Starting phenix.real_space_refine on Sat Jun 6 00:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l36_62782/06_2026/9l36_62782.map" } resolution = 2.71 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= 0.069 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: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 Cl 8 4.86 5 C 15272 2.51 5 N 4456 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24368 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3016 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.49, per 1000 atoms: 0.14 Number of scatterers: 24368 At special positions: 0 Unit cell: (134.85, 134.85, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 72 16.00 O 4544 8.00 N 4456 7.00 C 15272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.04 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 271 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 271 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 271 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 271 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 271 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 43.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.641A pdb=" N ARG A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.922A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.605A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.611A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.728A pdb=" N ALA A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.642A pdb=" N ARG B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.922A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.605A pdb=" N GLN B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.611A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 3.728A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.642A pdb=" N ARG C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.921A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 removed outlier: 3.605A pdb=" N GLN C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.611A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 354 through 362 removed outlier: 4.148A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 383 removed outlier: 3.727A pdb=" N ALA C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.642A pdb=" N ARG D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.921A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.606A pdb=" N GLN D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.609A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 3.727A pdb=" N ALA D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.641A pdb=" N ARG E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.921A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 204 removed outlier: 3.605A pdb=" N GLN E 196 " --> pdb=" O ASP E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 305 removed outlier: 3.611A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 3.728A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.642A pdb=" N ARG F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.922A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.605A pdb=" N GLN F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 305 removed outlier: 3.610A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 383 removed outlier: 3.728A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 96 through 101 removed outlier: 3.641A pdb=" N ARG G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.921A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 204 removed outlier: 3.606A pdb=" N GLN G 196 " --> pdb=" O ASP G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 244 Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 305 removed outlier: 3.611A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 354 through 362 removed outlier: 4.148A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 383 removed outlier: 3.727A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 375 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.642A pdb=" N ARG H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.921A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 204 removed outlier: 3.606A pdb=" N GLN H 196 " --> pdb=" O ASP H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 244 Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 305 removed outlier: 3.610A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 Processing helix chain 'H' and resid 325 through 336 Processing helix chain 'H' and resid 354 through 362 removed outlier: 4.147A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 383 removed outlier: 3.727A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR H 375 " --> pdb=" O LEU H 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA H 378 " --> pdb=" O ALA H 374 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 14.101A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.450A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.544A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.654A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.451A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.544A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.450A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.545A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.451A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.543A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.556A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 14.101A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.450A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.544A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.672A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.450A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.543A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.450A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.544A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 39 removed outlier: 3.671A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.555A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 14.102A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.451A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.543A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 2928 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: 4.75 Time building geometry restraints