Starting phenix.real_space_refine on Sat Mar 7 12:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.map" model { file = "/net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lrr_0959/03_2026/6lrr_0959.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 28040 2.51 5 N 7534 2.21 5 O 8008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43706 Number of models: 1 Model: "" Number of chains: 24 Chain: "O" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1151 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 124} Chain: "P" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 140} Chain: "T" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "W" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 869 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "G" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3386 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1151 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 124} Chain: "N" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 140} Chain: "U" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "V" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 869 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3386 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1151 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 124} Chain: "L" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 140} Chain: "X" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "Y" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 869 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3370 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3386 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1151 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 124} Chain: "J" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 140} Chain: "R" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 869 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "Q" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 877 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3386 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 9.92, per 1000 atoms: 0.23 Number of scatterers: 43706 At special positions: 0 Unit cell: (196.56, 196.56, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 8008 8.00 N 7534 7.00 C 28040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 173 " - pdb=" SG CYS G 193 " distance=2.05 Simple disulfide: pdb=" SG CYS G 248 " - pdb=" SG CYS H 248 " distance=2.04 Simple disulfide: pdb=" SG CYS H 173 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 248 " - pdb=" SG CYS F 248 " distance=2.04 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 193 " distance=2.05 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 193 " distance=2.05 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS D 248 " distance=2.04 Simple disulfide: pdb=" SG CYS D 173 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS B 248 " distance=2.04 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 193 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10188 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 55 sheets defined 32.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'O' and resid 234 through 239 removed outlier: 4.313A pdb=" N LYS O 238 " --> pdb=" O ALA O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 285 No H-bonds generated for 'chain 'O' and resid 283 through 285' Processing helix chain 'P' and resid 233 through 239 removed outlier: 3.630A pdb=" N LEU P 237 " --> pdb=" O LYS P 233 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS P 238 " --> pdb=" O ALA P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 removed outlier: 3.603A pdb=" N ALA P 271 " --> pdb=" O GLN P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 353 removed outlier: 3.659A pdb=" N VAL P 352 " --> pdb=" O LEU P 348 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR P 353 " --> pdb=" O ASP P 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 348 through 353' Processing helix chain 'T' and resid 20 through 33 Processing helix chain 'T' and resid 65 through 78 removed outlier: 3.858A pdb=" N ALA T 71 " --> pdb=" O ARG T 67 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 32 removed outlier: 3.896A pdb=" N TYR W 30 " --> pdb=" O LYS W 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE W 31 " --> pdb=" O GLN W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 35 No H-bonds generated for 'chain 'W' and resid 33 through 35' Processing helix chain 'W' and resid 69 through 80 removed outlier: 3.733A pdb=" N GLN W 74 " --> pdb=" O LEU W 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 109 removed outlier: 3.850A pdb=" N LEU G 108 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 121 Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.544A pdb=" N LYS G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.884A pdb=" N GLY G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 233 removed outlier: 3.649A pdb=" N ALA G 225 " --> pdb=" O PHE G 221 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA G 231 " --> pdb=" O THR G 227 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 260 removed outlier: 3.594A pdb=" N ARG G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 311 through 322 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 384 through 388 Processing helix chain 'G' and resid 389 through 394 removed outlier: 3.605A pdb=" N GLU G 393 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 433 removed outlier: 3.541A pdb=" N THR G 419 " --> pdb=" O ALA G 415 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 425 " --> pdb=" O ASN G 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 448 removed outlier: 3.717A pdb=" N VAL G 445 " --> pdb=" O GLU G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 459 removed outlier: 3.661A pdb=" N VAL G 458 " --> pdb=" O PRO G 454 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 459 " --> pdb=" O GLU G 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.076A pdb=" N TYR H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.982A pdb=" N LEU H 108 " --> pdb=" O PRO H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 122 removed outlier: 3.612A pdb=" N LEU H 118 " --> pdb=" O ILE H 114 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 156 through 164 Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.975A pdb=" N GLY H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 233 removed outlier: 4.025A pdb=" N ALA H 225 " --> pdb=" O PHE H 221 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA H 231 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.602A pdb=" N TYR H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 287 removed outlier: 4.113A pdb=" N ALA H 277 " --> pdb=" O ALA H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 322 removed outlier: 3.515A pdb=" N LEU H 315 " --> pdb=" O HIS H 311 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 342 Processing helix chain 'H' and resid 342 through 350 removed outlier: 3.656A pdb=" N ASP H 348 " --> pdb=" O MET H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 388 Processing helix chain 'H' and resid 389 through 394 Processing helix chain 'H' and resid 414 through 433 removed outlier: 4.062A pdb=" N LEU H 425 " --> pdb=" O ASN H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 448 removed outlier: 3.910A pdb=" N VAL H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 458 removed outlier: 3.603A pdb=" N VAL H 458 " --> pdb=" O PRO H 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 removed outlier: 4.325A pdb=" N LYS M 238 " --> pdb=" O ALA M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 285 No H-bonds generated for 'chain 'M' and resid 283 through 285' Processing helix chain 'N' and resid 233 through 239 removed outlier: 3.584A pdb=" N LEU N 237 " --> pdb=" O LYS N 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 238 " --> pdb=" O ALA N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 271 removed outlier: 3.627A pdb=" N ALA N 271 " --> pdb=" O GLN N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 353 removed outlier: 3.672A pdb=" N VAL N 352 " --> pdb=" O LEU N 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR N 353 " --> pdb=" O ASP N 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 348 through 353' Processing helix chain 'U' and resid 20 through 33 Processing helix chain 'U' and resid 65 through 78 removed outlier: 3.793A pdb=" N ALA U 71 " --> pdb=" O ARG U 67 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 32 removed outlier: 3.776A pdb=" N TYR V 30 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE V 31 " --> pdb=" O GLN V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 35 No H-bonds generated for 'chain 'V' and resid 33 through 35' Processing helix chain 'V' and resid 69 through 80 removed outlier: 3.659A pdb=" N SER V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.831A pdb=" N LEU E 108 " --> pdb=" O PRO E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.547A pdb=" N LYS E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.883A pdb=" N GLY E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 233 removed outlier: 3.650A pdb=" N ALA E 225 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 231 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 removed outlier: 3.594A pdb=" N ARG E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.601A pdb=" N THR E 279 " --> pdb=" O PHE E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 322 Processing helix chain 'E' and resid 336 through 350 Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.604A pdb=" N GLU E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 433 removed outlier: 3.537A pdb=" N THR E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 425 " --> pdb=" O ASN E 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 448 removed outlier: 3.723A pdb=" N VAL E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 459 removed outlier: 3.659A pdb=" N VAL E 458 " --> pdb=" O PRO E 454 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 59 Processing helix chain 'F' and resid 77 through 82 removed outlier: 4.123A pdb=" N TYR F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.984A pdb=" N LEU F 108 " --> pdb=" O PRO F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.609A pdb=" N LEU F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.974A pdb=" N GLY F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 233 removed outlier: 4.025A pdb=" N ALA F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 261 removed outlier: 3.600A pdb=" N TYR F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 287 removed outlier: 4.111A pdb=" N ALA F 277 " --> pdb=" O ALA F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 322 removed outlier: 3.521A pdb=" N LEU F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 342 through 350 removed outlier: 3.654A pdb=" N ASP F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 414 through 433 removed outlier: 4.058A pdb=" N LEU F 425 " --> pdb=" O ASN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 448 removed outlier: 3.916A pdb=" N VAL F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.607A pdb=" N VAL F 458 " --> pdb=" O PRO F 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 239 removed outlier: 4.334A pdb=" N LYS K 238 " --> pdb=" O ALA K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 285 No H-bonds generated for 'chain 'K' and resid 283 through 285' Processing helix chain 'L' and resid 233 through 239 removed outlier: 3.607A pdb=" N LEU L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 271 removed outlier: 3.603A pdb=" N ALA L 271 " --> pdb=" O GLN L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 348 through 353 removed outlier: 3.652A pdb=" N VAL L 352 " --> pdb=" O LEU L 348 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR L 353 " --> pdb=" O ASP L 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 348 through 353' Processing helix chain 'X' and resid 20 through 33 Processing helix chain 'X' and resid 65 through 78 removed outlier: 3.841A pdb=" N ALA X 71 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER X 78 " --> pdb=" O GLN X 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 32 removed outlier: 3.678A pdb=" N TYR Y 30 " --> pdb=" O LYS Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 80 removed outlier: 4.784A pdb=" N GLU Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 removed outlier: 3.503A pdb=" N ALA C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.820A pdb=" N LEU C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.542A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.868A pdb=" N