Starting phenix.real_space_refine on Thu Dec 26 03:57:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lrr_0959/12_2024/6lrr_0959.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lrr_0959/12_2024/6lrr_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_0959/12_2024/6lrr_0959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lrr_0959/12_2024/6lrr_0959.map" model { file = "/net/cci-nas-00/data/ceres_data/6lrr_0959/12_2024/6lrr_0959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lrr_0959/12_2024/6lrr_0959.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 24.26, per 1000 atoms: 0.56 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: 11.53 Conformation dependent library (CDL) restraints added in 5.9 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: 5.90 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: 19.76 Time building geometry restraints manager: 12.92 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: 1.390 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: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 97.880 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.200 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.900 ------------------------------------------------------------------------------- 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 44822 Z= 0.926 Angle : 1.217 12.744 60956 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 : 9.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.054 0.005 TRP X 53 HIS 0.020 0.004 HIS G 326 PHE 0.046 0.005 PHE H 126 TYR 0.073 0.005 TYR T 15 ARG 0.016 0.002 ARG C 216 *********************** 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 : 4.211 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: 0.5696 (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: 0.7696 (m-80) REVERT: W 104 HIS cc_start: 0.7252 (t70) cc_final: 0.6773 (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: 0.7634 (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: 0.8185 (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: 0.6205 (mp) REVERT: N 236 GLU cc_start: 0.6087 (mt-10) cc_final: 0.5825 (mm-30) REVERT: N 252 VAL cc_start: 0.7819 (m) cc_final: 0.7600 (p) REVERT: U 15 TYR cc_start: 0.8285 (m-10) cc_final: 0.8014 (m-80) REVERT: U 44 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7569 (mt-10) REVERT: U 52 TYR cc_start: 0.8437 (m-80) cc_final: 0.7719 (m-80) REVERT: E 336 LEU cc_start: 0.8927 (mp) cc_final: 0.8520 (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: 0.8652 (mtmt) REVERT: F 432 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8206 (tmm160) REVERT: F 451 LYS cc_start: 0.8122 (mttm) cc_final: 0.7570 (tptp) REVERT: K 341 LEU cc_start: 0.7497 (mt) cc_final: 0.7291 (mt) REVERT: L 232 LEU cc_start: 0.6589 (mt) cc_final: 0.6216 (mp) REVERT: L 236 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5537 (mm-30) REVERT: X 52 TYR cc_start: 0.8412 (m-80) cc_final: 0.7770 (m-80) 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: 0.7590 (mt-10) REVERT: D 33 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8663 (mtmt) REVERT: D 137 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7916 (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: I 341 LEU cc_start: 0.7486 (mt) cc_final: 0.7274 (mt) REVERT: J 232 LEU cc_start: 0.6596 (mt) cc_final: 0.6208 (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: 0.7566 (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: 0.7577 (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: 0.7912 (mm-30) REVERT: B 432 ARG cc_start: 0.8672 (tmm-80) cc_final: 0.8155 (tmm160) REVERT: B 433 ASN cc_start: 0.8491 (m-40) cc_final: 0.7873 (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: 0.6034 time to fit residues: 936.7803 Evaluate side-chains 614 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 606 time to evaluate : 5.047 ------------------------------------------------------------------------------- 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 455 optimal weight: 3.9990 chunk 409 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 423 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 490 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 351 ASN W 97 GLN G 96 ASN G 150 GLN ** G 278 ASN ** 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 150 GLN 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 150 GLN E 308 HIS E 357 GLN E 402 GLN F 150 GLN 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** K 267 GLN L 351 ASN X 83 HIS Y 95 GLN C 96 ASN C 150 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS C 357 GLN C 402 GLN 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 R 97 GLN A 96 ASN 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: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 44822 Z= 0.336 Angle : 0.715 9.450 60956 Z= 0.366 Chirality : 0.048 0.198 6660 Planarity : 0.006 0.069 7966 Dihedral : 6.424 49.628 6010 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.96 % Allowed : 8.17 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.09), residues: 5430 helix: -2.91 (0.09), residues: 1650 sheet: -3.33 (0.15), residues: 747 loop : -2.13 (0.10), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 53 HIS 0.011 0.002 HIS D 326 PHE 0.034 0.002 PHE B 128 TYR 0.021 0.002 TYR T 15 ARG 0.004 0.001 ARG A 80 *********************** 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 772 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 681 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 235 GLU cc_start: 0.7766 (tp30) cc_final: 0.7539 (tp30) REVERT: O 236 GLU cc_start: 0.6638 (mp0) cc_final: 0.6294 (mp0) REVERT: P 232 LEU cc_start: 0.5673 (mt) cc_final: 0.5470 (mp) REVERT: P 236 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5610 (mm-30) REVERT: P 260 TRP cc_start: 0.6269 (m-10) cc_final: 0.5851 (m-10) REVERT: P 341 LEU cc_start: 0.5897 (mt) cc_final: 0.5470 (mt) REVERT: T 52 TYR cc_start: 0.8605 (m-80) cc_final: 0.8090 (m-80) REVERT: G 82 LYS cc_start: 0.8277 (ptpt) cc_final: 0.8074 (ptmt) REVERT: G 336 LEU cc_start: 0.8778 (mp) cc_final: 0.8298 (mp) REVERT: G 447 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.7016 (mtm110) REVERT: H 33 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8629 (mtmt) REVERT: H 81 TYR cc_start: 0.8826 (m-80) cc_final: 0.8531 (m-80) REVERT: H 129 LYS cc_start: 0.8644 (tptt) cc_final: 0.8158 (ttpp) REVERT: H 371 SER cc_start: 0.8919 (m) cc_final: 0.8714 (t) REVERT: H 443 ASN cc_start: 0.7502 (m-40) cc_final: 0.6346 (p0) REVERT: H 451 LYS cc_start: 0.8137 (mttm) cc_final: 0.7438 (tptp) REVERT: N 232 LEU cc_start: 0.5932 (mt) cc_final: 0.5722 (mp) REVERT: N 236 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5750 (mm-30) REVERT: N 341 LEU cc_start: 0.5811 (tp) cc_final: 0.5479 (mt) REVERT: U 52 TYR cc_start: 0.8666 (m-80) cc_final: 0.8146 (m-80) REVERT: U 66 SER cc_start: 0.8565 (p) cc_final: 0.8289 (m) REVERT: E 336 LEU cc_start: 0.8796 (mp) cc_final: 0.8305 (mp) REVERT: E 447 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7013 (mtm110) REVERT: F 33 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8634 (mtmt) REVERT: F 128 PHE cc_start: 0.8007 (t80) cc_final: 0.7753 (t80) REVERT: F 129 LYS cc_start: 0.8656 (tptt) cc_final: 0.8284 (ttpp) REVERT: F 433 ASN cc_start: 0.8623 (m-40) cc_final: 