manager: 2.84 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: 8406 1.34 - 1.46: 4240 1.46 - 1.58: 12082 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 24864 Sorted by residual: bond pdb=" CAD 97U G 503 " pdb=" CAG 97U G 503 " ideal model delta sigma weight residual 1.495 1.370 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" CAD 97U C 503 " pdb=" CAG 97U C 503 " ideal model delta sigma weight residual 1.495 1.370 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" CAD 97U E 503 " pdb=" CAG 97U E 503 " ideal model delta sigma weight residual 1.495 1.370 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CAD 97U A 503 " pdb=" CAG 97U A 503 " ideal model delta sigma weight residual 1.495 1.370 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CAD 97U F 503 " pdb=" CAG 97U F 503 " ideal model delta sigma weight residual 1.495 1.370 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 24859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 32619 1.45 - 2.91: 857 2.91 - 4.36: 164 4.36 - 5.81: 80 5.81 - 7.27: 16 Bond angle restraints: 33736 Sorted by residual: angle pdb=" CA PRO C 77 " pdb=" C PRO C 77 " pdb=" O PRO C 77 " ideal model delta sigma weight residual 122.08 118.87 3.21 1.28e+00 6.10e-01 6.28e+00 angle pdb=" CA PRO D 77 " pdb=" C PRO D 77 " pdb=" O PRO D 77 " ideal model delta sigma weight residual 122.08 118.88 3.20 1.28e+00 6.10e-01 6.25e+00 angle pdb=" CA PRO H 77 " pdb=" C PRO H 77 " pdb=" O PRO H 77 " ideal model delta sigma weight residual 122.08 118.88 3.20 1.28e+00 6.10e-01 6.24e+00 angle pdb=" CA PRO B 77 " pdb=" C PRO B 77 " pdb=" O PRO B 77 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.28e+00 6.10e-01 6.18e+00 angle pdb=" CA PRO G 77 " pdb=" C PRO G 77 " pdb=" O PRO G 77 " ideal model delta sigma weight residual 122.08 118.91 3.17 1.28e+00 6.10e-01 6.14e+00 ... (remaining 33731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12836 17.95 - 35.89: 1464 35.89 - 53.84: 369 53.84 - 71.79: 123 71.79 - 89.74: 24 Dihedral angle restraints: 14816 sinusoidal: 5856 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY F 346 " pdb=" C GLY F 346 " pdb=" N VAL F 347 " pdb=" CA VAL F 347 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY H 346 " pdb=" C GLY H 346 " pdb=" N VAL H 347 " pdb=" CA VAL H 347 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 14813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3247 0.068 - 0.136: 425 0.136 - 0.204: 0 0.204 - 0.272: 0 0.272 - 0.340: 8 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" C 97U G 503 " pdb=" CB 97U G 503 " both_signs ideal model delta sigma weight residual False 2.30 2.64 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA 97U F 503 " pdb=" N 97U F 503 " pdb=" C 97U F 503 " pdb=" CB 97U F 503 " both_signs ideal model delta sigma weight residual False 2.30 2.64 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA 97U B 503 " pdb=" N 97U B 503 " pdb=" C 97U B 503 " pdb=" CB 97U B 503 " both_signs ideal model delta sigma weight residual False 2.30 2.64 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3677 not shown) Planarity restraints: 4496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 91 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO E 92 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 92 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 91 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO G 92 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 92 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 92 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 91 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO F 92 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 92 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 92 " 0.027 5.00e-02 4.00e+02 ... (remaining 4493 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 28 1.54 - 2.38: 146 2.38 - 3.22: 23362 3.22 - 4.06: 63818 4.06 - 4.90: 122174 Warning: very small nonbonded interaction distances. Nonbonded interactions: 209528 Sorted by model distance: nonbonded pdb=" OD2 ASP D 102 " pdb=" OE2 GLU H 172 " model vdw 0.700 3.040 nonbonded pdb=" OD1 ASP C 102 " pdb=" OE1 GLU E 172 " model vdw 0.849 3.040 nonbonded pdb=" OE2 GLU B 172 " pdb=" OD2 ASP F 102 " model vdw 0.853 3.040 nonbonded pdb=" OE1 GLU A 172 " pdb=" OD1 ASP G 102 " model vdw 0.889 3.040 nonbonded pdb=" OE2 GLU D 172 " pdb=" OD2 ASP H 102 " model vdw 0.910 3.040 ... (remaining 209523 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: 0.09 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.400 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.009 0.382 24904 Z= 0.354 Angle : 0.637 7.268 33752 Z= 0.329 Chirality : 0.045 0.340 3680 Planarity : 0.005 0.061 4496 Dihedral : 16.933 89.736 9112 Min Nonbonded Distance : 0.700 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.17 % Allowed : 19.77 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1304 sheet: 0.64 (0.31), residues: 248 loop : -1.10 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 298 TYR 0.016 0.002 TYR C 359 PHE 0.024 0.002 PHE D 417 TRP 0.009 0.001 TRP A 289 HIS 0.006 0.001 HIS D 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.27 (24864) covalent geometry : angle 0.63654 / 0.33 (33736) SS BOND : bond 0.00403 / 0.21 ( 8) SS BOND : angle 1.00979 / 0.61 ( 16) hydrogen bonds : bond 0.14868 / 10.00 ( 1040) hydrogen bonds : angle 6.55836 / 4.68 ( 2928) metal coordination : bond 0.19074 / 14.05 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 401 time to evaluate : 0.899 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: B 155 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7579 (tptp) REVERT: B 229 PHE cc_start: 0.6599 (m-80) cc_final: 0.6177 (t80) REVERT: B 243 ASP cc_start: 0.7257 (m-30) cc_final: 0.6955 (m-30) REVERT: D 108 PHE cc_start: 0.7800 (m-10) cc_final: 0.7489 (m-80) REVERT: D 243 ASP cc_start: 0.7142 (m-30) cc_final: 0.6913 (t0) REVERT: F 207 ASP cc_start: 0.8559 (m-30) cc_final: 0.8275 (m-30) REVERT: F 397 ASP cc_start: 0.6514 (m-30) cc_final: 0.6303 (m-30) REVERT: H 338 ARG cc_start: 0.7406 (mtm180) cc_final: 0.7177 (ptm160) outliers start: 4 outliers final: 0 residues processed: 405 average time/residue: 0.8265 time to fit residues: 375.3246 Evaluate side-chains 247 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 135 HIS A 285 GLN B 263 GLN B 377 HIS D 