GLY C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 233 removed outlier: 3.628A pdb=" N ALA C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 removed outlier: 3.597A pdb=" N ARG C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.089A pdb=" N ALA C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 279 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 336 through 350 Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.606A pdb=" N GLU C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 433 removed outlier: 3.528A pdb=" N THR C 419 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 448 removed outlier: 3.717A pdb=" N VAL C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 459 removed outlier: 3.663A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 77 through 82 removed outlier: 4.021A pdb=" N TYR D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.964A pdb=" N LEU D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.611A pdb=" N LEU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.980A pdb=" N GLY D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 233 removed outlier: 4.021A pdb=" N ALA D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.601A pdb=" N TYR D 257 " --> pdb=" O LYS D 253 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 4.106A pdb=" N ALA D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.516A pdb=" N LEU D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 342 through 350 removed outlier: 3.654A pdb=" N ASP D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 414 through 433 removed outlier: 4.059A pdb=" N LEU D 425 " --> pdb=" O ASN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 448 removed outlier: 3.910A pdb=" N VAL D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.595A pdb=" N VAL D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 239 removed outlier: 4.321A pdb=" N LYS I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'J' and resid 233 through 239 removed outlier: 3.596A pdb=" N LEU J 237 " --> pdb=" O LYS J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 271 removed outlier: 3.602A pdb=" N ALA J 271 " --> pdb=" O GLN J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 353 removed outlier: 3.665A pdb=" N VAL J 352 " --> pdb=" O LEU J 348 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR J 353 " --> pdb=" O ASP J 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 348 through 353' Processing helix chain 'R' and resid 20 through 32 removed outlier: 3.616A pdb=" N TYR R 30 " --> pdb=" O LYS R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 35 No H-bonds generated for 'chain 'R' and resid 33 through 35' Processing helix chain 'R' and resid 66 through 80 removed outlier: 3.815A pdb=" N LEU R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU R 72 " --> pdb=" O GLU R 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 33 Processing helix chain 'Q' and resid 65 through 78 removed outlier: 3.791A pdb=" N ALA Q 71 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER Q 78 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.819A pdb=" N LEU A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.543A pdb=" N LYS A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.885A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.661A pdb=" N ALA A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.598A pdb=" N ARG A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 4.107A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.604A pdb=" N GLU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 removed outlier: 3.539A pdb=" N THR A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.715A pdb=" N VAL A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.659A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.023A pdb=" N TYR B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.969A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.614A pdb=" N LEU B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.977A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 4.014A pdb=" N ALA B 225 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.603A pdb=" N TYR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 4.108A pdb=" N ALA B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.518A pdb=" N LEU B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 342 through 350 removed outlier: 3.658A pdb=" N ASP B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 414 through 433 removed outlier: 4.059A pdb=" N LEU B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.910A pdb=" N VAL B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.591A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 223 through 225 Processing sheet with id=AA2, first strand: chain 'O' and resid 252 through 254 removed outlier: 3.837A pdb=" N PHE O 254 " --> pdb=" O GLN P 258 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN P 258 " --> pdb=" O PHE O 254 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA P 259 " --> pdb=" O VAL P 226 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU P 279 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN P 229 " --> pdb=" O LEU P 279 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR P 281 " --> pdb=" O GLN P 229 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE P 278 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU P 297 " --> pdb=" O LEU P 341 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU P 341 " --> pdb=" O LEU P 297 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL P 299 " --> pdb=" O ILE P 339 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS P 337 " --> pdb=" O ASP P 301 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL P 314 " --> pdb=" O LEU P 335 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS P 337 " --> pdb=" O TYR P 312 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR P 312 " --> pdb=" O LYS P 337 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE P 313 " --> pdb=" O GLN P 324 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN P 324 " --> pdb=" O PHE P 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 275 through 281 removed outlier: 5.289A pdb=" N ARG O 343 " --> pdb=" O PRO O 295 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU O 297 " --> pdb=" O LEU O 341 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU O 341 " --> pdb=" O LEU O 297 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL O 299 " --> pdb=" O ILE O 339 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL O 314 " --> pdb=" O LEU O 335 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE O 313 " --> pdb=" O GLN O 324 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN O 324 " --> pdb=" O PHE O 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 275 through 281 removed outlier: 5.289A pdb=" N ARG O 343 " --> pdb=" O PRO O 295 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU O 297 " --> pdb=" O LEU O 341 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU O 341 " --> pdb=" O LEU O 297 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL O 299 " --> pdb=" O ILE O 339 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE P 212 " --> pdb=" O ILE O 339 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU O 341 " --> pdb=" O PHE P 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 54 through 55 removed outlier: 6.985A pdb=" N ILE T 85 " --> pdb=" O ILE T 102 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE T 102 " --> pdb=" O ILE T 85 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL T 87 " --> pdb=" O SER T 100 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER T 100 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY T 89 " --> pdb=" O ILE T 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 37 through 39 Processing sheet with id=AA7, first strand: chain 'W' and resid 37 through 39 removed outlier: 6.347A pdb=" N VAL W 87 " --> pdb=" O ILE W 102 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE W 102 " --> pdb=" O VAL W 87 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY W 89 " --> pdb=" O SER W 100 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER W 100 " --> pdb=" O GLY W 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 84 through 87 removed outlier: 3.736A pdb=" N ARG G 84 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG G 42 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU G 136 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR G 44 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU G 134 " --> pdb=" O THR G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 200 through 202 removed outlier: 6.040A pdb=" N LEU G 171 " --> pdb=" O PHE G 200 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS G 202 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS G 173 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN G 402 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA G 379 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 241 through 242 removed outlier: 5.916A pdb=" N LEU G 241 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASP G 269 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE G 266 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS G 295 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N HIS G 268 " --> pdb=" O HIS G 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AB3, first strand: chain 'H' and resid 84 through 87 removed outlier: 3.569A pdb=" N ARG H 84 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU H 38 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 200 through 202 removed outlier: 6.141A pdb=" N LEU H 171 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS H 202 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS H 173 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS H 328 " --> pdb=" O ILE H 294 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU H 241 " --> pdb=" O MET H 267 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP H 269 " --> pdb=" O LEU H 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 354 through 355 Processing sheet with id=AB6, first strand: chain 'M' and resid 223 through 225 Processing sheet with id=AB7, first strand: chain 'M' and resid 252 through 254 removed outlier: 3.523A pdb=" N VAL M 252 " --> pdb=" O TRP N 260 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE M 254 " --> pdb=" O GLN N 258 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN N 258 " --> pdb=" O PHE M 254 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA N 259 " --> pdb=" O VAL N 226 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN N 229 " --> pdb=" O LEU N 279 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR N 281 " --> pdb=" O GLN N 229 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE N 278 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU N 297 " --> pdb=" O LEU N 341 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU N 341 " --> pdb=" O LEU N 297 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL N 299 " --> pdb=" O ILE N 339 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS N 337 " --> pdb=" O ASP N 301 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 336 " --> pdb=" O VAL N 314 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR N 312 " --> pdb=" O VAL N 338 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE N 313 " --> pdb=" O GLN N 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN N 324 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 275 through 281 removed outlier: 5.291A pdb=" N ARG M 343 " --> pdb=" O PRO M 295 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU M 297 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU M 341 " --> pdb=" O LEU M 297 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL M 299 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL M 314 " --> pdb=" O LEU M 335 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE M 313 " --> pdb=" O GLN M 324 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN M 324 " --> pdb=" O PHE M 313 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 275 through 281 removed outlier: 5.291A pdb=" N ARG M 343 " --> pdb=" O PRO M 295 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU M 297 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU M 341 " --> pdb=" O LEU M 297 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL M 299 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE N 212 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU M 341 " --> pdb=" O PHE N 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.998A pdb=" N ILE U 85 " --> pdb=" O ILE U 102 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE U 102 " --> pdb=" O ILE U 85 