0.8237 (m-40) REVERT: F 443 ASN cc_start: 0.7493 (m-40) cc_final: 0.6378 (p0) REVERT: F 451 LYS cc_start: 0.8105 (mttm) cc_final: 0.7475 (tptp) REVERT: L 260 TRP cc_start: 0.6165 (m-10) cc_final: 0.5959 (m-10) REVERT: X 52 TYR cc_start: 0.8601 (m-80) cc_final: 0.8156 (m-80) REVERT: C 178 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7925 (mtpp) REVERT: C 205 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: C 253 LYS cc_start: 0.8637 (ptpt) cc_final: 0.8431 (ptpt) REVERT: C 336 LEU cc_start: 0.8707 (mp) cc_final: 0.8227 (mp) REVERT: C 447 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.7018 (mtm110) REVERT: D 33 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8624 (mtmt) REVERT: D 81 TYR cc_start: 0.8680 (m-80) cc_final: 0.8328 (m-80) REVERT: D 371 SER cc_start: 0.8942 (m) cc_final: 0.8733 (t) REVERT: D 432 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8250 (tmm160) REVERT: D 433 ASN cc_start: 0.8309 (m-40) cc_final: 0.7896 (m-40) REVERT: D 443 ASN cc_start: 0.7432 (m-40) cc_final: 0.6386 (p0) REVERT: D 451 LYS cc_start: 0.8141 (mttm) cc_final: 0.7418 (tptp) REVERT: I 235 GLU cc_start: 0.7632 (tp30) cc_final: 0.7349 (tp30) REVERT: J 236 GLU cc_start: 0.5713 (mt-10) cc_final: 0.5414 (mm-30) REVERT: J 260 TRP cc_start: 0.6789 (m-10) cc_final: 0.6538 (m-10) REVERT: Q 52 TYR cc_start: 0.8645 (m-80) cc_final: 0.8110 (m-80) REVERT: A 336 LEU cc_start: 0.8730 (mp) cc_final: 0.8242 (mp) REVERT: A 447 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.7014 (mtm110) REVERT: B 33 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8602 (mtmt) REVERT: B 432 ARG cc_start: 0.8616 (tmm-80) cc_final: 0.8262 (tmm160) REVERT: B 433 ASN cc_start: 0.8420 (m-40) cc_final: 0.8211 (m-40) REVERT: B 443 ASN cc_start: 0.7540 (m-40) cc_final: 0.6398 (p0) REVERT: B 451 LYS cc_start: 0.8114 (mttm) cc_final: 0.7419 (tptp) outliers start: 91 outliers final: 36 residues processed: 753 average time/residue: 0.6016 time to fit residues: 743.8441 Evaluate side-chains 626 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 589 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 276 VAL Chi-restraints excluded: chain O residue 304 GLN Chi-restraints excluded: chain P residue 300 VAL 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 230 LEU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 304 GLN Chi-restraints excluded: chain N residue 269 LEU 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 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 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 205 GLU 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 230 LEU 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 272 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 408 optimal weight: 4.9990 chunk 333 optimal weight: 0.0050 chunk 135 optimal weight: 30.0000 chunk 491 optimal weight: 0.2980 chunk 530 optimal weight: 0.8980 chunk 437 optimal weight: 6.9990 chunk 487 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 83 HIS W 97 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 402 GLN ** 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** U 83 HIS V 97 GLN E 96 ASN E 288 ASN E 402 GLN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 288 ASN C 295 HIS C 402 GLN D 150 GLN D 164 ASN D 185 ASN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN R 97 GLN A 96 ASN A 288 ASN A 295 HIS A 402 GLN B 164 ASN B 387 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44822 Z= 0.226 Angle : 0.630 13.236 60956 Z= 0.318 Chirality : 0.046 0.168 6660 Planarity : 0.005 0.064 7966 Dihedral : 5.820 44.717 6010 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.98 % Allowed : 10.31 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.10), residues: 5430 helix: -1.77 (0.11), residues: 1682 sheet: -3.01 (0.15), residues: 797 loop : -1.87 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 260 HIS 0.008 0.001 HIS H 326 PHE 0.034 0.002 PHE G 346 TYR 0.017 0.001 TYR T 15 ARG 0.005 0.000 ARG H 188 *********************** 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 695 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 603 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 236 GLU cc_start: 0.6895 (mp0) cc_final: 0.6511 (mp0) REVERT: P 236 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5661 (mm-30) REVERT: P 260 TRP cc_start: 0.6142 (m-10) cc_final: 0.5860 (m-10) REVERT: T 52 TYR cc_start: 0.8441 (m-80) cc_final: 0.8105 (m-80) REVERT: G 96 ASN cc_start: 0.8245 (t0) cc_final: 0.8011 (t0) REVERT: G 178 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8121 (mtpp) REVERT: G 205 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: G 447 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.7034 (mtm110) REVERT: H 33 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8636 (mtmt) REVERT: H 64 THR cc_start: 0.8638 (p) cc_final: 0.8398 (p) REVERT: H 371 SER cc_start: 0.8894 (m) cc_final: 0.8644 (t) REVERT: H 443 ASN cc_start: 0.7440 (m-40) cc_final: 0.6609 (p0) REVERT: H 451 LYS cc_start: 0.8147 (mttm) cc_final: 0.7377 (tptp) REVERT: N 232 LEU cc_start: 0.5780 (mt) cc_final: 0.5570 (mp) REVERT: N 236 GLU cc_start: 0.5832 (mt-10) cc_final: 0.5506 (mm-30) REVERT: N 341 LEU cc_start: 0.5766 (tp) cc_final: 0.5429 (mt) REVERT: U 51 LEU cc_start: 0.8832 (tp) cc_final: 0.8620 (tp) REVERT: U 52 TYR cc_start: 0.8481 (m-80) cc_final: 0.8153 (m-80) REVERT: E 178 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8051 (mtpp) REVERT: E 205 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6285 (mt-10) REVERT: E 447 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.7043 (mtm110) REVERT: F 33 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8659 (mtmt) REVERT: F 433 ASN cc_start: 0.8540 (m-40) cc_final: 0.7709 (m-40) REVERT: F 443 ASN cc_start: 0.7408 (m-40) cc_final: 0.6571 (p0) REVERT: F 451 LYS cc_start: 0.8100 (mttm) cc_final: 0.7372 (tptp) REVERT: K 266 TRP cc_start: 0.7989 (m-90) cc_final: 0.7789 (m-90) REVERT: L 341 LEU cc_start: 0.6075 (tp) cc_final: 0.5675 (mt) REVERT: X 52 TYR cc_start: 0.8458 (m-80) cc_final: 0.8184 (m-80) REVERT: C 178 LYS cc_start: 0.8297 (mtpt) cc_final: 0.8004 (mtpp) REVERT: C 205 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6947 (pt0) REVERT: C 253 LYS cc_start: 0.8633 (ptpt) cc_final: 0.8430 (ptpt) REVERT: C 447 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7039 (mtm110) REVERT: D 33 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8633 (mtmt) REVERT: D 166 TYR cc_start: 0.9025 (m-80) cc_final: 0.8646 (m-80) REVERT: D 371 SER cc_start: 0.8871 (m) cc_final: 0.8649 (t) REVERT: D 432 ARG cc_start: 0.8564 (tmm-80) cc_final: 0.8287 (ttp-110) REVERT: D 433 ASN cc_start: 0.8183 (m-40) cc_final: 0.7896 (m-40) REVERT: D 443 ASN cc_start: 0.7462 (m-40) cc_final: 0.6604 (p0) REVERT: D 451 LYS cc_start: 0.8112 (mttm) cc_final: 0.7325 (tptp) REVERT: I 236 GLU cc_start: 0.6745 (mp0) cc_final: 0.6527 (mp0) REVERT: J 236 GLU cc_start: 0.5671 (mt-10) cc_final: 0.5337 (mm-30) REVERT: J 260 TRP cc_start: 0.6465 (m-10) cc_final: 0.6191 (m-10) REVERT: J 341 LEU cc_start: 0.6059 (tp) cc_final: 0.5673 (mt) REVERT: Q 51 LEU cc_start: 0.8865 (tp) cc_final: 0.8649 (tp) REVERT: Q 52 TYR cc_start: 0.8462 (m-80) cc_final: 0.8125 (m-80) REVERT: A 178 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7940 (mtpp) REVERT: A 205 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6291 (mt-10) REVERT: A 298 MET cc_start: 0.8437 (ttp) cc_final: 0.8211 (ttp) REVERT: A 447 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.7040 (mtm110) REVERT: B 33 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8643 (mtmt) REVERT: B 432 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8266 (ttp-110) REVERT: B 433 ASN cc_start: 0.8274 (m-40) cc_final: 0.8029 (m-40) REVERT: B 443 ASN cc_start: 0.7494 (m-40) cc_final: 0.6621 (p0) REVERT: B 451 LYS cc_start: 0.8092 (mttm) cc_final: 0.7336 (tptp) outliers start: 92 outliers final: 52 residues processed: 679 average time/residue: 0.6121 time to fit residues: 686.3033 Evaluate side-chains 605 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 550 time to evaluate : 5.532 ------------------------------------------------------------------------------- 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 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 36 ASP Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 205 GLU 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 M residue 230 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 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 E residue 173 CYS 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 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 K residue 304 GLN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain C residue 319 LEU 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 I residue 304 GLN 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 253 LYS Chi-restraints excluded: chain A residue 319 LEU 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 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 493 optimal weight: 6.9990 chunk 521 optimal weight: 0.8980 chunk 257 optimal weight: 9.9990 chunk 467 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 97 GLN G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 GLN E 96 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 288 ASN D 164 ASN ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN A 96 ASN A 288 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 44822 Z= 0.197 Angle : 0.595 9.714 60956 Z= 0.299 Chirality : 0.046 0.209 6660 Planarity : 0.005 0.061 7966 Dihedral : 5.415 43.369 6010 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.33 % Allowed : 11.02 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.11), residues: 5430 helix: -1.11 (0.12), residues: 1687 sheet: -2.84 (0.15), residues: 857 loop : -1.56 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 260 HIS 0.007 0.001 HIS B 326 PHE 0.033 0.002 PHE A 346 TYR 0.018 0.001 TYR H 81 ARG 0.008 0.000 ARG A 296 *********************** 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 710 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 602 time to evaluate : 5.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 178 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7919 (mtpp) REVERT: G 198 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8323 (mp) REVERT: G 205 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: G 288 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8152 (m110) REVERT: G 447 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7122 (mtm110) REVERT: H 33 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8566 (mtmt) REVERT: H 64 THR cc_start: 0.8676 (p) cc_final: 0.8413 (p) REVERT: H 371 SER cc_start: 0.8869 (m) cc_final: 0.8613 (t) REVERT: H 432 ARG cc_start: 0.8478 (tmm-80) cc_final: 0.8183 (tmm160) REVERT: H 443 ASN cc_start: 0.7366 (m-40) cc_final: 0.6690 (p0) REVERT: N 341 LEU cc_start: 0.5608 (tp) cc_final: 0.5296 (mt) REVERT: U 52 TYR cc_start: 0.8430 (m-80) cc_final: 0.8162 (m-80) REVERT: E 198 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8342 (mp) REVERT: E 205 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: E 447 ARG cc_start: 0.7480 (mtm-85) cc_final: 0.7119 (mtm110) REVERT: F 33 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8565 (mtmt) REVERT: F 432 ARG cc_start: 0.8502 (tmm-80) cc_final: 0.8220 (ttp-110) REVERT: F 443 ASN cc_start: 0.7367 (m-40) cc_final: 0.6679 (p0) REVERT: F 451 LYS cc_start: 0.8021 (mttm) cc_final: 0.7274 (tptp) REVERT: L 341 LEU cc_start: 0.5824 (tp) cc_final: 0.5486 (mt) REVERT: X 52 TYR cc_start: 0.8367 (m-80) cc_final: 0.8153 (m-80) REVERT: C 178 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7603 (mtpp) REVERT: C 205 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: C 253 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8457 (ptpt) REVERT: C 278 ASN cc_start: 0.8848 (t0) cc_final: 0.8234 (t0) REVERT: C 447 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.7120 (mtm110) REVERT: C 455 GLU cc_start: 0.7431 (mp0) cc_final: 0.7134 (mm-30) REVERT: D 33 LYS cc_start: 0.8891 (mtmm) cc_final: 0.8550 (mtmt) REVERT: D 166 TYR cc_start: 0.8941 (m-80) cc_final: 0.8704 (m-80) REVERT: D 371 SER cc_start: 0.8893 (m) cc_final: 0.8674 (t) REVERT: D 432 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.8110 (tmm160) REVERT: D 443 ASN cc_start: 0.7357 (m-40) cc_final: 0.6677 (p0) REVERT: I 304 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: J 341 LEU cc_start: 0.5840 (tp) cc_final: 0.5494 (mt) REVERT: Q 52 TYR cc_start: 0.8410 (m-80) cc_final: 0.8145 (m-80) REVERT: A 198 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8416 (mp) REVERT: A 205 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: A 298 MET cc_start: 0.8208 (ttp) cc_final: 0.7954 (ttp) REVERT: A 447 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.7120 (mtm110) REVERT: B 33 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8567 (mtmt) REVERT: B 61 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6606 (mm-30) REVERT: B 432 ARG cc_start: 0.8518 (tmm-80) cc_final: 0.8242 (ttp-110) REVERT: B 433 ASN cc_start: 0.8297 (m-40) cc_final: 0.8036 (m-40) REVERT: B 443 ASN cc_start: 0.7406 (m-40) cc_final: 0.6700 (p0) outliers start: 108 outliers final: 50 residues processed: 685 average time/residue: 0.5981 time to fit residues: 681.0129 Evaluate side-chains 616 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 557 time to evaluate : 5.116 ------------------------------------------------------------------------------- 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 T residue 45 VAL Chi-restraints excluded: chain T residue 88 VAL 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 205 GLU 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 448 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 277 THR 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 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 366 THR Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 247 THR 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 X residue 88 VAL Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 164 ASN 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 R residue 99 LEU Chi-restraints excluded: chain Q residue 45 VAL 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 205 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 266 optimal weight: 1.9990 chunk 468 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 267 GLN W 97 GLN G 116 ASN G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN H 124 