135 HIS E 85 HIS E 285 GLN F 285 GLN G 285 GLN H 196 GLN H 377 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157238 restraints weight = 21381.981| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.58 r_work: 0.3615 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.280 24904 Z= 0.193 Angle : 0.662 13.212 33752 Z= 0.330 Chirality : 0.048 0.248 3680 Planarity : 0.005 0.057 4496 Dihedral : 6.166 41.497 3760 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.82 % Allowed : 17.65 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3136 helix: 0.49 (0.14), residues: 1240 sheet: 1.21 (0.29), residues: 264 loop : -0.89 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 173 TYR 0.013 0.002 TYR D 95 PHE 0.034 0.003 PHE B 122 TRP 0.009 0.001 TRP C 79 HIS 0.011 0.001 HIS E 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (24864) covalent geometry : angle 0.66152 / 0.33 (33736) SS BOND : bond 0.00350 / 0.17 ( 8) SS BOND : angle 0.86210 / 0.49 ( 16) hydrogen bonds : bond 0.03363 / 2.30 ( 1040) hydrogen bonds : angle 4.50158 / 3.24 ( 2928) metal coordination : bond 0.06220 / 4.45 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 341 time to evaluate : 1.001 Fit side-chains REVERT: A 88 ARG cc_start: 0.7397 (ppt170) cc_final: 0.7132 (mtt90) REVERT: A 115 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: A 146 ARG cc_start: 0.8389 (mtp85) cc_final: 0.8156 (mtm180) REVERT: A 177 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 419 MET cc_start: 0.4828 (mpt) cc_final: 0.4351 (ttm) REVERT: B 45 LEU cc_start: 0.6224 (tp) cc_final: 0.5473 (mm) REVERT: B 88 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7228 (ppt170) REVERT: B 178 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6767 (p) REVERT: B 280 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.5557 (mpp) REVERT: C 247 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8874 (mtt-85) REVERT: D 45 LEU cc_start: 0.6417 (mp) cc_final: 0.5681 (tp) REVERT: D 172 GLU cc_start: 0.7253 (mp0) cc_final: 0.7042 (tm-30) REVERT: D 178 VAL cc_start: 0.7417 (OUTLIER) cc_final: 0.7024 (p) REVERT: D 324 LEU cc_start: 0.6846 (mt) cc_final: 0.6236 (mt) REVERT: E 259 LYS cc_start: 0.7566 (tttp) cc_final: 0.7313 (ttmm) REVERT: E 343 THR cc_start: 0.8030 (p) cc_final: 0.7818 (t) REVERT: F 131 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6930 (mm-30) REVERT: F 259 LYS cc_start: 0.8237 (tttp) cc_final: 0.7915 (mtmm) REVERT: F 275 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8325 (mtt) REVERT: G 173 ARG cc_start: 0.8197 (ttt90) cc_final: 0.7983 (ptm160) REVERT: G 222 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7658 (mtt180) REVERT: G 242 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7600 (mtt90) REVERT: G 360 MET cc_start: 0.7763 (mtt) cc_final: 0.7553 (mtp) REVERT: H 98 ASP cc_start: 0.7661 (t0) cc_final: 0.7302 (t0) REVERT: H 172 GLU cc_start: 0.6994 (mp0) cc_final: 0.6767 (pp20) REVERT: H 220 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: H 275 MET cc_start: 0.8714 (mtm) cc_final: 0.8485 (mtt) REVERT: H 284 LYS cc_start: 0.7412 (mtpt) cc_final: 0.7144 (mtmp) outliers start: 116 outliers final: 16 residues processed: 425 average time/residue: 0.9242 time to fit residues: 435.8956 Evaluate side-chains 287 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 220 TYR Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 103 optimal weight: 0.0370 chunk 129 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 93 GLN B 37 GLN C 93 GLN D 93 GLN E 85 HIS F 89 GLN G 372 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141587 restraints weight = 21232.609| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.46 r_work: 0.3414 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.465 24904 Z= 0.160 Angle : 0.524 10.356 33752 Z= 0.265 Chirality : 0.045 0.216 3680 Planarity : 0.004 0.040 4496 Dihedral : 5.580 41.434 3760 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.66 % Allowed : 20.68 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3136 helix: 0.89 (0.14), residues: 1240 sheet: 0.98 (0.27), residues: 336 loop : -0.78 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 315 TYR 0.009 0.001 TYR A 369 PHE 0.026 0.002 PHE A 417 TRP 0.008 0.001 TRP F 289 HIS 0.010 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24864) covalent geometry : angle 0.52439 / 0.26 (33736) SS BOND : bond 0.00149 / 0.08 ( 8) SS BOND : angle 0.47635 / 0.28 ( 16) hydrogen bonds : bond 0.03303 / 2.24 ( 1040) hydrogen bonds : angle 4.09737 / 2.98 ( 2928) metal coordination : bond 0.08331 / 5.97 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 0.983 Fit side-chains REVERT: A 155 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7677 (tttp) REVERT: A 172 GLU cc_start: 0.7495 (pt0) cc_final: 0.7135 (pt0) REVERT: A 173 ARG cc_start: 0.8449 (ttt90) cc_final: 0.8127 (ttt180) REVERT: A 419 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5412 (ttm) REVERT: B 45 LEU cc_start: 0.7254 (tp) cc_final: 0.6128 (mm) REVERT: B 52 ARG cc_start: 0.6619 (mtm110) cc_final: 0.6064 (mpt180) REVERT: B 88 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7746 (mpt180) REVERT: B 93 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: B 172 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6833 (tm-30) REVERT: B 178 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7079 (p) REVERT: B 320 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7527 (ttp-110) REVERT: B 389 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7606 (t) REVERT: B 407 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: C 173 ARG cc_start: 0.8410 (ttt90) cc_final: 0.8159 (ttt180) REVERT: C 298 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7705 (mtt-85) REVERT: C 397 ASP cc_start: 0.7935 (m-30) cc_final: 0.7705 (m-30) REVERT: D 45 LEU cc_start: 0.7158 (mp) cc_final: 0.6254 (tp) REVERT: D 52 ARG cc_start: 0.6455 (mtm110) cc_final: 0.5868 (mmp-170) REVERT: E 98 ASP cc_start: 0.8010 (t70) cc_final: 0.7629 (t0) REVERT: E 208 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (pt) REVERT: E 298 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7788 (mtt180) REVERT: E 419 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.4807 (mpt) REVERT: F 131 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6847 (mm-30) REVERT: F 235 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8001 (mptp) REVERT: F 280 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6368 (mtt) REVERT: F 320 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7173 (ttp-170) REVERT: G 127 ASP cc_start: 0.7902 (t70) cc_final: 0.7633 (t0) REVERT: G 131 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7083 (mm-30) REVERT: G 173 ARG cc_start: 0.8228 (ttt90) cc_final: 0.7998 (ptm160) REVERT: G 176 HIS cc_start: 0.7253 (t-90) cc_final: 0.7017 (t70) REVERT: G 222 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7686 (mtt180) REVERT: G 235 LYS cc_start: 0.8312 (mttt) cc_final: 0.8081 (mttm) REVERT: G 242 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7699 (mtt180) REVERT: G 284 LYS cc_start: 0.7397 (mtpt) cc_final: 0.7175 (mtmp) REVERT: H 98 ASP cc_start: 0.7812 (t0) cc_final: 0.7430 (t0) REVERT: H 127 ASP cc_start: 0.7796 (t70) cc_final: 0.7497 (t0) REVERT: H 131 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: H 284 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7545 (mtmp) REVERT: H 302 GLU cc_start: 0.7682 (pp20) cc_final: 0.7361 (mt-10) outliers start: 64 outliers final: 19 residues processed: 382 average time/residue: 0.9747 time to fit residues: 411.4199 Evaluate side-chains 311 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 262 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 171 ASN ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN D 350 HIS D 377 HIS E 271 HIS E 350 HIS F 89 GLN F 350 HIS G 53 GLN G 176 HIS G 350 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.153726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127304 restraints weight = 20903.205| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.29 r_work: 0.3318 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.185 24904 Z= 0.283 Angle : 0.557 12.008 33752 Z= 0.277 Chirality : 0.046 0.233 3680 Planarity : 0.004 0.049 4496 Dihedral : 5.606 36.334 3760 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.45 % Allowed : 20.81 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3136 helix: 0.95 (0.14), residues: 1248 sheet: 0.33 (0.25), residues: 432 loop : -0.62 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 29 TYR 0.013 0.001 TYR A 274 PHE 0.021 0.002 PHE D 122 TRP 0.006 0.001 TRP A 79 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (24864) covalent geometry : angle 0.55659 / 0.28 (33736) SS BOND : bond 0.00356 / 0.20 ( 8) SS BOND : angle 1.22771 / 0.72 ( 16) hydrogen bonds : bond 0.03118 / 2.14 ( 1040) hydrogen bonds : angle 4.22745 / 3.04 ( 2928) metal coordination : bond 0.20950 / 15.99 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 0.937 Fit side-chains REVERT: A 155 LYS cc_start: 0.8473 (ttpt) cc_final: 0.7416 (tptp) REVERT: A 173 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7784 (ptm160) REVERT: A 247 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.7770 (mtm180) REVERT: A 276 ASP cc_start: 0.7951 (p0) cc_final: 0.7641 (p0) REVERT: A 280 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.6430 (mtp) REVERT: B 37 GLN cc_start: 0.7323 (mt0) cc_final: 0.6611 (pt0) REVERT: B 45 LEU cc_start: 0.7469 (tp) cc_final: 0.6380 (mm) REVERT: B 52 ARG cc_start: 0.6559 (mtm110) cc_final: 0.5902 (mpt180) REVERT: B 178 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7314 (p) REVERT: B 320 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7305 (ttp-110) REVERT: B 407 GLU cc_start: 0.6736 (pt0) cc_final: 0.6468 (mt-10) REVERT: C 45 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.5934 (tp) REVERT: C 173 ARG cc_start: 0.8178 (ttt90) cc_final: 0.7814 (ptm160) REVERT: C 247 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8649 (mtt-85) REVERT: C 280 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.5213 (mpp) REVERT: D 45 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7120 (mm) REVERT: D 52 ARG cc_start: 0.6425 (mtm110) cc_final: 0.5394 (mmp-170) REVERT: D 222 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7942 (mtt-85) REVERT: D 327 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: E 242 ARG cc_start: 0.7422 (mtm110) cc_final: 0.7089 (ttm110) REVERT: E 360 MET cc_start: 0.7677 (mtt) cc_final: 0.7317 (mtp) REVERT: E 419 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.4631 (ttp) REVERT: F 127 ASP cc_start: 0.7842 (t70) cc_final: 0.7616 (t70) REVERT: F 131 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6573 (mm-30) REVERT: F 185 GLU cc_start: 0.8073 (mp0) cc_final: 0.7775 (mp0) REVERT: F 222 ARG cc_start: 0.8252 (mtm180) cc_final: 0.7993 (mmm160) REVERT: F 259 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7501 (mtmt) REVERT: F 320 ARG cc_start: 0.7108 (ttp80) cc_final: 0.6892 (ttp-170) REVERT: G 88 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7479 (ptm160) REVERT: G 127 ASP cc_start: 0.7813 (t70) cc_final: 0.7542 (t0) REVERT: G 131 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7012 (mm-30) REVERT: G 173 ARG cc_start: 0.7920 (ttt90) cc_final: 0.7637 (ptm160) REVERT: G 222 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8005 (mmm160) REVERT: G 235 LYS cc_start: 0.8279 (mttt) cc_final: 0.7948 (mttm) REVERT: G 284 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7702 (mtmp) REVERT: G 302 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: H 26 GLN cc_start: 0.7555 (mt0) cc_final: 0.6140 (tp40) REVERT: H 93 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: H 98 ASP cc_start: 0.7772 (t70) cc_final: 0.7307 (t0) REVERT: H 127 ASP cc_start: 0.7786 (t70) cc_final: 0.7482 (t0) REVERT: H 172 GLU cc_start: 0.7081 (mp0) cc_final: 0.6847 (mp0) REVERT: H 185 GLU cc_start: 0.8046 (mp0) cc_final: 0.7737 (mp0) REVERT: H 222 ARG cc_start: 0.8326 (mtm180) cc_final: 0.8064 (mmm160) REVERT: H 302 GLU cc_start: 0.7708 (pp20) cc_final: 0.7412 (mt-10) REVERT: H 320 ARG cc_start: 0.7001 (ttp80) cc_final: 0.6773 (ttp-170) outliers start: 83 outliers final: 30 residues processed: 380 average time/residue: 0.9353 time to fit residues: 394.8414 Evaluate side-chains 330 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 130 optimal weight: 5.9990 chunk 223 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 251 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 271 HIS B 37 GLN C 89 GLN C 176 HIS C 271 HIS E 285 GLN E 372 GLN F 89 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125984 restraints weight = 20869.693| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.16 