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL U 87 " --> pdb=" O SER U 100 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER U 100 " --> pdb=" O VAL U 87 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY U 89 " --> pdb=" O ILE U 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'V' and resid 37 through 39 removed outlier: 6.289A pdb=" N VAL V 87 " --> pdb=" O ILE V 102 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE V 102 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY V 89 " --> pdb=" O SER V 100 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER V 100 " --> pdb=" O GLY V 89 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.646A pdb=" N ARG E 84 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG E 42 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR E 44 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU E 134 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.046A pdb=" N LEU E 171 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 202 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS E 173 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN E 402 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA E 379 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.909A pdb=" N LEU E 241 " --> pdb=" O MET E 267 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP E 269 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE E 266 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS E 295 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS E 268 " --> pdb=" O HIS E 295 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AC8, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.571A pdb=" N ARG F 84 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU F 38 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 200 through 202 removed outlier: 6.136A pdb=" N LEU F 171 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS F 202 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS F 173 " --> pdb=" O LYS F 202 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS F 328 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 266 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N HIS F 295 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS F 268 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU F 241 " --> pdb=" O MET F 267 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP F 269 " --> pdb=" O LEU F 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 354 through 355 Processing sheet with id=AD2, first strand: chain 'K' and resid 223 through 225 Processing sheet with id=AD3, first strand: chain 'K' and resid 252 through 254 removed outlier: 3.747A pdb=" N PHE K 254 " --> pdb=" O GLN L 258 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 259 " --> pdb=" O VAL L 226 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 222 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 279 " --> pdb=" O VAL L 227 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN L 229 " --> pdb=" O LEU L 279 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR L 281 " --> pdb=" O GLN L 229 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 278 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU L 297 " --> pdb=" O LEU L 341 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU L 341 " --> pdb=" O LEU L 297 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL L 299 " --> pdb=" O ILE L 339 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS L 337 " --> pdb=" O ASP L 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL L 314 " --> pdb=" O LEU L 335 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS L 337 " --> pdb=" O TYR L 312 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR L 312 " --> pdb=" O LYS L 337 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE L 313 " --> pdb=" O GLN L 324 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN L 324 " --> pdb=" O PHE L 313 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 275 through 281 removed outlier: 5.295A pdb=" N ARG K 343 " --> pdb=" O PRO K 295 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU K 297 " --> pdb=" O LEU K 341 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU K 341 " --> pdb=" O LEU K 297 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL K 299 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL K 314 " --> pdb=" O LEU K 335 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE K 313 " --> pdb=" O GLN K 324 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN K 324 " --> pdb=" O PHE K 313 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 275 through 281 removed outlier: 5.295A pdb=" N ARG K 343 " --> pdb=" O PRO K 295 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU K 297 " --> pdb=" O LEU K 341 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU K 341 " --> pdb=" O LEU K 297 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL K 299 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE L 212 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU K 341 " --> pdb=" O PHE L 212 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 54 through 55 removed outlier: 6.884A pdb=" N ILE X 85 " --> pdb=" O ILE X 102 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE X 102 " --> pdb=" O ILE X 85 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL X 87 " --> pdb=" O SER X 100 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER X 100 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLY X 89 " --> pdb=" O ILE X 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 37 through 39 removed outlier: 3.539A pdb=" N GLU Y 41 " --> pdb=" O ARG Y 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 37 through 39 removed outlier: 7.109A pdb=" N ILE Y 85 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE Y 102 " --> pdb=" O ILE Y 85 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL Y 87 " --> pdb=" O SER Y 100 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER Y 100 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY Y 89 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS Y 96 " --> pdb=" O ASP Y 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.651A pdb=" N ARG C 84 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG C 42 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU C 136 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR C 44 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU C 134 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 200 through 202 removed outlier: 6.070A pdb=" N LEU C 171 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS C 202 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS C 173 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN C 402 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 379 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 241 through 242 removed outlier: 5.916A pdb=" N LEU C 241 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASP C 269 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE C 266 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS C 295 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS C 268 " --> pdb=" O HIS C 295 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.593A pdb=" N ARG D 84 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 38 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 202 removed outlier: 6.139A pdb=" N LEU D 171 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS D 202 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS D 173 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS D 328 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 266 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS D 295 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS D 268 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU D 241 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP D 269 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 354 through 355 Processing sheet with id=AE7, first strand: chain 'I' and resid 223 through 225 Processing sheet with id=AE8, first strand: chain 'I' and resid 252 through 254 removed outlier: 3.755A pdb=" N PHE I 254 " --> pdb=" O GLN J 258 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA J 259 " --> pdb=" O VAL J 226 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG J 222 " --> pdb=" O LEU J 263 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU J 279 " --> pdb=" O VAL J 227 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN J 229 " --> pdb=" O LEU J 279 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR J 281 " --> pdb=" O GLN J 229 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 278 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU J 297 " --> pdb=" O LEU J 341 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU J 341 " --> pdb=" O LEU J 297 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 299 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS J 337 " --> pdb=" O ASP J 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL J 314 " --> pdb=" O LEU J 335 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS J 337 " --> pdb=" O TYR J 312 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR J 312 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE J 313 " --> pdb=" O GLN J 324 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN J 324 " --> pdb=" O PHE J 313 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 275 through 281 removed outlier: 5.283A pdb=" N ARG I 343 " --> pdb=" O PRO I 295 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU I 297 " --> pdb=" O LEU I 341 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU I 341 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL I 299 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL I 314 " --> pdb=" O LEU I 335 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE I 313 " --> pdb=" O GLN I 324 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN I 324 " --> pdb=" O PHE I 313 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 275 through 281 removed outlier: 5.283A pdb=" N ARG I 343 " --> pdb=" O PRO I 295 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU I 297 " --> pdb=" O LEU I 341 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU I 341 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL I 299 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE J 212 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU I 341 " --> pdb=" O PHE J 212 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 54 through 55 removed outlier: 3.549A pdb=" N GLU R 41 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL R 87 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE R 102 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.994A pdb=" N ILE Q 85 " --> pdb=" O ILE Q 102 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE Q 102 " --> pdb=" O ILE Q 85 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL Q 87 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER Q 100 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY Q 89 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.607A pdb=" N ARG A 84 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 42 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 44 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU A 134 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.038A pdb=" N LEU A 171 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS A 202 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 173 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLN A 402 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 379 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 241 through 242 removed outlier: 5.923A pdb=" N LEU A 241 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP A 269 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 266 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS A 295 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 268 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AF8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.597A pdb=" N ARG B 84 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 38 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 200 through 202 removed outlier: 6.139A pdb=" N LEU B 171 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS B 202 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS B 173 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 328 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 266 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N HIS B 295 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS B 268 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 241 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP B 269 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 354 through 355 1349 hydrogen bonds defined for protein. 