Starting phenix.real_space_refine on Fri Mar 6 08:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lrs_0960/03_2026/6lrs_0960.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lrs_0960/03_2026/6lrs_0960.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/6lrs_0960/03_2026/6lrs_0960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lrs_0960/03_2026/6lrs_0960.map" model { file = "/net/cci-nas-00/data/ceres_data/6lrs_0960/03_2026/6lrs_0960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lrs_0960/03_2026/6lrs_0960.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 19228 2.51 5 N 5272 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30156 Number of models: 1 Model: "" Number of chains: 12 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: "G" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" 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: "E" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" 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: "C" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 392} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.39, per 1000 atoms: 0.21 Number of scatterers: 30156 At special positions: 0 Unit cell: (140.4, 140.4, 113.36, 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 112 16.00 O 5544 8.00 N 5272 7.00 C 19228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 248 " - pdb=" SG CYS H 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 173 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 248 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 193 " distance=2.05 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 173 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS B 248 " distance=2.03 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7000 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 38 sheets defined 37.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'T' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL T 28 " --> pdb=" O ILE T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 68 Processing helix chain 'T' and resid 69 through 74 Processing helix chain 'G' and resid 50 through 62 removed outlier: 3.682A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 62 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.785A pdb=" N LEU G 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 109 No H-bonds generated for 'chain 'G' and resid 107 through 109' Processing helix chain 'G' and resid 116 through 121 Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.577A pdb=" N LYS G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 182 through 195 removed outlier: 3.538A pdb=" N TYR G 191 " --> pdb=" O GLY G 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 230 removed outlier: 3.563A pdb=" N LEU G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 261 removed outlier: 3.760A pdb=" N GLU G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 311 through 316 removed outlier: 3.765A pdb=" N LEU G 315 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 323 Processing helix chain 'G' and resid 336 through 344 removed outlier: 4.019A pdb=" N GLY G 341 " --> pdb=" O GLU G 337 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.739A pdb=" N LEU G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 435 removed outlier: 3.582A pdb=" N ALA G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU G 425 " --> pdb=" O ASN G 421 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY G 435 " --> pdb=" O ALA G 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 64 removed outlier: 3.604A pdb=" N SER H 62 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.619A pdb=" N LEU H 108 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 109' Processing helix chain 'H' and resid 116 through 121 removed outlier: 3.654A pdb=" N SER H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 157 through 164 Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.516A pdb=" N ALA H 189 " --> pdb=" O ASN H 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 233 removed outlier: 3.555A pdb=" N LEU H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 231 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.685A pdb=" N ALA H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 288 Processing helix chain 'H' and resid 298 through 302 removed outlier: 3.651A pdb=" N VAL H 301 " --> pdb=" O MET H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 removed outlier: 3.692A pdb=" N LEU H 315 " --> pdb=" O HIS H 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 320 " --> pdb=" O ALA H 316 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 removed outlier: 3.769A pdb=" N ILE H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE H 346 " --> pdb=" O ILE H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 387 through 394 removed outlier: 3.707A pdb=" N LEU H 391 " --> pdb=" O HIS H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 420 Processing helix chain 'H' and resid 422 through 427 Processing helix chain 'H' and resid 427 through 433 Processing helix chain 'H' and resid 442 through 450 removed outlier: 4.002A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 447 " --> pdb=" O ASN H 443 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU H 448 " --> pdb=" O ASP H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 460 removed outlier: 3.992A pdb=" N ALA H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL S 28 " --> pdb=" O ILE S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 68 Processing helix chain 'S' and resid 69 through 74 Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.685A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.809A pdb=" N LEU E 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.575A pdb=" N LYS E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.538A pdb=" N TYR E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 230 removed outlier: 3.562A pdb=" N LEU E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 261 removed outlier: 3.761A pdb=" N GLU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.764A pdb=" N LEU E 315 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 336 through 344 removed outlier: 4.019A pdb=" N GLY E 341 " --> pdb=" O GLU E 337 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.725A pdb=" N LEU E 350 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.553A pdb=" N ALA E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU E 425 " --> pdb=" O ASN E 421 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.650A pdb=" N SER F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.605A pdb=" N LEU F 108 " --> pdb=" O PRO F 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 109 " --> pdb=" O LEU F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.661A pdb=" N SER F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 157 through 164 Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.880A pdb=" N CYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 233 removed outlier: 3.549A pdb=" N LEU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 261 removed outlier: 3.688A pdb=" N ALA F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 288 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.650A pdb=" N VAL F 301 " --> pdb=" O MET F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.692A pdb=" N LEU F 315 " --> pdb=" O HIS F 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 removed outlier: 3.770A pdb=" N ILE F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE F 346 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 387 through 394 removed outlier: 3.693A pdb=" N LEU F 391 " --> pdb=" O HIS F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 427 through 433 Processing helix chain 'F' and resid 442 through 450 removed outlier: 3.989A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.994A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 33 removed outlier: 3.593A pdb=" N VAL R 28 " --> pdb=" O ILE R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 68 Processing helix chain 'R' and resid 69 through 74 Processing helix chain 'C' and resid 50 through 64 removed outlier: 3.621A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.786A