r_work: 0.3312 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.257 24904 Z= 0.391 Angle : 0.506 11.477 33752 Z= 0.254 Chirality : 0.044 0.222 3680 Planarity : 0.004 0.057 4496 Dihedral : 5.438 36.118 3760 Min Nonbonded Distance : 1.361 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.99 % Allowed : 22.67 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3136 helix: 0.95 (0.14), residues: 1288 sheet: 0.32 (0.25), residues: 384 loop : -0.67 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 315 TYR 0.013 0.001 TYR F 333 PHE 0.017 0.001 PHE E 417 TRP 0.008 0.001 TRP C 289 HIS 0.032 0.001 HIS E 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (24864) covalent geometry : angle 0.50579 / 0.25 (33736) SS BOND : bond 0.00201 / 0.11 ( 8) SS BOND : angle 0.67289 / 0.40 ( 16) hydrogen bonds : bond 0.03054 / 2.08 ( 1040) hydrogen bonds : angle 4.06778 / 2.94 ( 2928) metal coordination : bond 0.31239 / 22.52 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 0.944 Fit side-chains REVERT: A 45 LEU cc_start: 0.7333 (mp) cc_final: 0.6658 (tp) REVERT: A 155 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7597 (tptp) REVERT: A 173 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7994 (ptm160) REVERT: A 276 ASP cc_start: 0.7993 (p0) cc_final: 0.7146 (p0) REVERT: A 280 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.6095 (mpp) REVERT: B 37 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6798 (pt0) REVERT: B 45 LEU cc_start: 0.7807 (tp) cc_final: 0.6905 (mm) REVERT: B 73 LYS cc_start: 0.6156 (mttp) cc_final: 0.5324 (mmtm) REVERT: B 177 LEU cc_start: 0.7228 (pp) cc_final: 0.6737 (mt) REVERT: B 320 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7611 (ttp-110) REVERT: C 45 LEU cc_start: 0.7329 (mp) cc_final: 0.6498 (tp) REVERT: C 88 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7698 (mmt-90) REVERT: C 119 MET cc_start: 0.8956 (mmm) cc_final: 0.8467 (mmp) REVERT: C 173 ARG cc_start: 0.8306 (ttt90) cc_final: 0.8057 (ptm160) REVERT: C 247 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8786 (mtt-85) REVERT: C 280 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.5860 (mpp) REVERT: D 37 GLN cc_start: 0.6727 (mp10) cc_final: 0.6183 (mm110) REVERT: D 45 LEU cc_start: 0.7845 (mp) cc_final: 0.7436 (mm) REVERT: D 52 ARG cc_start: 0.6646 (mtm110) cc_final: 0.5745 (mpt180) REVERT: D 222 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: D 283 MET cc_start: 0.8723 (mtp) cc_final: 0.8325 (mtt) REVERT: D 327 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: E 127 ASP cc_start: 0.7908 (t70) cc_final: 0.7677 (t70) REVERT: E 222 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7952 (mmm160) REVERT: E 419 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5195 (ttp) REVERT: F 26 GLN cc_start: 0.7615 (mt0) cc_final: 0.6448 (tp40) REVERT: F 127 ASP cc_start: 0.7749 (t70) cc_final: 0.7513 (t0) REVERT: F 131 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6641 (mm-30) REVERT: F 185 GLU cc_start: 0.8357 (mp0) cc_final: 0.8149 (mp0) REVERT: F 259 LYS cc_start: 0.8477 (mtpt) cc_final: 0.7919 (mtmt) REVERT: F 320 ARG cc_start: 0.7313 (ttp80) cc_final: 0.7098 (ttp-170) REVERT: G 26 GLN cc_start: 0.7153 (mt0) cc_final: 0.5998 (tp40) REVERT: G 127 ASP cc_start: 0.7834 (t70) cc_final: 0.7551 (t0) REVERT: G 131 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6840 (mm-30) REVERT: G 302 GLU cc_start: 0.7706 (pp20) cc_final: 0.7194 (mt-10) REVERT: H 26 GLN cc_start: 0.7788 (mt0) cc_final: 0.6514 (tp40) REVERT: H 127 ASP cc_start: 0.7754 (t70) cc_final: 0.7512 (t0) REVERT: H 131 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: H 185 GLU cc_start: 0.8355 (mp0) cc_final: 0.8146 (mp0) REVERT: H 222 ARG cc_start: 0.8400 (mtm180) cc_final: 0.7749 (mmm160) outliers start: 72 outliers final: 34 residues processed: 358 average time/residue: 0.8786 time to fit residues: 350.6240 Evaluate side-chains 316 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 56 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 89 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS B 42 HIS B 271 HIS B 350 HIS C 42 HIS C 89 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS D 271 HIS D 327 GLN ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 377 HIS F 89 GLN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS G 53 GLN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 350 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110608 restraints weight = 20550.398| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.07 r_work: 0.3084 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.498 24904 Z= 0.517 Angle : 0.670 11.966 33752 Z= 0.342 Chirality : 0.050 0.243 3680 Planarity : 0.005 0.058 4496 Dihedral : 7.206 59.817 3760 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.03 % Allowed : 21.93 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3136 helix: 0.76 (0.15), residues: 1248 sheet: 0.67 (0.30), residues: 224 loop : -0.71 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 50 TYR 0.026 0.002 TYR H 333 PHE 0.030 0.003 PHE E 417 TRP 0.004 0.001 TRP E 289 HIS 0.028 0.002 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (24864) covalent geometry : angle 0.66842 / 0.34 (33736) SS BOND : bond 0.00791 / 0.42 ( 8) SS BOND : angle 2.45205 / 1.41 ( 16) hydrogen bonds : bond 0.04370 / 2.97 ( 1040) hydrogen bonds : angle 4.57653 / 3.33 ( 2928) metal coordination : bond 0.37314 / 22.26 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 317 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.7523 (mp10) cc_final: 0.7308 (mp10) REVERT: A 73 LYS cc_start: 0.6348 (mttm) cc_final: 0.5574 (mmtm) REVERT: A 247 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7900 (mtm180) REVERT: A 280 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.6712 (mpp) REVERT: B 37 GLN cc_start: 0.7527 (mt0) cc_final: 0.6822 (mp10) REVERT: B 45 LEU cc_start: 0.7858 (tp) cc_final: 0.6966 (mm) REVERT: B 73 LYS cc_start: 0.6686 (mttp) cc_final: 0.5909 (mmtt) REVERT: B 177 LEU cc_start: 0.7690 (pp) cc_final: 0.7024 (mt) REVERT: B 408 ASP cc_start: 0.7541 (t0) cc_final: 0.7116 (t0) REVERT: C 45 LEU cc_start: 0.7902 (mp) cc_final: 0.7427 (mm) REVERT: C 52 ARG cc_start: 0.6809 (mtm110) cc_final: 0.5704 (mpt180) REVERT: C 73 LYS cc_start: 0.6391 (mttm) cc_final: 0.5669 (mmtm) REVERT: C 88 ARG cc_start: 0.8062 (mtt90) cc_final: 0.7773 (mpt180) REVERT: C 173 ARG cc_start: 0.8358 (ttt90) cc_final: 0.8009 (ptm160) REVERT: C 247 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7603 (mtm180) REVERT: C 320 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7548 (ttm170) REVERT: D 109 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7950 (mtp180) REVERT: D 177 LEU cc_start: 0.7552 (pp) cc_final: 0.6926 (mt) REVERT: D 222 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8048 (mtt180) REVERT: D 327 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: D 408 ASP cc_start: 0.7410 (t0) cc_final: 0.7011 (t0) REVERT: E 127 ASP cc_start: 0.8119 (t70) cc_final: 0.7894 (t0) REVERT: E 259 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8245 (mtpt) REVERT: E 302 GLU cc_start: 0.7750 (pp20) cc_final: 0.7415 (mt-10) REVERT: E 320 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7194 (ttp-170) REVERT: E 389 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8264 (m) REVERT: F 131 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6909 (mm-30) REVERT: F 222 ARG cc_start: 0.8327 (mmm160) cc_final: 0.7885 (mmm160) REVERT: F 320 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7297 (ttp-170) REVERT: F 331 LYS cc_start: 0.7651 (ttpp) cc_final: 0.7430 (tttt) REVERT: G 131 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7010 (mm-30) REVERT: G 222 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8049 (mmm160) REVERT: H 222 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7763 (mmm160) REVERT: H 327 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6321 (pm20) outliers start: 97 outliers final: 33 residues processed: 387 average time/residue: 0.8714 time to fit residues: 376.5640 Evaluate side-chains 317 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 327 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 141 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 410 ASN B 176 HIS C 89 GLN C 176 HIS D 37 GLN D 176 HIS D 327 GLN F 89 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 ASN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116105 restraints weight = 20678.825| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.10 r_work: 0.3136 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.8580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24904 Z= 0.148 Angle : 0.547 12.004 33752 Z= 0.279 Chirality : 0.046 0.232 3680 Planarity : 0.004 0.060 4496 Dihedral : 6.479 58.882 3760 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.57 % Allowed : 23.84 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3136 helix: 0.89 (0.15), residues: 1248 sheet: 0.20 (0.28), residues: 280 loop : -0.56 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 50 TYR 0.016 0.001 TYR G 333 PHE 0.015 0.002 PHE E 122 TRP 0.008 0.001 TRP E 289 HIS 0.024 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (24864) covalent geometry : angle 0.54590 / 0.28 (33736) SS BOND : bond 0.00508 / 0.27 ( 8) SS BOND : angle 1.46092 / 0.85 ( 16) hydrogen bonds : bond 0.03444 / 2.33 ( 1040) hydrogen bonds : angle 4.28676 / 3.11 ( 2928) metal coordination : bond 0.02372 / 1.37 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.6311 (mttm) cc_final: 0.5516 (mmtt) REVERT: A 280 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.6481 (mtp) REVERT: B 45 LEU cc_start: 0.7713 (tp) cc_final: 0.6943 (mm) REVERT: B 73 LYS cc_start: 0.6722 (mttp) cc_final: 0.6080 (mmtt) REVERT: B 88 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7737 (mpt180) REVERT: B 177 LEU cc_start: 0.7585 (pp) cc_final: 0.6976 (mt) REVERT: B 408 ASP cc_start: 0.7483 (t0) cc_final: 0.7090 (t0) REVERT: C 45 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 52 ARG cc_start: 0.6760 (mtm110) cc_final: 0.5668 (mpt180) REVERT: C 73 LYS cc_start: 0.6480 (mttm) cc_final: 0.5614 (mmtt) REVERT: C 88 ARG cc_start: 0.7959 (mtt90) cc_final: 0.7748 (mmt-90) REVERT: C 119 MET cc_start: 0.9010 (mmm) cc_final: 0.8667 (mmp) REVERT: C 173 ARG cc_start: 0.8298 (ttt90) cc_final: 0.7991 (ptm160) REVERT: C 247 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8778 (mtt-85) REVERT: D 45 LEU cc_start: 0.7973 (mp) cc_final: 0.7555 (mm) REVERT: D 177 LEU cc_start: 0.7636 (pp) cc_final: 0.6991 (mt) REVERT: D 222 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7903 (mtt-85) REVERT: D 327 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: D 408 ASP cc_start: 0.7568 (t0) cc_final: 0.7082 (t0) REVERT: E 259 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: E 280 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6479 (mtt) REVERT: E 331 LYS cc_start: 0.7680 (tttt) cc_final: 0.7235 (tttt) REVERT: E 416 ARG cc_start: 0.8565 (mmt90) cc_final: 0.8278 (mmm-85) REVERT: F 131 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6865 (mm-30) REVERT: F 259 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7937 (mtmt) REVERT: F 283 MET cc_start: 0.8975 (mtp) cc_final: 0.8691 (mtp) REVERT: F 320 ARG cc_start: 0.7588 (ttp80) cc_final: 0.7335 (ttp-170) REVERT: F 389 VAL cc_start: 0.8660 (m) cc_final: 0.8420 (p) REVERT: G 131 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6954 (mm-30) REVERT: G 222 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: G 389 VAL cc_start: 0.8729 (m) cc_final: 0.8509 (p) REVERT: H 259 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8489 (ttmt) outliers start: 62 outliers final: 30 residues processed: 348 average time/residue: 0.8751 time to fit residues: 339.9175 Evaluate side-chains 321 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 235 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 173 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 243 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS B 176 HIS C 89 GLN C 176 HIS D 37 GLN D 327 GLN F 89 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 404 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111945 restraints weight = 20193.900| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.12 r_work: 0.3099 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.8763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24904 Z= 0.221 Angle : 0.608 12.423 33752 Z= 0.312 Chirality : 0.048 0.234 3680 Planarity : 0.005 0.067 4496 Dihedral : 6.918 56.311 3760 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.78 % Allowed : 23.55 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3136 helix: 0.81 (0.15), residues: 