3726 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: 9.98 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13889 1.33 - 1.46: 11394 1.46 - 1.59: 19363 1.59 - 1.72: 0 1.72 - 1.85: 176 Bond restraints: 44822 Sorted by residual: bond pdb=" CA PHE H 200 " pdb=" CB PHE H 200 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.52e-02 4.33e+03 1.56e+01 bond pdb=" CA PHE D 200 " pdb=" CB PHE D 200 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.52e-02 4.33e+03 1.52e+01 bond pdb=" CA PHE F 200 " pdb=" CB PHE F 200 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.52e-02 4.33e+03 1.52e+01 bond pdb=" CA PHE B 200 " pdb=" CB PHE B 200 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.52e-02 4.33e+03 1.52e+01 bond pdb=" CB ASN E 278 " pdb=" CG ASN E 278 " ideal model delta sigma weight residual 1.516 1.422 0.094 2.50e-02 1.60e+03 1.42e+01 ... (remaining 44817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 57971 2.55 - 5.10: 2590 5.10 - 7.65: 301 7.65 - 10.20: 62 10.20 - 12.74: 32 Bond angle restraints: 60956 Sorted by residual: angle pdb=" N VAL G 392 " pdb=" CA VAL G 392 " pdb=" C VAL G 392 " ideal model delta sigma weight residual 113.42 104.70 8.72 1.17e+00 7.31e-01 5.55e+01 angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 113.42 104.70 8.72 1.17e+00 7.31e-01 5.55e+01 angle pdb=" N VAL E 392 " pdb=" CA VAL E 392 " pdb=" C VAL E 392 " ideal model delta sigma weight residual 113.42 104.73 8.69 1.17e+00 7.31e-01 5.51e+01 angle pdb=" N VAL C 392 " pdb=" CA VAL C 392 " pdb=" C VAL C 392 " ideal model delta sigma weight residual 113.42 104.74 8.68 1.17e+00 7.31e-01 5.50e+01 angle pdb=" C ILE I 246 " pdb=" N GLU I 247 " pdb=" CA GLU I 247 " ideal model delta sigma weight residual 120.58 128.21 -7.63 1.32e+00 5.74e-01 3.34e+01 ... (remaining 60951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 25123 16.60 - 33.20: 1388 33.20 - 49.80: 177 49.80 - 66.40: 28 66.40 - 83.00: 36 Dihedral angle restraints: 26752 sinusoidal: 10910 harmonic: 15842 Sorted by residual: dihedral pdb=" CA SER G 63 " pdb=" C SER G 63 " pdb=" N THR G 64 " pdb=" CA THR G 64 " ideal model delta harmonic sigma weight residual 180.00 134.85 45.15 0 5.00e+00 4.00e-02 8.15e+01 dihedral pdb=" CA SER H 63 " pdb=" C SER H 63 " pdb=" N THR H 64 " pdb=" CA THR H 64 " ideal model delta harmonic sigma weight residual 180.00 135.45 44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA SER F 63 " pdb=" C SER F 63 " pdb=" N THR F 64 " pdb=" CA THR F 64 " ideal model delta harmonic sigma weight residual 180.00 135.70 44.30 0 5.00e+00 4.00e-02 7.85e+01 ... (remaining 26749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4659 0.068 - 0.135: 1647 0.135 - 0.203: 270 0.203 - 0.271: 66 0.271 - 0.339: 18 Chirality restraints: 6660 Sorted by residual: chirality pdb=" CG LEU G 425 " pdb=" CB LEU G 425 " pdb=" CD1 LEU G 425 " pdb=" CD2 LEU G 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CG LEU C 425 " pdb=" CB LEU C 425 " pdb=" CD1 LEU C 425 " pdb=" CD2 LEU C 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CG LEU E 425 " pdb=" CB LEU E 425 " pdb=" CD1 LEU E 425 " pdb=" CD2 LEU E 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 6657 not shown) Planarity restraints: 7966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR T 15 " 0.045 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" CG TYR T 15 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR T 15 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR T 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR T 15 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR T 15 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR T 15 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 15 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 15 " 0.044 2.00e-02 2.50e+03 3.32e-02 2.21e+01 pdb=" CG TYR Q 15 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 15 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 15 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 15 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 15 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR Q 15 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR Q 15 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 15 " 0.044 2.00e-02 2.50e+03 3.30e-02 2.17e+01 pdb=" CG TYR U 15 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR U 15 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR U 15 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR U 15 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR U 15 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR U 15 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR U 15 " 0.017 2.00e-02 2.50e+03 ... (remaining 7963 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 12267 2.80 - 3.32: 39518 3.32 - 3.85: 77322 3.85 - 4.37: 94823 4.37 - 4.90: 161155 Nonbonded interactions: 385085 Sorted by model distance: nonbonded pdb=" OD1 ASP B 161 " pdb=" OH TYR B 166 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP H 161 " pdb=" OH TYR H 166 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP F 161 " pdb=" OH TYR F 166 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR P 281 " pdb=" OD1 ASP P 283 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR N 281 " pdb=" OD1 ASP N 283 " model vdw 2.292 3.040 ... (remaining 385080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 22 through 65 or resid 77 through 462)) selection = (chain 'C' and (resid 22 through 65 or resid 77 through 462)) selection = (chain 'D' and (resid 22 through 65 or resid 77 through 462)) selection = chain 'E' selection = (chain 'F' and (resid 22 through 65 or resid 77 through 462)) selection = chain 'G' selection = (chain 'H' and (resid 22 through 65 or resid 77 through 462)) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 206 through 346) selection = chain 'K' selection = (chain 'L' and resid 206 through 346) selection = chain 'M' selection = (chain 'N' and resid 206 through 346) selection = chain 'O' selection = (chain 'P' and resid 206 through 346) } ncs_group { reference = (chain 'Q' and resid 2 through 106) selection = chain 'R' selection = (chain 'T' and resid 2 through 106) selection = (chain 'U' and resid 2 through 106) selection = chain 'V' selection = chain 'W' selection = (chain 'X' and resid 2 through 106) selection = chain 'Y' } 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: 1.140 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 40.250 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.014 0.124 44834 Z= 0.594 Angle : 1.219 12.744 60980 Z= 0.652 Chirality : 0.071 0.339 6660 Planarity : 0.009 0.084 7966 Dihedral : 11.038 83.002 16528 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 0.52 % Allowed : 3.36 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.20 % 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: -5.11 (0.09), residues: 5430 helix: -4.62 (0.05), residues: 1669 sheet: -3.57 (0.14), residues: 805 loop : -2.55 (0.10), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG C 216 TYR 0.073 0.005 TYR T 15 PHE 0.046 0.005 PHE H 126 TRP 0.054 0.005 TRP X 53 HIS 0.020 0.004 HIS G 326 Details of bonding type rmsd covalent geometry : bond 0.01430 (44822) covalent geometry : angle 1.21725 (60956) SS BOND : bond 0.01726 ( 12) SS BOND : angle 3.14042 ( 24) hydrogen bonds : bond 0.29381 ( 1301) hydrogen bonds : angle 11.48484 ( 3726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 922 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 232 LEU cc_start: 0.6624 (mt) cc_final: 0.6240 (mp) REVERT: P 236 GLU cc_start: 0.6004 (mt-10) cc_final: 0.5697 (mm-30) REVERT: P 252 VAL cc_start: 0.7912 (m) cc_final: 0.7658 (p) REVERT: T 52 TYR cc_start: 0.8410 (m-80) cc_final: 0.7697 (m-80) REVERT: W 104 HIS cc_start: 0.7252 (t70) cc_final: 0.6774 (t-170) REVERT: G 336 LEU cc_start: 0.8921 (mp) cc_final: 0.8475 (mp) REVERT: G 339 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7635 (mt-10) REVERT: H 33 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8664 (mtmt) REVERT: H 371 SER cc_start: 0.8955 (m) cc_final: 0.8740 (t) REVERT: H 432 ARG cc_start: 0.8618 (tmm-80) cc_final: 0.8184 (tmm160) REVERT: H 451 LYS cc_start: 0.8141 (mttm) cc_final: 0.7567 (tptp) REVERT: M 247 GLU cc_start: 0.4605 (mm-30) cc_final: 0.4135 (mm-30) REVERT: N 232 LEU cc_start: 0.6511 (mt) cc_final: 0.6204 (mp) REVERT: N 236 GLU cc_start: 0.6087 (mt-10) cc_final: 0.5826 (mm-30) REVERT: N 252 VAL cc_start: 0.7819 (m) cc_final: 0.7599 (p) REVERT: U 15 TYR cc_start: 0.8285 (m-10) cc_final: 0.8015 (m-80) REVERT: U 44 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7568 (mt-10) REVERT: U 52 TYR cc_start: 0.8437 (m-80) cc_final: 0.7717 (m-80) REVERT: E 336 LEU cc_start: 0.8927 (mp) cc_final: 0.8519 (mp) REVERT: E 339 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 33 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8651 (mtmt) REVERT: F 432 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8204 (tmm160) REVERT: F 451 LYS cc_start: 0.8122 (mttm) cc_final: 0.7569 (tptp) REVERT: L 232 LEU cc_start: 0.6589 (mt) cc_final: 0.6213 (mp) REVERT: L 236 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5536 (mm-30) REVERT: X 52 TYR cc_start: 0.8412 (m-80) cc_final: 0.7771 (m-80) REVERT: C 253 LYS cc_start: 0.8815 (ptmt) cc_final: 0.8611 (ptpt) REVERT: C 336 LEU cc_start: 0.8876 (mp) cc_final: 0.8418 (mp) REVERT: C 339 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 33 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8665 (mtmt) REVERT: D 137 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7917 (mm-30) REVERT: D 371 SER cc_start: 0.8955 (m) cc_final: 0.8754 (t) REVERT: D 432 ARG cc_start: 0.8682 (tmm-80) cc_final: 0.8190 (tmm160) REVERT: D 451 LYS cc_start: 0.8151 (mttm) cc_final: 0.7546 (tptp) REVERT: J 232 LEU cc_start: 0.6596 (mt) cc_final: 0.6206 (mp) REVERT: J 236 GLU cc_start: 0.5813 (mt-10) cc_final: 0.5584 (mm-30) REVERT: R 20 THR cc_start: 0.7881 (p) cc_final: 0.7526 (t) REVERT: Q 44 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7565 (mt-10) REVERT: Q 52 TYR cc_start: 0.8429 (m-80) cc_final: 0.7706 (m-80) REVERT: A 336 LEU cc_start: 0.8887 (mp) cc_final: 0.8454 (mp) REVERT: A 339 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 33 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8657 (mtmt) REVERT: B 137 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 432 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8154 (tmm160) REVERT: B 433 ASN cc_start: 0.8491 (m-40) cc_final: 0.7874 (m-40) REVERT: B 451 LYS cc_start: 0.8119 (mttm) cc_final: 0.7554 (tptp) outliers start: 24 outliers final: 8 residues processed: 942 average time/residue: 0.2602 time to fit residues: 403.3331 Evaluate side-chains 610 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 602 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain A residue 319 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 97 GLN G 96 ASN G 97 GLN G 150 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS G 357 GLN G 402 GLN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN H 230 GLN H 263 GLN ** H 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 HIS H 308 HIS H 357 GLN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 GLN E 96 ASN E 97 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 HIS E 402 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 230 GLN F 263 GLN F 299 HIS F 308 HIS F 357 GLN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN C 96 ASN C 97 GLN C 150 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS C 357 GLN C 402 GLN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 230 GLN D 263 GLN D 299 HIS D 308 HIS D 357 GLN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN A 96 ASN A 97 GLN A 150 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 357 GLN A 402 GLN ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 230 GLN B 263 GLN B 299 HIS B 308 HIS B 357 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.199490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.163806 restraints weight = 46879.540| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.52 r_work: 0.3266 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44834 Z= 0.152 Angle : 0.673 8.711 60980 Z= 0.345 Chirality : 0.047 0.201 6660 Planarity : 0.006 0.069 7966 Dihedral : 6.271 45.117 6010 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.75 % Allowed : 8.34 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.14 % 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: -3.82 (0.09), residues: 5430 helix: -2.82 (0.10), residues: 1651 sheet: -3.30 (0.15), residues: 768 loop : -2.13 (0.10), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 80 TYR 0.018 0.001 TYR T 15 PHE 0.028 0.002 PHE E 346 TRP 0.016 0.002 TRP O 260 HIS 0.009 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00348 (44822) covalent geometry : angle 0.67322 (60956) SS BOND : bond 0.00641 ( 12) SS BOND : angle 1.14311 ( 24) hydrogen bonds : bond 0.04380 ( 1301) hydrogen bonds : angle 6.44956 ( 3726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 694 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 235 GLU cc_start: 0.7651 (tp30) cc_final: 0.7448 (tp30) REVERT: O 236 GLU cc_start: 0.6764 (mp0) cc_final: 0.6224 (mp0) REVERT: P 232 LEU cc_start: 0.5645 (mt) cc_final: 0.5322 (mp) REVERT: P 260 TRP cc_start: 0.6107 (m-10) cc_final: 0.5676 (m-10) REVERT: P 341 LEU cc_start: 0.5914 (mt) cc_final: 0.5472 (mt) REVERT: T 44 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8002 (mt-10) REVERT: T 52 TYR cc_start: 0.8679 (m-80) cc_final: 0.8188 (m-80) REVERT: G 80 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8194 (ttp80) REVERT: G 82 LYS cc_start: 0.8341 (ptpt) cc_final: 0.8075 (ptmt) REVERT: G 178 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8109 (mtpt) REVERT: G 205 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7367 (pt0) REVERT: G 447 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7554 (mtm110) REVERT: H 33 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8673 (mtmt) REVERT: H 64 THR cc_start: 0.8844 (p) cc_final: 0.8544 (p) REVERT: H 81 TYR cc_start: 0.8974 (m-80) cc_final: 0.8732 (m-80) REVERT: H 129 LYS cc_start: 0.9064 (tptt) cc_final: 0.8821 (mmtm) REVERT: H 271 LEU cc_start: 0.9120 (mt) cc_final: 0.8837 (mt) REVERT: H 443 ASN cc_start: 0.7451 (m-40) cc_final: 0.6391 (p0) REVERT: H 451 LYS cc_start: 0.8269 (mttm) cc_final: 0.7473 (tptp) REVERT: N 232 LEU cc_start: 0.5864 (mt) cc_final: 0.5541 (mp) REVERT: N 236 GLU cc_start: 0.5850 (mt-10) cc_final: 0.5609 (mm-30) REVERT: N 260 TRP cc_start: 0.6299 (m-10) cc_final: 0.5931 (m-10) REVERT: N 341 LEU cc_start: 0.5811 (tp) cc_final: 0.5470 (mt) REVERT: U 44 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7988 (mt-10) REVERT: U 52 TYR cc_start: 0.8672 (m-80) cc_final: 0.8181 (m-80) REVERT: U 66 SER cc_start: 0.8646 (p) cc_final: 0.8323 (m) REVERT: E 178 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8166 (mtpt) REVERT: E 447 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7505 (mtm110) REVERT: F 33 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8644 (mtmt) REVERT: F 271 LEU cc_start: 0.9118 (mt) cc_final: 0.8847 (mt) REVERT: F 433 ASN cc_start: 0.8855 (m-40) cc_final: 0.8504 (m-40) REVERT: F 443 ASN cc_start: 0.7475 (m-40) cc_final: 0.6403 (p0) REVERT: F 451 LYS cc_start: 0.8247 (mttm) cc_final: 0.7491 (tptp) REVERT: L 232 LEU cc_start: 0.6396 (mt) cc_final: 0.6116 (mp) REVERT: L 260 TRP cc_start: 0.6144 (m-10) cc_final: 0.5815 (m-10) REVERT: X 52 TYR cc_start: 0.8661 (m-80) cc_final: 0.8142 (m-80) REVERT: C 96 ASN cc_start: 0.8410 (t0) cc_final: 0.8117 (t0) REVERT: C 178 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8030 (mtpp) REVERT: C 205 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7527 (pt0) REVERT: C 447 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7487 (mtm110) REVERT: D 33 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8647 (mtmt) REVERT: D 81 TYR cc_start: 0.8832 (m-80) cc_final: 0.8473 (m-80) REVERT: D 129 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8321 (mmtm) REVERT: D 271 LEU cc_start: 0.9136 (mt) cc_final: 0.8853 (mt) REVERT: D 371 SER cc_start: 0.9150 (m) cc_final: 0.8940 (t) REVERT: D 432 ARG cc_start: 0.8709 (tmm-80) cc_final: 0.8404 (tmm160) REVERT: D 433 ASN cc_start: 0.8633 (m-40) cc_final: 0.8281 (m-40) REVERT: D 443 ASN cc_start: 0.7511 (m-40) cc_final: 0.6443 (p0) REVERT: D 451 LYS cc_start: 0.8232 (mttm) cc_final: 0.7471 (tptp) REVERT: I 235 GLU cc_start: 0.7606 (tp30) cc_final: 0.7380 (tp30) REVERT: I 236 GLU cc_start: 0.6556 (mp0) cc_final: 0.6353 (mp0) REVERT: J 232 LEU cc_start: 0.6325 (mt) cc_final: 0.5964 (mp) REVERT: J 236 GLU cc_start: 0.5595 (mt-10) cc_final: 0.5339 (mm-30) REVERT: J 260 TRP cc_start: 0.6751 (m-10) cc_final: 0.6391 (m-10) REVERT: Q 44 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7987 (mt-10) REVERT: Q 52 TYR cc_start: 0.8677 (m-80) cc_final: 0.8180 (m-80) REVERT: A 96 ASN cc_start: 0.8417 (t0) cc_final: 0.8126 (t0) REVERT: A 178 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8142 (mtpt) REVERT: A 447 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7542 (mtm110) REVERT: B 33 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8663 (mtmt) REVERT: B 271 LEU cc_start: 0.9134 (mt) cc_final: 0.8830 (mt) REVERT: B 432 ARG cc_start: 0.8716 (tmm-80) cc_final: 0.8404 (tmm160) REVERT: B 443 ASN cc_start: 0.7447 (m-40) cc_final: 0.6376 (p0) REVERT: B 451 LYS cc_start: 0.8266 (mttm) cc_final: 0.7469 (tptp) outliers start: 81 outliers final: 31 residues processed: 760 average time/residue: 0.2636 time to fit residues: 327.0176 Evaluate side-chains 601 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 570 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 247 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 328 optimal weight: 0.8980 chunk 476 optimal weight: 0.9980 chunk 265 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 428 optimal weight: 7.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 97 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN H 278 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 GLN E 150 GLN ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN R 97 GLN A 288 ASN A 295 HIS ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.200305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164298 restraints weight = 46851.987| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.54 r_work: 0.3295 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44834 Z= 0.121 Angle : 0.612 13.609 60980 Z= 0.306 Chirality : 0.046 0.169 6660 Planarity : 0.005 0.065 7966 Dihedral : 5.574 41.556 6010 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.77 % Allowed : 10.76 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.10), residues: 5430 helix: -1.66 (0.11), residues: 1698 sheet: -2.91 (0.15), residues: 806 loop : -1.79 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 188 TYR 0.016 0.001 TYR T 15 PHE 0.037 0.002 PHE B 128 TRP 0.015 0.001 TRP O 260 HIS 0.008 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00272 (44822) covalent geometry : angle 0.61157 (60956) SS BOND : bond 0.00459 ( 12) SS BOND : angle 0.75865 ( 24) hydrogen bonds : bond 0.03793 ( 1301) hydrogen bonds : angle 5.61366 ( 3726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 637 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 260 TRP cc_start: 0.6125 (m-10) cc_final: 0.5792 (m-10) REVERT: P 341 LEU cc_start: 0.5928 (mt) cc_final: 0.5712 (mt) REVERT: T 44 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7797 (mt-10) REVERT: T 52 TYR cc_start: 0.8423 (m-80) cc_final: 0.8194 (m-80) REVERT: G 174 THR cc_start: 0.7427 (m) cc_final: 0.7215 (p) REVERT: G 178 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8085 (mtpt) REVERT: G 198 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8453 (mp) REVERT: G 205 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7059 (pm20) REVERT: G 447 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7395 (mtm110) REVERT: H 33 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8647 (mtmt) REVERT: H 433 ASN cc_start: 0.8509 (m-40) cc_final: 0.8055 (m-40) REVERT: H 443 ASN cc_start: 0.7444 (m-40) cc_final: 0.6602 (p0) REVERT: H 447 ARG cc_start: 0.7369 (mtt180) cc_final: 0.6917 (mtt180) REVERT: H 451 LYS cc_start: 0.8145 (mttm) cc_final: 0.7925 (mmtp) REVERT: N 236 GLU cc_start: 0.5703 (mt-10) cc_final: 0.5306 (mm-30) REVERT: N 341 LEU cc_start: 0.5809 (tp) cc_final: 0.5451 (mt) REVERT: U 52 TYR cc_start: 0.8421 (m-80) cc_final: 0.8184 (m-80) REVERT: E 96 ASN cc_start: 0.8289 (t0) cc_final: 0.7934 (t0) REVERT: E 178 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8097 (mtpp) REVERT: E 198 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 205 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: E 263 GLN cc_start: 0.8146 (mm110) cc_final: 0.7860 (mm-40) REVERT: E 270 TYR cc_start: 0.9097 (p90) cc_final: 0.8651 (p90) REVERT: E 447 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7347 (mtm110) REVERT: F 33 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8660 (mtmt) REVERT: F 433 ASN cc_start: 0.8634 (m-40) cc_final: 0.8306 (m-40) REVERT: F 443 ASN cc_start: 0.7470 (m-40) cc_final: 0.6645 (p0) REVERT: F 451 LYS cc_start: 0.8150 (mttm) cc_final: 0.7315 (tptp) REVERT: L 341 LEU cc_start: 0.5910 (tp) cc_final: 0.5519 (mt) REVERT: C 96 ASN cc_start: 0.8286 (t0) cc_final: 0.7924 (t0) REVERT: C 174 THR cc_start: 0.7517 (m) cc_final: 0.7304 (p) REVERT: C 178 LYS cc_start: 0.8400 (mtpt) cc_final: 0.7960 (mtpp) REVERT: C 205 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: C 447 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7350 (mtm110) REVERT: D 33 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8650 (mtmt) REVERT: D 129 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7925 (mmtm) REVERT: D 166 TYR cc_start: 0.8871 (m-80) cc_final: 0.8535 (m-80) REVERT: D 371 SER cc_start: 0.9067 (m) cc_final: 0.8827 (t) REVERT: D 432 ARG cc_start: 0.8652 (tmm-80) cc_final: 0.8374 (tmm160) REVERT: D 443 ASN cc_start: 0.7467 (m-40) cc_final: 0.6629 (p0) REVERT: D 447 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6882 (mtt180) REVERT: J 236 GLU cc_start: 0.5556 (mt-10) cc_final: 0.5304 (mm-30) REVERT: J 260 TRP cc_start: 0.6436 (m-10) cc_final: 0.6094 (m-10) REVERT: J 341 LEU cc_start: 0.5906 (tp) cc_final: 0.5542 (mt) REVERT: Q 44 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7805 (mt-10) REVERT: Q 52 TYR cc_start: 0.8414 (m-80) cc_final: 0.8178 (m-80) REVERT: A 96 ASN cc_start: 0.8297 (t0) cc_final: 0.7945 (t0) REVERT: A 174 THR cc_start: 0.7392 (m) cc_final: 0.7165 (p) REVERT: A 205 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: A 447 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7348 (mtm110) REVERT: B 33 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8645 (mtmt) REVERT: B 52 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: B 61 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6595 (pm20) REVERT: B 432 ARG cc_start: 0.8665 (tmm-80) cc_final: 0.8363 (tmm160) REVERT: B 443 ASN cc_start: 0.7471 (m-40) cc_final: 0.6617 (p0) REVERT: B 447 ARG cc_start: 0.7347 (mtt180) cc_final: 0.6862 (mtt180) REVERT: B 451 LYS cc_start: 0.8068 (mttm) cc_final: 0.7863 (mmtp) outliers start: 82 outliers final: 43 residues processed: 707 average time/residue: 0.2690 time to fit residues: 312.1035 Evaluate side-chains 600 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 550 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 244 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 437 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 431 optimal weight: 5.9990 chunk 373 optimal weight: 0.5980 chunk 277 optimal weight: 30.0000 chunk 210 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 499 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 267 GLN ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 97 GLN G 116 ASN G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN H 164 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 267 GLN ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 HIS ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN B 164 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161392 restraints weight = 46719.390| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.67 r_work: 0.3191 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 44834 Z= 0.181 Angle : 0.619 9.617 60980 Z= 0.311 Chirality : 0.047 0.197 6660 Planarity : 0.005 0.059 7966 Dihedral : 5.308 34.899 6002 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.72 % Allowed : 11.41 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.11), residues: 5430 helix: -1.19 (0.12), residues: 1712 sheet: -2.86 (0.15), residues: 876 loop : -1.61 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.018 0.001 TYR T 15 PHE 0.035 0.002 PHE B 128 TRP 0.016 0.001 TRP O 260 HIS 0.008 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00430 (44822) covalent geometry : angle 0.61884 (60956) SS BOND : bond 0.00560 ( 12) SS BOND : angle 1.29823 ( 24) hydrogen bonds : bond 0.03719 ( 1301) hydrogen bonds : angle 5.38823 ( 3726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 