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 267 GLN ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 116 ASN E 213 GLN E 288 ASN F 124 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 116 ASN D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 HIS A 96 ASN A 116 ASN A 213 GLN ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 44822 Z= 0.316 Angle : 0.626 8.933 60956 Z= 0.315 Chirality : 0.047 0.172 6660 Planarity : 0.005 0.060 7966 Dihedral : 5.297 48.508 6004 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.41 % Allowed : 12.55 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.11), residues: 5430 helix: -0.85 (0.12), residues: 1663 sheet: -2.86 (0.15), residues: 865 loop : -1.50 (0.11), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 260 HIS 0.008 0.001 HIS F 326 PHE 0.030 0.002 PHE E 346 TYR 0.019 0.002 TYR U 36 ARG 0.004 0.000 ARG F 188 *********************** 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 679 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 567 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 242 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6287 (mt) REVERT: P 341 LEU cc_start: 0.5867 (mt) cc_final: 0.5587 (mt) REVERT: T 15 TYR cc_start: 0.8165 (m-80) cc_final: 0.7586 (m-80) REVERT: T 19 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7953 (pp) REVERT: G 198 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8500 (mp) REVERT: G 447 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7123 (mtm110) REVERT: H 33 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8613 (mtmt) REVERT: H 371 SER cc_start: 0.8912 (m) cc_final: 0.8641 (t) REVERT: H 432 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8074 (tmm160) REVERT: H 443 ASN cc_start: 0.7404 (m-40) cc_final: 0.6700 (p0) REVERT: H 451 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7256 (tptp) REVERT: M 219 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7187 (mp0) REVERT: M 236 GLU cc_start: 0.6665 (mp0) cc_final: 0.6465 (mp0) REVERT: N 254 PHE cc_start: 0.6630 (t80) cc_final: 0.6345 (t80) REVERT: N 260 TRP cc_start: 0.6335 (m-10) cc_final: 0.6002 (m-10) REVERT: N 341 LEU cc_start: 0.5645 (tp) cc_final: 0.5334 (mt) REVERT: U 19 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7842 (pp) REVERT: U 52 TYR cc_start: 0.8501 (m-80) cc_final: 0.8221 (m-80) REVERT: E 198 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8510 (mp) REVERT: E 205 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: E 447 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7111 (mtm110) REVERT: F 33 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8611 (mtmt) REVERT: F 61 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6304 (mm-30) REVERT: F 432 ARG cc_start: 0.8580 (tmm-80) cc_final: 0.8075 (tmm160) REVERT: F 443 ASN cc_start: 0.7382 (m-40) cc_final: 0.6685 (p0) REVERT: F 451 LYS cc_start: 0.7984 (mttm) cc_final: 0.7319 (tptp) REVERT: L 260 TRP cc_start: 0.6920 (m-10) cc_final: 0.6609 (m-10) REVERT: L 341 LEU cc_start: 0.5887 (tp) cc_final: 0.5607 (mt) REVERT: X 19 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (pp) REVERT: X 52 TYR cc_start: 0.8461 (m-80) cc_final: 0.8185 (m-80) REVERT: C 447 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7130 (mtm110) REVERT: D 33 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8589 (mtmt) REVERT: D 371 SER cc_start: 0.8933 (m) cc_final: 0.8681 (t) REVERT: D 432 ARG cc_start: 0.8581 (tmm-80) cc_final: 0.8242 (ttp-110) REVERT: D 443 ASN cc_start: 0.7366 (m-40) cc_final: 0.6678 (p0) REVERT: D 451 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7231 (tptp) REVERT: I 304 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: J 341 LEU cc_start: 0.5875 (tp) cc_final: 0.5599 (mt) REVERT: Q 15 TYR cc_start: 0.8146 (m-80) cc_final: 0.7605 (m-80) REVERT: Q 19 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7920 (pp) REVERT: Q 52 TYR cc_start: 0.8482 (m-80) cc_final: 0.8203 (m-80) REVERT: A 198 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 447 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7118 (mtm110) REVERT: B 33 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8615 (mtmt) REVERT: B 432 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8209 (ttp-110) REVERT: B 433 ASN cc_start: 0.8418 (m-40) cc_final: 0.8109 (m-40) REVERT: B 443 ASN cc_start: 0.7416 (m-40) cc_final: 0.6701 (p0) REVERT: B 451 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7248 (tptp) outliers start: 112 outliers final: 77 residues processed: 653 average time/residue: 0.6161 time to fit residues: 662.6820 Evaluate side-chains 628 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 541 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE 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 269 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 319 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 117 VAL 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 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 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 U residue 19 LEU Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 51 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 448 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain K residue 214 PHE 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 267 MET Chi-restraints excluded: chain C residue 319 LEU 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 D residue 117 VAL 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 I residue 214 PHE 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 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 179 LEU 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 445 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 3.9990 chunk 470 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 128 optimal weight: 0.0670 chunk 522 optimal weight: 3.9990 chunk 433 optimal weight: 30.0000 chunk 241 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 274 optimal weight: 0.0370 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 267 GLN T 34 GLN W 97 GLN G 96 ASN G 213 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 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** U 34 GLN E 96 ASN E 288 ASN F 164 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN 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 96 ASN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 44822 Z= 0.241 Angle : 0.592 8.572 60956 Z= 0.297 Chirality : 0.046 0.165 6660 Planarity : 0.005 0.065 7966 Dihedral : 5.137 46.050 6004 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.70 % Allowed : 12.98 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.11), residues: 5430 helix: -0.61 (0.13), residues: 1662 sheet: -2.79 (0.15), residues: 870 loop : -1.39 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 260 HIS 0.007 0.001 HIS F 326 PHE 0.029 0.002 PHE E 346 TYR 0.016 0.001 TYR T 36 ARG 0.010 0.000 ARG B 80 *********************** 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 681 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 556 time to evaluate : 5.