1248 sheet: 0.71 (0.32), residues: 224 loop : -0.69 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.021 0.002 TYR G 333 PHE 0.016 0.002 PHE H 122 TRP 0.006 0.001 TRP C 289 HIS 0.018 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (24864) covalent geometry : angle 0.60718 / 0.31 (33736) SS BOND : bond 0.00606 / 0.32 ( 8) SS BOND : angle 1.92577 / 1.10 ( 16) hydrogen bonds : bond 0.03969 / 2.69 ( 1040) hydrogen bonds : angle 4.47189 / 3.24 ( 2928) metal coordination : bond 0.01829 / 1.16 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 292 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.6460 (mttm) cc_final: 0.5762 (mmtt) REVERT: A 247 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7921 (mtm180) REVERT: A 280 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.6772 (mtp) REVERT: B 45 LEU cc_start: 0.7747 (tp) cc_final: 0.6860 (mm) REVERT: B 52 ARG cc_start: 0.6998 (mtm110) cc_final: 0.6166 (mpt180) REVERT: B 73 LYS cc_start: 0.6672 (mttp) cc_final: 0.6056 (mmtt) REVERT: B 88 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7952 (mpt180) REVERT: B 177 LEU cc_start: 0.7634 (pp) cc_final: 0.6942 (mt) REVERT: C 52 ARG cc_start: 0.6859 (mtm110) cc_final: 0.5696 (mpt180) REVERT: C 73 LYS cc_start: 0.6693 (mttm) cc_final: 0.5853 (mmtt) REVERT: C 119 MET cc_start: 0.9074 (mmm) cc_final: 0.8652 (mmp) REVERT: C 173 ARG cc_start: 0.8354 (ttt90) cc_final: 0.8034 (ptm160) REVERT: C 247 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8813 (mtt-85) REVERT: D 177 LEU cc_start: 0.7609 (pp) cc_final: 0.7006 (mt) REVERT: D 222 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (mtt180) REVERT: D 283 MET cc_start: 0.8891 (mtp) cc_final: 0.8509 (mtt) REVERT: E 26 GLN cc_start: 0.7509 (mt0) cc_final: 0.6204 (tp40) REVERT: E 127 ASP cc_start: 0.8068 (t70) cc_final: 0.7827 (t0) REVERT: E 131 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7132 (mm-30) REVERT: E 242 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7624 (mtt90) REVERT: E 280 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6584 (mtt) REVERT: E 331 LYS cc_start: 0.7699 (tttt) cc_final: 0.7487 (tttt) REVERT: F 131 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7396 (mm-30) REVERT: F 259 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8035 (mtmt) REVERT: F 320 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7454 (ttp-170) REVERT: F 331 LYS cc_start: 0.7627 (tttt) cc_final: 0.7336 (tptm) REVERT: G 29 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7387 (ttp-170) REVERT: G 127 ASP cc_start: 0.8026 (t70) cc_final: 0.7802 (t0) REVERT: G 131 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6915 (mm-30) REVERT: G 222 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7756 (mtt180) REVERT: H 222 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.8017 (mmm160) outliers start: 67 outliers final: 44 residues processed: 342 average time/residue: 0.8658 time to fit residues: 330.3477 Evaluate side-chains 336 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 235 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 168 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN C 176 HIS F 89 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113620 restraints weight = 20402.166| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.08 r_work: 0.3135 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24904 Z= 0.149 Angle : 0.542 12.633 33752 Z= 0.277 Chirality : 0.046 0.230 3680 Planarity : 0.005 0.064 4496 Dihedral : 6.481 57.149 3760 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.20 % Allowed : 24.04 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3136 helix: 0.92 (0.15), residues: 1248 sheet: 0.12 (0.29), residues: 280 loop : -0.55 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 50 TYR 0.016 0.001 TYR G 333 PHE 0.014 0.002 PHE H 122 TRP 0.007 0.001 TRP E 289 HIS 0.013 0.001 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24864) covalent geometry : angle 0.54164 / 0.28 (33736) SS BOND : bond 0.00454 / 0.25 ( 8) SS BOND : angle 1.29188 / 0.74 ( 16) hydrogen bonds : bond 0.03426 / 2.34 ( 1040) hydrogen bonds : angle 4.31471 / 3.12 ( 2928) metal coordination : bond 0.01393 / 0.91 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7018 (mtm110) cc_final: 0.5900 (mpt180) REVERT: A 73 LYS cc_start: 0.6286 (mttm) cc_final: 0.5633 (mmtt) REVERT: A 247 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8734 (mtt-85) REVERT: A 280 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.6461 (mtp) REVERT: B 45 LEU cc_start: 0.7624 (tp) cc_final: 0.6802 (mm) REVERT: B 52 ARG cc_start: 0.6866 (mtm110) cc_final: 0.6127 (mpt180) REVERT: B 73 LYS cc_start: 0.6693 (mttp) cc_final: 0.6039 (mmtt) REVERT: B 88 ARG cc_start: 0.8081 (mmt-90) cc_final: 0.7875 (mpt180) REVERT: B 177 LEU cc_start: 0.7500 (pp) cc_final: 0.6912 (mt) REVERT: C 45 LEU cc_start: 0.8047 (mp) cc_final: 0.7496 (mm) REVERT: C 52 ARG cc_start: 0.6761 (mtm110) cc_final: 0.5739 (mpt180) REVERT: C 73 LYS cc_start: 0.6550 (mttm) cc_final: 0.5893 (mmtt) REVERT: C 88 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.7765 (mpt180) REVERT: C 119 MET cc_start: 0.9000 (mmm) cc_final: 0.8633 (mmp) REVERT: C 173 ARG cc_start: 0.8328 (ttt90) cc_final: 0.7998 (ptm160) REVERT: C 247 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8791 (mtt-85) REVERT: C 283 MET cc_start: 0.8790 (mtp) cc_final: 0.8493 (mtt) REVERT: C 356 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: D 45 LEU cc_start: 0.7901 (mp) cc_final: 0.7415 (mm) REVERT: D 177 LEU cc_start: 0.7554 (pp) cc_final: 0.6963 (mt) REVERT: D 222 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: E 26 GLN cc_start: 0.7535 (mt0) cc_final: 0.6228 (tp40) REVERT: E 131 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6728 (mm-30) REVERT: E 242 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7649 (mtt90) REVERT: E 259 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8402 (ttmt) REVERT: E 280 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6403 (mtt) REVERT: E 331 LYS cc_start: 0.7552 (tttt) cc_final: 0.7248 (tttt) REVERT: F 131 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6897 (mm-30) REVERT: F 259 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7987 (mtmt) REVERT: F 320 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7459 (ttp-170) REVERT: G 131 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 