrogen bonds : angle 3.85703 ( 4371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7414.16 seconds wall clock time: 129 minutes 0.65 seconds (7740.65 seconds total)