552 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 242 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6166 (mt) REVERT: P 341 LEU cc_start: 0.6010 (mt) cc_final: 0.5511 (mt) REVERT: T 44 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7956 (mt-10) REVERT: T 52 TYR cc_start: 0.8532 (m-80) cc_final: 0.8205 (m-80) REVERT: G 96 ASN cc_start: 0.8319 (t0) cc_final: 0.8032 (t0) REVERT: G 198 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8615 (mp) REVERT: G 403 PHE cc_start: 0.8129 (m-80) cc_final: 0.7912 (m-80) REVERT: G 447 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7429 (mtm110) REVERT: H 33 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8754 (mtmt) REVERT: H 81 TYR cc_start: 0.8959 (m-80) cc_final: 0.8252 (m-80) REVERT: H 432 ARG cc_start: 0.8645 (tmm-80) cc_final: 0.8319 (tmm160) REVERT: H 433 ASN cc_start: 0.8629 (m-40) cc_final: 0.8241 (m-40) REVERT: H 443 ASN cc_start: 0.7489 (m-40) cc_final: 0.6564 (p0) REVERT: H 447 ARG cc_start: 0.7395 (mtt180) cc_final: 0.6903 (mtt180) REVERT: H 451 LYS cc_start: 0.8149 (mttm) cc_final: 0.7935 (mmtp) REVERT: N 341 LEU cc_start: 0.5805 (tp) cc_final: 0.5472 (mt) REVERT: U 52 TYR cc_start: 0.8525 (m-80) cc_final: 0.8203 (m-80) REVERT: E 96 ASN cc_start: 0.8370 (t0) cc_final: 0.8074 (t0) REVERT: E 198 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8641 (mp) REVERT: E 205 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: E 447 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7384 (mtm110) REVERT: F 33 LYS cc_start: 0.8977 (mtmm) cc_final: 0.8654 (mtmt) REVERT: F 432 ARG cc_start: 0.8669 (tmm-80) cc_final: 0.8293 (tmm160) REVERT: F 433 ASN cc_start: 0.8672 (m-40) cc_final: 0.8282 (m-40) REVERT: F 443 ASN cc_start: 0.7401 (m-40) cc_final: 0.6681 (p0) REVERT: F 451 LYS cc_start: 0.8183 (mttm) cc_final: 0.7341 (tptp) REVERT: L 260 TRP cc_start: 0.6861 (m-10) cc_final: 0.6467 (m-10) REVERT: L 341 LEU cc_start: 0.6104 (tp) cc_final: 0.5805 (mt) REVERT: C 96 ASN cc_start: 0.8353 (t0) cc_final: 0.8059 (t0) REVERT: C 174 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7317 (p) REVERT: C 178 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7796 (mtpp) REVERT: C 447 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7407 (mtm110) REVERT: D 33 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8626 (mtmt) REVERT: D 129 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8060 (mmtm) REVERT: D 371 SER cc_start: 0.9109 (m) cc_final: 0.8892 (t) REVERT: D 432 ARG cc_start: 0.8678 (tmm-80) cc_final: 0.8371 (tmm160) REVERT: D 443 ASN cc_start: 0.7472 (m-40) cc_final: 0.6638 (p0) REVERT: D 451 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7336 (tptp) REVERT: J 260 TRP cc_start: 0.6264 (m-10) cc_final: 0.6051 (m-10) REVERT: J 341 LEU cc_start: 0.6044 (tp) cc_final: 0.5737 (mt) REVERT: Q 44 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7953 (mt-10) REVERT: Q 52 TYR cc_start: 0.8533 (m-80) cc_final: 0.8206 (m-80) REVERT: A 96 ASN cc_start: 0.8360 (t0) cc_final: 0.8069 (t0) REVERT: A 174 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7329 (p) REVERT: A 178 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8174 (mtpt) REVERT: A 198 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 205 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7095 (pt0) REVERT: A 447 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7404 (mtm110) REVERT: B 33 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8681 (mtmt) REVERT: B 81 TYR cc_start: 0.8794 (m-80) cc_final: 0.8514 (m-80) REVERT: B 432 ARG cc_start: 0.8714 (tmm-80) cc_final: 0.8349 (tmm160) REVERT: B 443 ASN cc_start: 0.7521 (m-40) cc_final: 0.6566 (p0) REVERT: B 447 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6866 (mtt180) REVERT: B 451 LYS cc_start: 0.8136 (mttm) cc_final: 0.7920 (mmtp) outliers start: 126 outliers final: 67 residues processed: 646 average time/residue: 0.2664 time to fit residues: 281.8451 Evaluate side-chains 603 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 528 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 304 GLN Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 97 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 151 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 428 optimal weight: 40.0000 chunk 230 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN H 164 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.196612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161620 restraints weight = 46535.329| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.71 r_work: 0.3163 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 44834 Z= 0.210 Angle : 0.627 8.952 60980 Z= 0.316 Chirality : 0.047 0.169 6660 Planarity : 0.005 0.062 7966 Dihedral : 5.248 35.337 6002 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.80 % Allowed : 12.27 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.11), residues: 5430 helix: -0.90 (0.12), residues: 1686 sheet: -2.84 (0.15), residues: 866 loop : -1.53 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 80 TYR 0.018 0.002 TYR T 15 PHE 0.031 0.002 PHE G 346 TRP 0.014 0.001 TRP O 260 HIS 0.009 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00501 (44822) covalent geometry : angle 0.62675 (60956) SS BOND : bond 0.00642 ( 12) SS BOND : angle 1.43988 ( 24) hydrogen bonds : bond 0.03697 ( 1301) hydrogen bonds : angle 5.30103 ( 3726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 556 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 242 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6216 (mt) REVERT: P 213 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7957 (mtt-85) REVERT: P 341 LEU cc_start: 0.6005 (mt) cc_final: 0.5764 (mt) REVERT: T 15 TYR cc_start: 0.8222 (m-80) cc_final: 0.7579 (m-80) REVERT: T 19 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7946 (pp) REVERT: T 52 TYR cc_start: 0.8544 (m-80) cc_final: 0.8208 (m-80) REVERT: G 96 ASN cc_start: 0.8324 (t0) cc_final: 0.8056 (t0) REVERT: G 198 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8680 (mp) REVERT: G 288 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: G 447 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7408 (mtm110) REVERT: H 33 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8735 (mtmt) REVERT: H 432 ARG cc_start: 0.8688 (tmm-80) cc_final: 0.8303 (tmm160) REVERT: H 433 ASN cc_start: 0.8733 (m-40) cc_final: 0.8307 (m-40) REVERT: H 443 ASN cc_start: 0.7433 (m-40) cc_final: 0.6589 (p0) REVERT: H 451 LYS cc_start: 0.8094 (mttm) cc_final: 0.7389 (tptp) REVERT: N 341 LEU cc_start: 0.5758 (tp) cc_final: 0.5440 (mt) REVERT: U 19 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7901 (pp) REVERT: U 52 TYR cc_start: 0.8538 (m-80) cc_final: 0.8203 (m-80) REVERT: E 96 ASN cc_start: 0.8357 (t0) cc_final: 0.8088 (t0) REVERT: E 178 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8177 (mtpp) REVERT: E 198 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8701 (mp) REVERT: E 205 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: E 447 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7383 (mtm110) REVERT: F 33 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8695 (mtmt) REVERT: F 61 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6821 (mm-30) REVERT: F 443 ASN cc_start: 0.7448 (m-40) cc_final: 0.6743 (p0) REVERT: F 451 LYS cc_start: 0.8186 (mttm) cc_final: 0.7450 (tptp) REVERT: L 260 TRP cc_start: 0.6907 (m-10) cc_final: 0.6394 (m-10) REVERT: L 341 LEU cc_start: 0.6095 (tp) cc_final: 0.5788 (mt) REVERT: X 19 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (pp) REVERT: C 96 ASN cc_start: 0.8353 (t0) cc_final: 0.8091 (t0) REVERT: C 174 THR cc_start: 0.7562 (m) cc_final: 0.7321 (p) REVERT: C 178 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7790 (mtpp) REVERT: C 198 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8612 (mp) REVERT: C 447 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7387 (mtm110) REVERT: D 33 LYS cc_start: 0.9063 (mtmm) cc_final: 0.8703 (mtmt) REVERT: D 129 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7968 (mmtm) REVERT: D 371 SER cc_start: 0.9123 (m) cc_final: 0.8909 (t) REVERT: D 432 ARG cc_start: 0.8696 (tmm-80) cc_final: 0.8322 (tmm160) REVERT: D 443 ASN cc_start: 0.7458 (m-40) cc_final: 0.6656 (p0) REVERT: D 447 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7106 (mtt180) REVERT: J 260 TRP cc_start: 0.6286 (m-10) cc_final: 0.5911 (m-10) REVERT: J 341 LEU cc_start: 0.6118 (tp) cc_final: 0.5816 (mt) REVERT: Q 19 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7978 (pp) REVERT: Q 52 TYR cc_start: 0.8550 (m-80) cc_final: 0.8216 (m-80) REVERT: A 96 ASN cc_start: 0.8361 (t0) cc_final: 0.8077 (t0) REVERT: A 174 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 198 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 447 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7382 (mtm110) REVERT: B 33 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8712 (mtmt) REVERT: B 432 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8328 (tmm160) REVERT: B 443 ASN cc_start: 0.7495 (m-40) cc_final: 0.6614 (p0) REVERT: B 451 LYS cc_start: 0.8128 (mttm) cc_final: 0.7413 (tptp) outliers start: 130 outliers final: 93 residues processed: 645 average time/residue: 0.2654 time to fit residues: 281.1518 Evaluate side-chains 626 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 521 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 304 GLN Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 288 ASN Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 185 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 391 optimal weight: 4.9990 chunk 528 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 443 optimal weight: 0.0030 chunk 143 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 375 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 512 optimal weight: 3.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 HIS G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS E 213 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN Q 83 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.196361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160892 restraints weight = 46660.220| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.64 r_work: 0.3197 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44834 Z= 0.156 Angle : 0.597 8.855 60980 Z= 0.299 Chirality : 0.046 0.170 6660 Planarity : 0.005 0.077 7966 Dihedral : 5.101 34.977 6002 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.11), residues: 5430 helix: -0.66 (0.12), residues: 1686 sheet: -2.78 (0.15), residues: 863 loop : -1.43 (0.11), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 80 TYR 0.016 0.001 TYR U 15 PHE 0.030 0.002 PHE G 346 TRP 0.013 0.001 TRP O 260 HIS 0.007 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00372 (44822) covalent geometry : angle 0.59679 (60956) SS BOND : bond 0.00526 ( 12) SS BOND : angle 1.30676 ( 24) hydrogen bonds : bond 0.03470 ( 1301) hydrogen bonds : angle 5.18222 ( 3726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 545 time to evaluate : 1.659 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: P 341 LEU cc_start: 0.5968 (mt) cc_final: 0.5693 (mt) REVERT: T 15 TYR cc_start: 0.8094 (m-80) cc_final: 0.7407 (m-80) REVERT: T 19 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8051 (pp) REVERT: T 52 TYR cc_start: 0.8439 (m-80) cc_final: 0.8166 (m-80) REVERT: G 96 ASN cc_start: 0.8272 (t0) cc_final: 0.8023 (t0) REVERT: G 178 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7890 (mtpp) REVERT: G 198 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8634 (mp) REVERT: G 447 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7410 (mtm110) REVERT: H 33 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8720 (mtmt) REVERT: H 433 ASN cc_start: 0.8691 (m-40) cc_final: 0.8250 (m-40) REVERT: H 443 ASN cc_start: 0.7424 (m-40) cc_final: 0.6541 (p0) REVERT: H 451 LYS cc_start: 0.8125 (mttm) cc_final: 0.7396 (tptp) REVERT: N 341 LEU cc_start: 0.5690 (tp) cc_final: 0.5403 (mt) REVERT: U 15 TYR cc_start: 0.8093 (m-80) cc_final: 0.7441 (m-80) REVERT: U 19 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8035 (pp) REVERT: U 52 TYR cc_start: 0.8437 (m-80) cc_final: 0.8097 (m-80) REVERT: E 96 ASN cc_start: 0.8322 (t0) cc_final: 0.8060 (t0) REVERT: E 198 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8648 (mp) REVERT: E 205 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: E 270 TYR cc_start: 0.9044 (p90) cc_final: 0.8519 (p90) REVERT: E 447 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7398 (mtm110) REVERT: F 33 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8696 (mtmt) REVERT: F 