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 242 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6142 (mt) REVERT: P 341 LEU cc_start: 0.5790 (mt) cc_final: 0.5260 (mt) REVERT: T 15 TYR cc_start: 0.8093 (m-80) cc_final: 0.7488 (m-80) REVERT: T 19 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (pp) REVERT: G 198 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8486 (mp) REVERT: G 288 ASN cc_start: 0.8545 (m-40) cc_final: 0.8341 (m-40) REVERT: G 447 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7117 (mtm110) REVERT: H 33 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8635 (mtmt) REVERT: H 371 SER cc_start: 0.8907 (m) cc_final: 0.8653 (t) REVERT: H 432 ARG cc_start: 0.8566 (tmm-80) cc_final: 0.8184 (tmm160) REVERT: H 443 ASN cc_start: 0.7375 (m-40) cc_final: 0.6705 (p0) REVERT: H 451 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7258 (tptp) REVERT: M 219 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7114 (mp0) REVERT: N 260 TRP cc_start: 0.6235 (m-10) cc_final: 0.5953 (m-10) REVERT: N 341 LEU cc_start: 0.5575 (tp) cc_final: 0.5291 (mt) REVERT: U 15 TYR cc_start: 0.8056 (m-80) cc_final: 0.7488 (m-80) REVERT: U 19 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8002 (pp) REVERT: U 52 TYR cc_start: 0.8409 (m-80) cc_final: 0.8124 (m-80) REVERT: E 198 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8486 (mp) REVERT: E 205 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6827 (mt-10) REVERT: E 447 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7103 (mtm110) REVERT: F 33 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8624 (mtmt) REVERT: F 432 ARG cc_start: 0.8572 (tmm-80) cc_final: 0.8202 (ttp-110) REVERT: F 443 ASN cc_start: 0.7341 (m-40) cc_final: 0.6676 (p0) REVERT: F 451 LYS cc_start: 0.8019 (mttm) cc_final: 0.7350 (tptp) REVERT: L 260 TRP cc_start: 0.6757 (m-10) cc_final: 0.6308 (m-10) REVERT: L 341 LEU cc_start: 0.5954 (tp) cc_final: 0.5714 (mt) REVERT: X 52 TYR cc_start: 0.8398 (m-80) cc_final: 0.8180 (m-80) REVERT: C 178 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7627 (mtpp) REVERT: C 447 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7116 (mtm110) REVERT: D 33 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8617 (mtmt) REVERT: D 371 SER cc_start: 0.8868 (m) cc_final: 0.8652 (t) REVERT: D 432 ARG cc_start: 0.8564 (tmm-80) cc_final: 0.8232 (tmm160) REVERT: D 443 ASN cc_start: 0.7338 (m-40) cc_final: 0.6721 (p0) REVERT: D 451 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7246 (tptp) REVERT: I 304 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: J 260 TRP cc_start: 0.6641 (m-10) cc_final: 0.6079 (m-10) REVERT: J 341 LEU cc_start: 0.5815 (tp) cc_final: 0.5539 (mt) REVERT: Q 15 TYR cc_start: 0.8059 (m-80) cc_final: 0.7465 (m-80) REVERT: Q 19 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8024 (pp) REVERT: Q 52 TYR cc_start: 0.8406 (m-80) cc_final: 0.8122 (m-80) REVERT: A 198 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8503 (mp) REVERT: A 447 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.7114 (mtm110) REVERT: B 33 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8639 (mtmt) REVERT: B 432 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.8198 (ttp-110) REVERT: B 433 ASN cc_start: 0.8478 (m-40) cc_final: 0.8139 (m-40) REVERT: B 443 ASN cc_start: 0.7384 (m-40) cc_final: 0.6702 (p0) REVERT: B 451 LYS cc_start: 0.8050 (mmtp) cc_final: 0.7256 (tptp) outliers start: 125 outliers final: 81 residues processed: 654 average time/residue: 0.6185 time to fit residues: 667.7007 Evaluate side-chains 615 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 525 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 214 PHE 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 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 319 LEU Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain M residue 214 PHE 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 263 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 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 319 LEU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 117 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 K residue 214 PHE 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 45 VAL 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 173 CYS Chi-restraints excluded: chain C residue 319 LEU 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 117 VAL Chi-restraints excluded: chain D residue 164 ASN 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 I residue 214 PHE 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 300 VAL 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 179 LEU 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 448 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 6.9990 chunk 58 optimal weight: 0.0000 chunk 297 optimal weight: 6.9990 chunk 381 optimal weight: 2.9990 chunk 295 optimal weight: 0.0770 chunk 439 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 520 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 240 optimal weight: 0.3980 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 258 GLN O 267 GLN W 97 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 288 ASN ** E 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** 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 96 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44822 Z= 0.183 Angle : 0.569 8.658 60956 Z= 0.284 Chirality : 0.045 0.166 6660 Planarity : 0.005 0.060 7966 Dihedral : 4.948 43.164 6004 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.35 % Allowed : 13.48 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.11), residues: 5430 helix: -0.37 (0.13), residues: 1666 sheet: -2.74 (0.15), residues: 837 loop : -1.29 (0.11), residues: 2927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 260 HIS 0.006 0.001 HIS F 326 PHE 0.029 0.002 PHE E 346 TYR 0.015 0.001 TYR U 36 ARG 0.019 0.000 ARG B 80 *********************** 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 656 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 547 time to evaluate : 5.379 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: 0.5724 (mt) cc_final: 0.5448 (mt) REVERT: T 15 TYR cc_start: 0.7964 (m-80) cc_final: 0.7363 (m-80) REVERT: T 19 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (pp) REVERT: G 80 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7791 (ptp90) REVERT: G 178 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7550 (mtpp) REVERT: G 198 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8477 (mp) REVERT: G 288 ASN cc_start: 0.8499 (m-40) cc_final: 0.8263 (m110) REVERT: G 298 MET cc_start: 0.8456 (ttp) cc_final: 0.8242 (ttp) REVERT: G 386 TRP cc_start: 0.8294 (m100) cc_final: 0.7959 (m-10) REVERT: G 447 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7122 (mtm110) REVERT: G 455 GLU cc_start: 0.7589 (mp0) cc_final: 0.7326 (mm-30) REVERT: H 33 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8618 (mtmt) REVERT: H 371 SER cc_start: 0.8900 (m) cc_final: 0.8528 (t) REVERT: H 432 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8172 (tmm160) REVERT: H 443 ASN cc_start: 0.7172 (m-40) cc_final: 0.6705 (p0) REVERT: M 235 GLU cc_start: 0.7663 (tp30) cc_final: 0.7398 (tp30) REVERT: M 343 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7541 (mtp180) REVERT: N 341 LEU cc_start: 0.5484 (tp) cc_final: 0.5159 (mt) REVERT: U 15 TYR cc_start: 0.7927 (m-80) cc_final: 0.7336 (m-80) REVERT: U 19 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8041 (pp) REVERT: U 52 TYR cc_start: 0.8342 (m-80) cc_final: 0.8135 (m-80) REVERT: E 198 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8463 (mp) REVERT: E 205 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: E 386 TRP cc_start: 0.8277 (m100) cc_final: 0.7956 (m-10) REVERT: E 447 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7112 (mtm110) REVERT: F 33 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8627 (mtmt) REVERT: F 432 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8209 (tmm160) REVERT: F 443 ASN cc_start: 0.7131 (m-40) cc_final: 0.6670 (p0) REVERT: F 451 LYS cc_start: 0.7990 (mttm) cc_final: 0.7236 (tptp) REVERT: L 260 TRP cc_start: 0.6822 (m-10) cc_final: 0.6428 (m-10) REVERT: L 341 LEU cc_start: 0.5817 (tp) cc_final: 0.5493 (mt) REVERT: C 178 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7470 (mtpp) REVERT: C 386 TRP cc_start: 0.8284 (m100) cc_final: 0.7911 (m-10) REVERT: C 447 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7120 (mtm110) REVERT: D 33 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8616 (mtmt) REVERT: D 80 ARG cc_start: 0.7550 (ttt-90) cc_final: 0.7335 (ttt-90) REVERT: D 371 SER cc_start: 0.8868 (m) cc_final: 0.8638 (t) REVERT: D 432 ARG cc_start: 0.8532 (tmm-80) cc_final: 0.8232 (tmm160) REVERT: D 443 ASN cc_start: 0.7157 (m-40) cc_final: 0.6684 (p0) REVERT: I 304 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: J 260 TRP cc_start: 0.6456 (m-10) cc_final: 0.6000 (m-10) REVERT: J 341 LEU cc_start: 0.6028 (tp) cc_final: 0.5709 (mt) REVERT: Q 15 TYR cc_start: 0.7949 (m-80) cc_final: 0.7351 (m-80) REVERT: Q 52 TYR cc_start: 0.8335 (m-80) cc_final: 0.8128 (m-80) REVERT: A 128 PHE cc_start: 0.7684 (t80) cc_final: 0.7390 (t80) REVERT: A 198 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8505 (mp) REVERT: A 386 TRP cc_start: 0.8308 (m100) cc_final: 0.7972 (m-10) REVERT: A 447 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7122 (mtm110) REVERT: A 455 GLU cc_start: 0.7548 (mp0) cc_final: 0.7267 (mm-30) REVERT: B 33 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8624 (mtmt) REVERT: B 432 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8153 (tmm160) REVERT: B 433 ASN cc_start: 0.8447 (m-40) cc_final: 0.8104 (m-40) REVERT: B 443 ASN cc_start: 0.7177 (m-40) cc_final: 0.6696 (p0) outliers start: 109 outliers final: 69 residues processed: 626 average time/residue: 0.6441 time to fit residues: 655.7368 Evaluate side-chains 586 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 510 time to evaluate : 5.145 ------------------------------------------------------------------------------- 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 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 319 LEU Chi-restraints excluded: chain H residue 117 VAL 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 M residue 214 PHE Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 236 GLU 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 263 LEU Chi-restraints excluded: chain N residue 276 VAL Chi-restraints excluded: chain N residue 277 THR 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 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 F residue 117 VAL Chi-restraints excluded: chain F residue 247 THR 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 276 VAL Chi-restraints excluded: chain X residue 45 VAL 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 173 CYS Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 302 ILE 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 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 B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 354 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 258 GLN W 97 GLN W 104 HIS G 96 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 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** V 104 HIS ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** 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 96 ASN D 164 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN Q 34 GLN A 96 ASN A 213 GLN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 44822 Z= 0.342 Angle : 0.639 9.679 60956 Z= 0.319 Chirality : 0.048 0.212 6660 Planarity : 0.005 0.063 7966 Dihedral : 5.102 49.018 6000 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.48 % Allowed : 13.93 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5430 helix: -0.49 (0.13), residues: 1655 sheet: -2.75 (0.15), residues: 872 loop : -1.24 (0.11), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 260 HIS 0.008 0.001 HIS B 326 PHE 0.029 0.002 PHE E 128 TYR 0.018 0.002 TYR Q 15 ARG 0.009 0.000 ARG D 80 *********************** 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 641 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 526 time to evaluate : 4.886 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: P 341 LEU cc_start: 0.5817 (mt) cc_final: 0.5545 (mt) REVERT: T 15 TYR cc_start: 0.8110 (m-80) cc_final: 0.7451 (m-80) REVERT: G 80 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7785 (ptt-90) REVERT: G 198 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8549 (mp) REVERT: G 288 ASN cc_start: 0.8644 (m-40) cc_final: 0.8395 (m110) REVERT: G 447 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7144 (mtm110) REVERT: H 33 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8625 (mtmt) REVERT: H 371 SER cc_start: 0.8919 (m) cc_final: 0.8644 (t) REVERT: H 443 ASN cc_start: 0.7434 (m-40) cc_final: 0.6742 (p0) REVERT: H 451 LYS cc_start: 0.7874 (mmtm) cc_final: 0.7164 (tptp) REVERT: M 235 GLU cc_start: 0.7702 (tp30) cc_final: 0.7390 (tp30) REVERT: N 341 LEU cc_start: 0.5565 (tp) cc_final: 0.5251 (mt) REVERT: U 15 TYR cc_start: 0.8112 (m-80) cc_final: 0.7443 (m-80) REVERT: U 52 TYR cc_start: 0.8487 (m-80) cc_final: 0.8202 (m-80) REVERT: E 96 ASN cc_start: 0.8596 (t0) cc_final: 0.8360 (t0) REVERT: E 198 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8558 (mp) REVERT: E 205 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: E 288 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8370 (m-40) REVERT: E 447 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7117 (mtm110) REVERT: F 33 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8638 (mtmt) REVERT: F 443 ASN cc_start: 0.7400 (m-40) cc_final: 0.6711 (p0) REVERT: F 451 LYS cc_start: 0.7991 (mttm) cc_final: 0.7349 (tptp) REVERT: L 260 TRP cc_start: 0.6816 (m-10) cc_final: 0.6368 (m-10) REVERT: L 341 LEU cc_start: 0.5853 (tp) cc_final: 0.5546 (mt) REVERT: C 178 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7616 (mtpp) REVERT: C 447 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.7128 (mtm110) REVERT: D 33 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8614 (mtmt) REVERT: D 80 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7368 (ttt-90) REVERT: D 371 SER cc_start: 0.8912 (m) cc_final: 0.8660 (t) REVERT: D 443 ASN cc_start: 0.7424 (m-40) cc_final: 0.6720 (p0) REVERT: D 451 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7146 (tptp) REVERT: I 247 GLU cc_start: 0.6608 (tt0) cc_final: 0.5922 (tp30) REVERT: J 260 TRP cc_start: 0.6518 (m-10) cc_final: 0.6006 (m-10) REVERT: J 341 LEU cc_start: 0.6004 (tp) cc_final: 0.5758 (mt) REVERT: Q 15 TYR cc_start: 0.8103 (m-80) cc_final: 0.7447 (m-80) REVERT: Q 52 TYR cc_start: 