pdb=" N LEU C 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.573A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.539A pdb=" N TYR C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 192 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 230 removed outlier: 3.568A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.760A pdb=" N GLU C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.764A pdb=" N LEU C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 323 Processing helix chain 'C' and resid 336 through 344 removed outlier: 4.028A pdb=" N GLY C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.722A pdb=" N LEU C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 414 through 435 removed outlier: 3.552A pdb=" N ALA C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.601A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.622A pdb=" N LEU D 108 " --> pdb=" O PRO D 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 109' Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.651A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 157 through 164 Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.882A pdb=" N CYS D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 233 removed outlier: 3.556A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.693A pdb=" N ALA D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 298 through 302 removed outlier: 3.660A pdb=" N VAL D 301 " --> pdb=" O MET D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.690A pdb=" N LEU D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.772A pdb=" N ILE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE D 346 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 387 through 394 removed outlier: 3.708A pdb=" N LEU D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 427 through 433 Processing helix chain 'D' and resid 442 through 450 removed outlier: 4.003A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.995A pdb=" N ALA D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 33 removed outlier: 3.592A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 68 Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'A' and resid 50 through 62 removed outlier: 3.682A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.809A pdb=" N LEU A 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.575A pdb=" N LYS A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.525A pdb=" N TYR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.569A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.759A pdb=" N GLU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.765A pdb=" N LEU A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 Processing helix chain 'A' and resid 336 through 344 removed outlier: 4.028A pdb=" N GLY A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.714A pdb=" N LEU A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 414 through 435 removed outlier: 3.551A pdb=" N ALA A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.641A pdb=" N SER B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.624A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.657A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.873A pdb=" N CYS B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.538A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.687A pdb=" N ALA B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.660A pdb=" N VAL B 301 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.691A pdb=" N LEU B 315 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.771A pdb=" N ILE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 394 removed outlier: 3.691A pdb=" N LEU B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.987A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.997A pdb=" N ALA B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 54 through 55 removed outlier: 3.743A pdb=" N PHE T 101 " --> pdb=" O VAL T 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'G' and resid 84 through 85 removed outlier: 6.536A pdb=" N LEU G 38 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE G 139 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 40 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLY G 309 " --> pdb=" O ARG G 132 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 134 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 170 through 173 removed outlier: 7.204A pdb=" N LEU G 170 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE G 403 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY G 172 " --> pdb=" O PHE G 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 241 through 242 removed outlier: 5.318A pdb=" N LEU G 241 " --> pdb=" O MET G 267 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP G 269 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE G 266 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS G 295 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS G 268 " --> pdb=" O HIS G 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 355 Processing sheet with id=AA8, first strand: chain 'H' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE H 88 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE H 99 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU H 38 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE H 139 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA H 40 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY H 309 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 134 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 174 removed outlier: 6.355A pdb=" N LEU H 171 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS H 202 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS H 173 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR H 201 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN H 242 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N HIS H 239 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N MET H 267 " --> pdb=" O HIS H 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU H 241 " --> pdb=" O MET H 267 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP H 269 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE H 266 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS H 295 " --> pdb=" O ILE H 266 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N HIS H 268 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS H 328 " --> pdb=" O LEU H 292 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE H 294 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE H 327 " --> pdb=" O VAL H 378 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER H 380 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 54 through 55 removed outlier: 3.742A pdb=" N PHE S 101 " --> pdb=" O VAL S 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.538A pdb=" N LEU E 38 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 139 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA E 40 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N GLY E 309 " --> pdb=" O ARG E 132 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU E 134 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 170 through 173 removed outlier: 7.202A pdb=" N LEU E 170 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE E 403 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY E 172 " --> pdb=" O PHE E 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 241 through 242 removed outlier: 5.333A pdb=" N LEU E 241 " --> pdb=" O MET E 267 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP E 269 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE E 266 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N HIS E 295 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS E 268 " --> pdb=" O HIS E 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB7, first strand: chain 'E' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 88 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 99 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 90 removed outlier: 6.702A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 88 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 99 