443 ASN cc_start: 0.7254 (m-40) cc_final: 0.6729 (p0) REVERT: F 451 LYS cc_start: 0.8137 (mttm) cc_final: 0.7375 (tptp) REVERT: L 260 TRP cc_start: 0.6779 (m-10) cc_final: 0.6316 (m-10) REVERT: L 341 LEU cc_start: 0.6065 (tp) cc_final: 0.5809 (mt) REVERT: X 19 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8194 (pp) REVERT: X 72 GLU cc_start: 0.6372 (tt0) cc_final: 0.6159 (tt0) REVERT: C 96 ASN cc_start: 0.8307 (t0) cc_final: 0.8038 (t0) REVERT: C 174 THR cc_start: 0.7519 (m) cc_final: 0.7307 (p) REVERT: C 198 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8590 (mp) REVERT: C 447 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7408 (mtm110) REVERT: D 33 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8687 (mtmt) REVERT: D 198 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8212 (mp) REVERT: D 371 SER cc_start: 0.9085 (m) cc_final: 0.8871 (t) REVERT: D 432 ARG cc_start: 0.8662 (tmm-80) cc_final: 0.8299 (tmm160) REVERT: D 443 ASN cc_start: 0.7465 (m-40) cc_final: 0.6641 (p0) REVERT: D 451 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7258 (tptp) REVERT: I 235 GLU cc_start: 0.7575 (tp30) cc_final: 0.7283 (tp30) REVERT: J 260 TRP cc_start: 0.6246 (m-10) cc_final: 0.5861 (m-10) REVERT: J 341 LEU cc_start: 0.6065 (tp) cc_final: 0.5815 (mt) REVERT: Q 15 TYR cc_start: 0.8116 (m-80) cc_final: 0.7422 (m-80) REVERT: Q 52 TYR cc_start: 0.8457 (m-80) cc_final: 0.8189 (m-80) REVERT: A 96 ASN cc_start: 0.8321 (t0) cc_final: 0.8055 (t0) REVERT: A 198 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 447 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7402 (mtm110) REVERT: B 33 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8731 (mtmt) REVERT: B 432 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8315 (tmm160) REVERT: B 443 ASN cc_start: 0.7450 (m-40) cc_final: 0.6574 (p0) REVERT: B 451 LYS cc_start: 0.8073 (mttm) cc_final: 0.7390 (tptp) outliers start: 118 outliers final: 81 residues processed: 628 average time/residue: 0.2725 time to fit residues: 280.8153 Evaluate side-chains 608 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 518 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 304 GLN Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 213 GLN Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 19 LEU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 52 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 466 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 382 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 chunk 287 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 444 optimal weight: 7.9990 chunk 477 optimal weight: 0.0370 overall best weight: 2.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN W 104 HIS ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN H 164 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 288 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN A 213 GLN A 288 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.195201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159147 restraints weight = 46635.444| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.78 r_work: 0.3132 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44834 Z= 0.181 Angle : 0.605 7.244 60980 Z= 0.303 Chirality : 0.046 0.175 6660 Planarity : 0.005 0.062 7966 Dihedral : 5.059 34.530 6002 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.89 % Allowed : 13.24 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.11), residues: 5430 helix: -0.55 (0.13), residues: 1686 sheet: -2.78 (0.15), residues: 868 loop : -1.36 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 80 TYR 0.016 0.001 TYR U 15 PHE 0.029 0.002 PHE E 346 TRP 0.012 0.001 TRP O 260 HIS 0.008 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00434 (44822) covalent geometry : angle 0.60473 (60956) SS BOND : bond 0.00586 ( 12) SS BOND : angle 1.39915 ( 24) hydrogen bonds : bond 0.03497 ( 1301) hydrogen bonds : angle 5.13376 ( 3726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 511 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 15 TYR cc_start: 0.8068 (m-80) cc_final: 0.7324 (m-80) REVERT: T 52 TYR cc_start: 0.8470 (m-80) cc_final: 0.8125 (m-80) REVERT: G 96 ASN cc_start: 0.8330 (t0) cc_final: 0.8065 (t0) REVERT: G 178 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7945 (mtpp) REVERT: G 198 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8670 (mp) REVERT: G 447 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7404 (mtm110) REVERT: H 33 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8718 (mtmt) REVERT: H 124 ASN cc_start: 0.6769 (m-40) cc_final: 0.6457 (m110) REVERT: H 433 ASN cc_start: 0.8701 (m-40) cc_final: 0.8309 (m-40) REVERT: H 443 ASN cc_start: 0.7346 (m-40) cc_final: 0.6637 (p0) REVERT: H 451 LYS cc_start: 0.8144 (mttm) cc_final: 0.7849 (mmtm) REVERT: N 341 LEU cc_start: 0.5692 (tp) cc_final: 0.5328 (mt) REVERT: U 15 TYR cc_start: 0.8116 (m-80) cc_final: 0.7375 (m-80) REVERT: U 52 TYR cc_start: 0.8474 (m-80) cc_final: 0.8124 (m-80) REVERT: E 96 ASN cc_start: 0.8376 (t0) cc_final: 0.8100 (t0) REVERT: E 198 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8688 (mp) REVERT: E 205 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: E 336 LEU cc_start: 0.8669 (mt) cc_final: 0.8439 (mt) REVERT: E 447 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7404 (mtm110) REVERT: F 33 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8737 (mtmt) REVERT: F 443 ASN cc_start: 0.7438 (m-40) cc_final: 0.6724 (p0) REVERT: F 451 LYS cc_start: 0.8189 (mttm) cc_final: 0.7383 (tptp) REVERT: K 236 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: L 260 TRP cc_start: 0.6734 (m-10) cc_final: 0.6310 (m-10) REVERT: L 341 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5872 (mt) REVERT: X 72 GLU cc_start: 0.6426 (tt0) cc_final: 0.6174 (tt0) REVERT: C 96 ASN cc_start: 0.8371 (t0) cc_final: 0.8078 (t0) REVERT: C 174 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7317 (p) REVERT: C 178 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7879 (mtpp) REVERT: C 198 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8650 (mp) REVERT: C 206 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8656 (p0) REVERT: C 288 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8453 (m-40) REVERT: C 447 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7414 (mtm110) REVERT: D 33 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8703 (mtmt) REVERT: D 129 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (ttpp) REVERT: D 198 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8304 (mp) REVERT: D 371 SER cc_start: 0.9141 (m) cc_final: 0.8921 (t) REVERT: D 432 ARG cc_start: 0.8693 (tmm-80) cc_final: 0.8207 (tmm160) REVERT: D 443 ASN cc_start: 0.7393 (m-40) cc_final: 0.6722 (p0) REVERT: D 451 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7304 (tptp) REVERT: J 260 TRP cc_start: 0.6238 (m-10) cc_final: 0.5825 (m-10) REVERT: J 341 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5804 (mt) REVERT: Q 15 TYR cc_start: 0.8132 (m-80) cc_final: 0.7403 (m-80) REVERT: Q 52 TYR cc_start: 0.8505 (m-80) cc_final: 0.8163 (m-80) REVERT: A 96 ASN cc_start: 0.8366 (t0) cc_final: 0.8087 (t0) REVERT: A 174 THR cc_start: 0.7564 (m) cc_final: 0.7336 (p) REVERT: A 178 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7874 (mtpt) REVERT: A 198 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 288 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8451 (m-40) REVERT: A 336 LEU cc_start: 0.8614 (mt) cc_final: 0.8390 (mt) REVERT: A 447 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7397 (mtm110) REVERT: B 33 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8755 (mtmt) REVERT: B 443 ASN cc_start: 0.7418 (m-40) cc_final: 0.6687 (p0) REVERT: B 451 LYS cc_start: 0.8100 (mttm) cc_final: 0.7354 (tptp) outliers start: 134 outliers final: 96 residues processed: 604 average time/residue: 0.2665 time to fit residues: 266.9166 Evaluate side-chains 603 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 493 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 307 optimal weight: 8.9990 chunk 379 optimal weight: 7.9990 chunk 459 optimal weight: 7.9990 chunk 410 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 299 optimal weight: 30.0000 chunk 194 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 HIS ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 GLN A 288 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** 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 = 0.4120 r_free = 0.4120 target = 0.195448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.160291 restraints weight = 46949.232| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.72 r_work: 0.3177 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44834 Z= 0.171 Angle : 0.602 8.614 60980 Z= 0.300 Chirality : 0.046 0.209 6660 Planarity : 0.005 0.066 7966 Dihedral : 5.024 34.287 6002 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.72 % Allowed : 13.63 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.11), residues: 5430 helix: -0.47 (0.13), residues: 1685 sheet: -2.76 (0.15), residues: 865 loop : -1.30 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 432 TYR 0.016 0.001 TYR U 15 PHE 0.029 0.002 PHE C 346 TRP 0.012 0.001 TRP O 260 HIS 0.007 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00411 (44822) covalent geometry : angle 0.60148 (60956) SS BOND : bond 0.00569 ( 12) SS BOND : angle 1.28312 ( 24) hydrogen bonds : bond 0.03463 ( 1301) hydrogen bonds : angle 5.10072 ( 3726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 506 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 15 TYR cc_start: 0.8085 (m-80) cc_final: 0.7325 (m-80) REVERT: T 52 TYR cc_start: 0.8452 (m-80) cc_final: 0.8111 (m-80) REVERT: G 96 ASN cc_start: 0.8297 (t0) cc_final: 0.8053 (t0) REVERT: G 178 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7900 (mtpp) REVERT: G 198 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8657 (mp) REVERT: G 447 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7396 (mtm110) REVERT: H 33 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8708 (mtmt) REVERT: H 443 ASN cc_start: 0.7200 (m-40) cc_final: 0.6704 (p0) REVERT: H 451 LYS cc_start: 0.8123 (mttm) cc_final: 0.7855 (mmtm) REVERT: N 341 LEU cc_start: 0.5718 (tp) cc_final: 0.5415 (mt) REVERT: U 15 TYR cc_start: 0.8064 (m-80) cc_final: 0.7361 (m-80) REVERT: U 52 TYR cc_start: 0.8464 (m-80) cc_final: 0.8117 (m-80) REVERT: E 96 ASN cc_start: 0.8338 (t0) cc_final: 0.8085 (t0) REVERT: E 198 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8687 (mp) REVERT: E 205 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: E 447 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7387 (mtm110) REVERT: F 33 LYS cc_start: 0.9101 (mtmm) cc_final: 0.8730 (mtmt) REVERT: F 443 ASN cc_start: 0.7462 (m-40) cc_final: 0.6779 (p0) REVERT: F 451 LYS cc_start: 0.8168 (mttm) cc_final: 0.7893 (mmtm) REVERT: K 236 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6538 (tp30) REVERT: L 260 TRP cc_start: 0.6729 (m-10) cc_final: 0.6334 (m-10) REVERT: L 341 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5827 (mt) REVERT: C 96 ASN cc_start: 0.8323 (t0) cc_final: 0.8054 (t0) REVERT: C 174 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7317 (p) REVERT: C 198 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 447 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7407 (mtm110) REVERT: D 33 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8699 (mtmt) REVERT: D 129 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (ttpp) REVERT: D 198 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 371 SER cc_start: 0.9129 (m) cc_final: 0.8904 (t) REVERT: D 432 ARG cc_start: 0.8720 (tmm-80) cc_final: 0.8233 (tmm160) REVERT: D 443 ASN cc_start: 0.7416 (m-40) cc_final: 0.6783 (p0) REVERT: D 451 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7297 (tptp) REVERT: I 247 GLU cc_start: 0.6608 (tt0) cc_final: 0.5912 (tp30) REVERT: J 260 TRP cc_start: 0.6279 (m-10) cc_final: 0.5989 (m-10) REVERT: J 341 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5774 (mt) REVERT: Q 15 TYR cc_start: 0.8073 (m-80) cc_final: 0.7330 (m-80) REVERT: Q 52 TYR cc_start: 0.8487 (m-80) cc_final: 0.8223 (m-80) REVERT: A 96 ASN cc_start: 0.8337 (t0) cc_final: 0.8078 (t0) REVERT: A 174 THR cc_start: 0.7539 (m) cc_final: 0.7323 (p) REVERT: A 178 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7814 (mtpt) REVERT: A 198 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8665 (mp) REVERT: A 447 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7421 (mtm110) REVERT: B 33 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8737 (mtmt) REVERT: B 