222 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7727 (mtt180) REVERT: G 389 VAL cc_start: 0.8809 (m) cc_final: 0.8470 (p) REVERT: H 222 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.7970 (mmm160) REVERT: H 331 LYS cc_start: 0.7683 (tttt) cc_final: 0.7455 (tptm) outliers start: 53 outliers final: 40 residues processed: 342 average time/residue: 0.9179 time to fit residues: 348.8425 Evaluate side-chains 335 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 235 LYS Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 4 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 0.0070 chunk 207 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 228 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS D 37 GLN D 176 HIS F 89 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 404 ASN H 404 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120215 restraints weight = 20729.457| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.01 r_work: 0.3222 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24904 Z= 0.103 Angle : 0.496 11.723 33752 Z= 0.254 Chirality : 0.044 0.227 3680 Planarity : 0.004 0.064 4496 Dihedral : 5.929 59.119 3760 Min Nonbonded Distance : 1.455 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.79 % Allowed : 24.79 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3136 helix: 1.16 (0.15), residues: 1248 sheet: 1.02 (0.33), residues: 224 loop : -0.60 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 50 TYR 0.012 0.001 TYR G 333 PHE 0.015 0.001 PHE H 122 TRP 0.008 0.001 TRP E 289 HIS 0.012 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (24864) covalent geometry : angle 0.49604 / 0.25 (33736) SS BOND : bond 0.00304 / 0.17 ( 8) SS BOND : angle 0.76057 / 0.44 ( 16) hydrogen bonds : bond 0.02997 / 2.05 ( 1040) hydrogen bonds : angle 4.14551 / 2.99 ( 2928) metal coordination : bond 0.01112 / 0.75 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6904 (mtm110) cc_final: 0.5795 (mpt180) REVERT: A 73 LYS cc_start: 0.6344 (mttm) cc_final: 0.5755 (mmtt) REVERT: A 280 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.6122 (mpp) REVERT: B 45 LEU cc_start: 0.7548 (tp) cc_final: 0.6875 (mm) REVERT: B 73 LYS cc_start: 0.6654 (mttp) cc_final: 0.6079 (mmtt) REVERT: C 37 GLN cc_start: 0.6902 (mp10) cc_final: 0.6651 (pm20) REVERT: C 45 LEU cc_start: 0.8003 (mp) cc_final: 0.7452 (mm) REVERT: C 52 ARG cc_start: 0.6688 (mtm110) cc_final: 0.5694 (mpt180) REVERT: C 73 LYS cc_start: 0.6370 (mttm) cc_final: 0.5820 (mmtt) REVERT: C 88 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.7720 (mpt180) REVERT: C 119 MET cc_start: 0.8955 (mmm) cc_final: 0.8514 (mmp) REVERT: C 173 ARG cc_start: 0.8329 (ttt90) cc_final: 0.8011 (ptm160) REVERT: C 356 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: D 37 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7220 (mm110) REVERT: D 45 LEU cc_start: 0.7926 (mp) cc_final: 0.7501 (mm) REVERT: D 177 LEU cc_start: 0.7376 (pp) cc_final: 0.6827 (mt) REVERT: D 283 MET cc_start: 0.8777 (mtp) cc_final: 0.8477 (mtt) REVERT: E 26 GLN cc_start: 0.7483 (mt0) cc_final: 0.6151 (tp40) REVERT: E 127 ASP cc_start: 0.7901 (t70) cc_final: 0.7571 (t0) REVERT: E 131 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6636 (mm-30) REVERT: E 176 HIS cc_start: 0.7603 (t70) cc_final: 0.7390 (t70) REVERT: E 242 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7573 (mtt90) REVERT: E 280 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6082 (mtt) REVERT: E 331 LYS cc_start: 0.7422 (tttt) cc_final: 0.7132 (tttt) REVERT: F 39 LYS cc_start: 0.7034 (mtpm) cc_final: 0.6141 (mmtt) REVERT: F 127 ASP cc_start: 0.7825 (t70) cc_final: 0.7482 (t0) REVERT: F 131 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6784 (mm-30) REVERT: F 259 LYS cc_start: 0.8486 (mtpt) cc_final: 0.7939 (mtmt) REVERT: G 39 LYS cc_start: 0.6618 (mtpp) cc_final: 0.6023 (mmtt) REVERT: G 127 ASP cc_start: 0.7842 (t70) cc_final: 0.7540 (t0) REVERT: G 131 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6766 (mm-30) REVERT: G 222 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7760 (mtt180) REVERT: G 331 LYS cc_start: 0.7622 (tttt) cc_final: 0.7383 (tptm) REVERT: H 39 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6146 (mmtt) REVERT: H 127 ASP cc_start: 0.7887 (t70) cc_final: 0.7654 (t0) REVERT: H 242 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7707 (mtt90) REVERT: H 259 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8039 (mttp) outliers start: 43 outliers final: 32 residues processed: 350 average time/residue: 0.9067 time to fit residues: 352.9936 Evaluate side-chains 334 residues out of total 2408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 171 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 91 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 290 optimal weight: 1.9990 chunk 214 optimal weight: 0.0050 chunk 156 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS C 89 GLN C 176 HIS ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS F 89 GLN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 HIS ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 HIS ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110699 restraints weight = 20730.634| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.08 r_work: 0.3048 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.8969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.534 24904 Z= 0.542 Angle : 0.669 12.195 33752 Z= 0.342 Chirality : 0.052 0.287 3680 Planarity : 0.006 0.067 4496 Dihedral : 7.217 54.417 3760 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.53 % Allowed : 24.38 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3136 helix: 0.78 (0.15), residues: 1248 sheet: 0.55 (0.33), residues: 224 loop : -0.72 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.026 0.003 TYR G 333 PHE 0.017 0.003 PHE A 417 TRP 0.006 0.001 TRP C 289 HIS 0.016 0.002 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.29 (24864) covalent geometry : angle 0.66720 / 0.34 (33736) SS BOND : bond 0.00612 / 0.32 ( 8) SS BOND : angle 2.04727 / 1.17 ( 16) hydrogen bonds : bond 0.04388 / 2.99 ( 1040) hydrogen bonds : angle 4.60740 / 3.34 ( 2928) metal coordination : bond 0.38242 / 29.82 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9151.70 seconds wall clock time: 156 minutes 37.79 seconds (9397.79 seconds total)