0.8463 (m-80) cc_final: 0.8170 (m-80) REVERT: A 198 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 447 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7152 (mtm110) REVERT: B 33 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8615 (mtmt) REVERT: B 188 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7234 (ptm160) REVERT: B 443 ASN cc_start: 0.7432 (m-40) cc_final: 0.6734 (p0) REVERT: B 451 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7169 (tptp) outliers start: 115 outliers final: 94 residues processed: 608 average time/residue: 0.6268 time to fit residues: 625.5696 Evaluate side-chains 603 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 504 time to evaluate : 5.217 ------------------------------------------------------------------------------- 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 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 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 H residue 117 VAL 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 230 LEU Chi-restraints excluded: chain M residue 236 GLU 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 263 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 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 288 ASN 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 117 VAL Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 207 ILE 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 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 K residue 340 ILE Chi-restraints excluded: chain L residue 276 VAL 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 51 LEU Chi-restraints excluded: chain Y residue 99 LEU Chi-restraints excluded: chain C residue 173 CYS 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 117 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 207 ILE 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 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 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 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 4.9990 chunk 498 optimal weight: 3.9990 chunk 454 optimal weight: 7.9990 chunk 485 optimal weight: 0.6980 chunk 291 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 380 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 438 optimal weight: 30.0000 chunk 458 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 34 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 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 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** 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 27 GLN R 104 HIS Q 34 GLN ** A 96 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 44822 Z= 0.305 Angle : 0.621 8.765 60956 Z= 0.311 Chirality : 0.047 0.232 6660 Planarity : 0.005 0.069 7966 Dihedral : 5.099 47.689 6000 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.11), residues: 5430 helix: -0.40 (0.13), residues: 1646 sheet: -2.74 (0.15), residues: 869 loop : -1.21 (0.11), residues: 2915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 260 HIS 0.008 0.001 HIS B 326 PHE 0.028 0.002 PHE E 346 TYR 0.017 0.002 TYR U 15 ARG 0.008 0.000 ARG D 80 *********************** 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 629 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 517 time to evaluate : 4.997 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: 0.5792 (mt) cc_final: 0.5512 (mt) REVERT: T 15 TYR cc_start: 0.8062 (m-80) cc_final: 0.7422 (m-80) REVERT: G 80 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7796 (ptp90) REVERT: G 178 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7800 (mtpp) REVERT: G 198 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8562 (mp) REVERT: G 288 ASN cc_start: 0.8645 (m-40) cc_final: 0.8394 (m110) REVERT: G 447 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7131 (mtm110) REVERT: H 33 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8620 (mtmt) REVERT: H 371 SER cc_start: 0.8919 (m) cc_final: 0.8642 (t) REVERT: H 443 ASN cc_start: 0.7414 (m-40) cc_final: 0.6754 (p0) REVERT: H 451 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7187 (tptp) REVERT: M 235 GLU cc_start: 0.7708 (tp30) cc_final: 0.7398 (tp30) REVERT: N 341 LEU cc_start: 0.5585 (tp) cc_final: 0.5288 (mt) REVERT: U 15 TYR cc_start: 0.8068 (m-80) cc_final: 0.7429 (m-80) REVERT: U 52 TYR cc_start: 0.8438 (m-80) cc_final: 0.8140 (m-80) REVERT: E 96 ASN cc_start: 0.8596 (t0) cc_final: 0.8322 (t0) REVERT: E 198 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8541 (mp) REVERT: E 205 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: E 447 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7126 (mtm110) REVERT: F 33 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8627 (mtmt) REVERT: F 443 ASN cc_start: 0.7429 (m-40) cc_final: 0.6735 (p0) REVERT: F 451 LYS cc_start: 0.7997 (mttm) cc_final: 0.7353 (tptp) REVERT: L 260 TRP cc_start: 0.6819 (m-10) cc_final: 0.6431 (m-10) REVERT: L 313 PHE cc_start: 0.6018 (m-80) cc_final: 0.5811 (m-10) REVERT: L 341 LEU cc_start: 0.5798 (tp) cc_final: 0.5490 (mt) REVERT: Y 51 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7040 (mp) REVERT: C 178 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7588 (mtpp) REVERT: C 447 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7107 (mtm110) REVERT: D 33 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8735 (mtmt) REVERT: D 371 SER cc_start: 0.8907 (m) cc_final: 0.8659 (t) REVERT: D 443 ASN cc_start: 0.7420 (m-40) cc_final: 0.6725 (p0) REVERT: I 247 GLU cc_start: 0.6633 (tt0) cc_final: 0.5926 (tp30) REVERT: J 260 TRP cc_start: 0.6497 (m-10) cc_final: 0.6067 (m-10) REVERT: J 341 LEU cc_start: 0.5969 (tp) cc_final: 0.5720 (mt) REVERT: Q 15 TYR cc_start: 0.8057 (m-80) cc_final: 0.7403 (m-80) REVERT: Q 52 TYR cc_start: 0.8448 (m-80) cc_final: 0.8147 (m-80) REVERT: A 198 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 447 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7142 (mtm110) REVERT: B 33 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8611 (mtmt) REVERT: B 443 ASN cc_start: 0.7436 (m-40) cc_final: 0.6777 (p0) outliers start: 112 outliers final: 102 residues processed: 599 average time/residue: 0.6046 time to fit residues: 602.3632 Evaluate side-chains 611 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 504 time to evaluate : 5.334 ------------------------------------------------------------------------------- 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 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 300 VAL 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 117 VAL Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 205 GLU 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 230 LEU Chi-restraints excluded: chain M residue 236 GLU 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 263 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 267 MET 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 117 VAL Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 247 THR 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 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 K residue 340 ILE Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 297 LEU Chi-restraints excluded: chain X residue 45 VAL 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 