443 ASN cc_start: 0.7445 (m-40) cc_final: 0.6759 (p0) REVERT: B 451 LYS cc_start: 0.8096 (mttm) cc_final: 0.7834 (mmtm) outliers start: 126 outliers final: 100 residues processed: 591 average time/residue: 0.2591 time to fit residues: 252.3186 Evaluate side-chains 604 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 493 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 311 SER Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 240 VAL Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 486 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 HIS Q 34 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.192375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159466 restraints weight = 46554.399| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.65 r_work: 0.3164 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 44834 Z= 0.241 Angle : 0.649 7.480 60980 Z= 0.326 Chirality : 0.048 0.221 6660 Planarity : 0.005 0.066 7966 Dihedral : 5.150 34.064 6001 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.85 % Allowed : 13.61 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.11), residues: 5430 helix: -0.52 (0.13), residues: 1658 sheet: -2.81 (0.15), residues: 842 loop : -1.22 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.022 0.002 TYR B 25 PHE 0.030 0.002 PHE C 346 TRP 0.014 0.002 TRP O 260 HIS 0.009 0.002 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00583 (44822) covalent geometry : angle 0.64793 (60956) SS BOND : bond 0.00708 ( 12) SS BOND : angle 1.69276 ( 24) hydrogen bonds : bond 0.03742 ( 1301) hydrogen bonds : angle 5.21363 ( 3726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 531 time to evaluate : 1.610 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: T 15 TYR cc_start: 0.8171 (m-80) cc_final: 0.7427 (m-80) REVERT: T 52 TYR cc_start: 0.8563 (m-80) cc_final: 0.8128 (m-80) REVERT: G 96 ASN cc_start: 0.8286 (t0) cc_final: 0.8062 (t0) REVERT: G 178 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8011 (mtpp) REVERT: G 198 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8704 (mp) REVERT: G 447 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7427 (mtm110) REVERT: H 33 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8788 (mtmt) REVERT: H 443 ASN cc_start: 0.7400 (m-40) cc_final: 0.6844 (p0) REVERT: H 451 LYS cc_start: 0.8195 (mttm) cc_final: 0.7558 (tptp) REVERT: N 341 LEU cc_start: 0.5820 (tp) cc_final: 0.5509 (mt) REVERT: U 15 TYR cc_start: 0.8181 (m-80) cc_final: 0.7481 (m-80) REVERT: U 52 TYR cc_start: 0.8563 (m-80) cc_final: 0.8115 (m-80) REVERT: E 96 ASN cc_start: 0.8327 (t0) cc_final: 0.8096 (t0) REVERT: E 198 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8739 (mp) REVERT: E 205 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: E 447 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7427 (mtm110) REVERT: F 33 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8721 (mtmt) REVERT: F 443 ASN cc_start: 0.7386 (m-40) cc_final: 0.6807 (p0) REVERT: F 451 LYS cc_start: 0.8212 (mttm) cc_final: 0.7573 (tptp) REVERT: K 219 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: K 236 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: L 260 TRP cc_start: 0.6633 (m-10) cc_final: 0.6274 (m-10) REVERT: L 341 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5793 (mt) REVERT: C 96 ASN cc_start: 0.8299 (t0) cc_final: 0.8057 (t0) REVERT: C 174 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 198 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8704 (mp) REVERT: C 447 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7438 (mtm110) REVERT: D 33 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8757 (mtmt) REVERT: D 198 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8403 (mp) REVERT: D 371 SER cc_start: 0.9131 (m) cc_final: 0.8894 (t) REVERT: D 443 ASN cc_start: 0.7410 (m-40) cc_final: 0.6844 (p0) REVERT: D 451 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7426 (tptp) REVERT: I 247 GLU cc_start: 0.6643 (tt0) cc_final: 0.5927 (tp30) REVERT: J 341 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5798 (mt) REVERT: Q 15 TYR cc_start: 0.8172 (m-80) cc_final: 0.7429 (m-80) REVERT: Q 52 TYR cc_start: 0.8558 (m-80) cc_final: 0.8220 (m-80) REVERT: A 96 ASN cc_start: 0.8314 (t0) cc_final: 0.8084 (t0) REVERT: A 174 THR cc_start: 0.7611 (m) cc_final: 0.7372 (p) REVERT: A 178 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7954 (mtpt) REVERT: A 198 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 447 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7428 (mtm110) REVERT: B 33 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8739 (mtmt) REVERT: B 443 ASN cc_start: 0.7420 (m-40) cc_final: 0.6840 (p0) outliers start: 132 outliers final: 111 residues processed: 623 average time/residue: 0.2510 time to fit residues: 257.9747 Evaluate side-chains 630 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 508 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 304 GLN Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 458 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 351 ASN Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 360 optimal weight: 9.9990 chunk 340 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 373 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 361 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 397 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161607 restraints weight = 46833.341| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.68 r_work: 0.3182 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44834 Z= 0.128 Angle : 0.584 7.732 60980 Z= 0.293 Chirality : 0.045 0.174 6660 Planarity : 0.005 0.070 7966 Dihedral : 4.938 34.078 6001 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.35 % Allowed : 14.38 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.11), residues: 5430 helix: -0.28 (0.13), residues: 1666 sheet: -2.70 (0.15), residues: 862 loop : -1.19 (0.11), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 80 TYR 0.014 0.001 TYR U 15 PHE 0.028 0.002 PHE C 346 TRP 0.014 0.001 TRP O 260 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00303 (44822) covalent geometry : angle 0.58435 (60956) SS BOND : bond 0.00453 ( 12) SS BOND : angle 0.87781 ( 24) hydrogen bonds : bond 0.03304 ( 1301) hydrogen bonds : angle 5.04788 ( 3726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10860 Ramachandran restraints generated. 5430 Oldfield, 0 Emsley, 5430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 528 time to evaluate : 1.662 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: T 15 TYR cc_start: 0.8024 (m-80) cc_final: 0.7254 (m-80) REVERT: T 52 TYR cc_start: 0.8394 (m-80) cc_final: 0.8113 (m-80) REVERT: G 96 ASN cc_start: 0.8268 (t0) cc_final: 0.8021 (t0) REVERT: G 178 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7811 (mtpp) REVERT: G 198 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8665 (mp) REVERT: G 447 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7364 (mtm110) REVERT: H 33 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8764 (mtmt) REVERT: H 443 ASN cc_start: 0.7392 (m-40) cc_final: 0.6729 (p0) REVERT: H 451 LYS cc_start: 0.8113 (mttm) cc_final: 0.7361 (tptp) REVERT: N 341 LEU cc_start: 0.5668 (tp) cc_final: 0.5364 (mt) REVERT: U 15 TYR cc_start: 0.8004 (m-80) cc_final: 0.7285 (m-80) REVERT: U 52 TYR cc_start: 0.8394 (m-80) cc_final: 0.8113 (m-80) REVERT: E 96 ASN cc_start: 0.8320 (t0) cc_final: 0.8057 (t0) REVERT: E 198 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8686 (mp) REVERT: E 205 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: E 447 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7344 (mtm110) REVERT: F 33 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8705 (mtmt) REVERT: F 388 MET cc_start: 0.8831 (tpp) cc_final: 0.8585 (tpt) REVERT: F 443 ASN cc_start: 0.7395 (m-40) cc_final: 0.6730 (p0) REVERT: F 451 LYS cc_start: 0.8148 (mttm) cc_final: 0.7405 (tptp) REVERT: K 219 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: K 236 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6687 (tp30) REVERT: L 260 TRP cc_start: 0.6432 (m-10) cc_final: 0.6150 (m-10) REVERT: L 341 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5521 (mt) REVERT: X 15 TYR cc_start: 0.8209 (m-80) cc_final: 0.7625 (m-80) REVERT: C 96 ASN cc_start: 0.8316 (t0) cc_final: 0.8029 (t0) REVERT: C 174 THR cc_start: 0.7471 (m) cc_final: 0.7247 (p) REVERT: C 198 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8663 (mp) REVERT: C 447 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7382 (mtm110) REVERT: D 33 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8739 (mtmt) REVERT: D 198 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8319 (mp) REVERT: D 371 SER cc_start: 0.9071 (m) cc_final: 0.8821 (t) REVERT: D 388 MET cc_start: 0.8839 (tpp) cc_final: 0.8592 (tpt) REVERT: D 443 ASN cc_start: 0.7414 (m-40) cc_final: 0.6748 (p0) REVERT: D 451 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7308 (tptp) REVERT: I 247 GLU cc_start: 0.6677 (tt0) cc_final: 0.5918 (tp30) REVERT: J 260 TRP cc_start: 0.6256 (m-10) cc_final: 0.5940 (m-10) REVERT: J 341 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5438 (mt) REVERT: Q 15 TYR cc_start: 0.8010 (m-80) cc_final: 0.7247 (m-80) REVERT: Q 52 TYR cc_start: 0.8406 (m-80) cc_final: 0.8124 (m-80) REVERT: A 96 ASN cc_start: 0.8324 (t0) cc_final: 0.8064 (t0) REVERT: A 198 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 447 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7375 (mtm110) REVERT: B 33 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8723 (mtmt) REVERT: B 443 ASN cc_start: 0.7418 (m-40) cc_final: 0.6747 (p0) outliers start: 109 outliers final: 79 residues processed: 602 average time/residue: 0.2619 time to fit residues: 260.5841 Evaluate side-chains 591 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 502 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE Chi-restraints excluded: chain O residue 216 THR Chi-restraints excluded: chain O residue 219 GLU Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain O residue 300 VAL Chi-restraints excluded: chain O residue 311 SER Chi-restraints excluded: chain O residue 340 ILE Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 297 LEU Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 351 ASN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain M residue 214 PHE Chi-restraints excluded: chain M residue 216 THR Chi-restraints excluded: chain M residue 219 GLU Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain M residue 311 SER Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 351 ASN Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 458 VAL Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain K residue 214 PHE Chi-restraints excluded: chain K residue 216 THR Chi-restraints excluded: chain K residue 219 GLU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 304 GLN Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 340 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain I residue 214 PHE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 219 GLU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 351 ASN Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 107 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 505 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 467 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 239 optimal weight: 0.0870 chunk 453 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 288 ASN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.198795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164171 restraints weight = 46742.007| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.57 r_work: 0.3250 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44834 Z= 0.118 Angle : 0.574 7.755 60980 Z= 0.287 Chirality : 0.045 0.222 6660 Planarity : 0.005 0.061 7966 Dihedral : 4.783 32.370 5998 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.13 % Allowed : 14.77 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.11), residues: 5430 helix: -0.16 (0.13), residues: 1666 sheet: -2.54 (0.16), residues: 857 loop : -1.07 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 432 TYR 0.020 0.001 TYR Q 10 PHE 0.029 0.001 PHE C 346 TRP 0.023 0.001 TRP O 260 HIS 0.006 0.001 HIS F 326 Details of bonding type rmsd covalent geometry : bond 0.00279 (44822) covalent geometry : angle 0.57388 (60956) SS BOND : bond 0.00370 ( 12) SS BOND : angle 0.70422 ( 24) hydrogen bonds : bond 0.03199 ( 1301) hydrogen bonds : angle 4.94653 ( 3726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9740.39 seconds wall clock time: 168 minutes 55.37 seconds (10135.37 seconds total)