173 CYS 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 117 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS 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 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 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 319 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 179 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 4.9990 chunk 512 optimal weight: 0.9990 chunk 313 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 537 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 330 optimal weight: 0.0060 chunk 262 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 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 96 ASN E 288 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 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** ** A 96 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44822 Z= 0.257 Angle : 0.608 8.977 60956 Z= 0.304 Chirality : 0.046 0.281 6660 Planarity : 0.005 0.064 7966 Dihedral : 5.024 46.123 6000 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.39 % Allowed : 14.58 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5430 helix: -0.30 (0.13), residues: 1652 sheet: -2.70 (0.15), residues: 869 loop : -1.17 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 260 HIS 0.007 0.001 HIS B 326 PHE 0.028 0.002 PHE G 346 TYR 0.016 0.001 TYR Q 15 ARG 0.005 0.000 ARG B 432 ********************** 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 633 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 522 time to evaluate : 4.931 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: P 341 LEU cc_start: 0.5734 (mt) cc_final: 0.5459 (mt) REVERT: T 15 TYR cc_start: 0.8064 (m-80) cc_final: 0.7401 (m-80) REVERT: G 80 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7757 (ptp90) REVERT: G 178 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7735 (mtpp) REVERT: G 198 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8556 (mp) REVERT: G 288 ASN cc_start: 0.8625 (m-40) cc_final: 0.8371 (m110) REVERT: G 447 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7110 (mtm110) REVERT: H 33 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8666 (mtmt) REVERT: H 371 SER cc_start: 0.8927 (m) cc_final: 0.8651 (t) REVERT: H 443 ASN cc_start: 0.7412 (m-40) cc_final: 0.6756 (p0) REVERT: H 451 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7158 (tptp) REVERT: M 235 GLU cc_start: 0.7577 (tp30) cc_final: 0.7248 (tp30) REVERT: N 341 LEU cc_start: 0.5590 (tp) cc_final: 0.5268 (mt) REVERT: U 15 TYR cc_start: 0.8029 (m-80) cc_final: 0.7399 (m-80) REVERT: U 52 TYR cc_start: 0.8409 (m-80) cc_final: 0.8113 (m-80) REVERT: E 96 ASN cc_start: 0.8542 (t0) cc_final: 0.8277 (t0) REVERT: E 198 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8537 (mp) REVERT: E 205 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: E 447 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7099 (mtm110) REVERT: F 33 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8606 (mtmt) REVERT: F 443 ASN cc_start: 0.7428 (m-40) cc_final: 0.6740 (p0) REVERT: F 451 LYS cc_start: 0.7986 (mttm) cc_final: 0.7320 (tptp) REVERT: L 260 TRP cc_start: 0.6779 (m-10) cc_final: 0.6403 (m-10) REVERT: L 313 PHE cc_start: 0.6020 (m-80) cc_final: 0.5801 (m-10) REVERT: L 341 LEU cc_start: 0.5684 (tp) cc_final: 0.5366 (mt) REVERT: X 15 TYR cc_start: 0.8244 (m-80) cc_final: 0.7696 (m-80) REVERT: Y 51 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6976 (mp) REVERT: C 178 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7572 (mtpp) REVERT: C 447 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7100 (mtm110) REVERT: D 33 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8587 (mtmt) REVERT: D 371 SER cc_start: 0.8915 (m) cc_final: 0.8664 (t) REVERT: D 443 ASN cc_start: 0.7420 (m-40) cc_final: 0.6728 (p0) REVERT: I 247 GLU cc_start: 0.6640 (tt0) cc_final: 0.5934 (tp30) REVERT: J 260 TRP cc_start: 0.6377 (m-10) cc_final: 0.6017 (m-10) REVERT: J 341 LEU cc_start: 0.5776 (tp) cc_final: 0.5479 (mt) REVERT: Q 15 TYR cc_start: 0.8015 (m-80) cc_final: 0.7365 (m-80) REVERT: Q 52 TYR cc_start: 0.8376 (m-80) cc_final: 0.8080 (m-80) REVERT: A 178 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7903 (mtpp) REVERT: A 198 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 447 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7119 (mtm110) REVERT: B 33 LYS cc_start: 0.8993 (mtmm) cc_final: 0.8669 (mtmt) REVERT: B 443 ASN cc_start: 0.7418 (m-40) cc_final: 0.6742 (p0) outliers start: 111 outliers final: 94 residues processed: 604 average time/residue: 0.6317 time to fit residues: 638.8766 Evaluate side-chains 606 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 507 time to evaluate : 5.208 ------------------------------------------------------------------------------- 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 311 SER Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 276 VAL 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 448 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 173 CYS Chi-restraints excluded: chain H residue 205 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 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 263 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 399 SER Chi-restraints excluded: chain E residue 448 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 247 THR 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 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 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 351 ASN Chi-restraints excluded: chain X residue 45 VAL 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 173 CYS 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 117 VAL Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 173 CYS 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 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 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 319 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 179 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.9990 chunk 456 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 395 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 429 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 258 GLN T 34 GLN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 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** U 34 GLN E 288 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** 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 96 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158056 restraints weight = 46741.424| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.75 r_work: 0.3382 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 44822 Z= 0.332 Angle : 0.637 10.683 60956 Z= 0.319 Chirality : 0.048 0.247 6660 Planarity : 0.005 0.065 7966 Dihedral : 5.098 48.789 6000 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5430 helix: -0.36 (0.13), residues: 1670 sheet: -2.72 (0.15), residues: 849 loop : -1.14 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 260 HIS 0.008 0.001 HIS B 326 PHE 0.029 0.002 PHE E 346 TYR 0.023 0.002 TYR H 81 ARG 0.005 0.000 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11032.99 seconds wall clock time: 202 minutes 25.42 seconds (12145.42 seconds total)