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU F 38 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE F 139 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA F 40 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 170 through 174 removed outlier: 6.357A pdb=" N LEU F 171 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS F 202 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS F 173 " --> pdb=" O LYS F 202 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR F 201 " --> pdb=" O TYR F 240 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN F 242 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N HIS F 239 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET F 267 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU F 241 " --> pdb=" O MET F 267 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP F 269 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE F 266 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS F 295 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS F 268 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N HIS F 328 " --> pdb=" O LEU F 292 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE F 294 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F 327 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER F 380 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 54 through 55 removed outlier: 3.743A pdb=" N PHE R 101 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.534A pdb=" N LEU C 38 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C 139 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 40 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY C 309 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 134 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 170 through 173 removed outlier: 7.205A pdb=" N LEU C 170 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE C 403 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY C 172 " --> pdb=" O PHE C 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 241 through 242 removed outlier: 5.322A pdb=" N LEU C 241 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP C 269 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE C 266 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N HIS C 295 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS C 268 " --> pdb=" O HIS C 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC9, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.701A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE D 88 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 99 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 38 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE D 139 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 40 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLY D 309 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 134 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.350A pdb=" N LEU D 171 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS D 202 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS D 173 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 201 " --> pdb=" O TYR D 240 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN D 242 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS D 239 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N MET D 267 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU D 241 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP D 269 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D 266 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS D 295 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS D 268 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N HIS D 328 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE D 294 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE D 327 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER D 380 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 54 through 55 removed outlier: 3.742A pdb=" N PHE Q 101 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.537A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 139 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 40 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N GLY A 309 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 134 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 170 through 173 removed outlier: 7.222A pdb=" N LEU A 170 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE A 403 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY A 172 " --> pdb=" O PHE A 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 241 through 242 removed outlier: 5.319A pdb=" N LEU A 241 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP A 269 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE A 266 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS A 295 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 268 " --> pdb=" O HIS A 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.700A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 88 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 99 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.700A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 88 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 99 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 38 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 139 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 40 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.358A pdb=" N LEU B 171 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS B 202 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 173 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 201 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 242 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N HIS B 239 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N MET B 267 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU B 241 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP B 269 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE B 266 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS B 295 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS B 268 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS B 328 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE B 294 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 327 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER B 380 " --> pdb=" O ILE B 327 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2568 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: 5.72 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9960 1.34 - 1.46: 7295 1.46 - 1.58: 13485 1.58 - 1.70: 0 1.70 - 1.83: 164 Bond restraints: 30904 Sorted by residual: bond pdb=" CB THR H 280 " pdb=" CG2 THR H 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR F 280 " pdb=" CG2 THR F 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR D 280 " pdb=" CG2 THR D 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CB THR B 280 " pdb=" CG2 THR B 280 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.21e+00 bond pdb=" C HIS C 410 " pdb=" N PRO C 411 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.82e+00 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 39302 1.88 - 3.77: 2209 3.77 - 5.65: 345 5.65 - 7.53: 102 7.53 - 9.42: 42 Bond angle restraints: 42000 Sorted by residual: angle pdb=" C TYR T 36 " pdb=" N ILE T 37 " pdb=" CA ILE T 37 " ideal model delta sigma weight residual 123.25 131.48 -8.23 1.10e+00 8.26e-01 5.60e+01 angle pdb=" C TYR Q 36 " pdb=" N ILE Q 37 " pdb=" CA ILE Q 37 " ideal model delta sigma weight residual 123.25 131.48 -8.23 1.10e+00 8.26e-01 5.59e+01 angle pdb=" C TYR S 36 " pdb=" N ILE S 37 " pdb=" CA ILE S 37 " ideal model delta sigma weight residual 123.25 131.42 -8.17 1.10e+00 8.26e-01 5.52e+01 angle pdb=" C TYR R 36 " pdb=" N ILE R 37 " pdb=" CA ILE R 37 " ideal model delta sigma weight residual 123.25 131.42 -8.17 1.10e+00 8.26e-01 5.51e+01 angle pdb=" N VAL E 158 " pdb=" CA VAL E 158 " pdb=" C VAL E 158 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.26e+01 ... (remaining 41995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 17306 15.71 - 31.42: 738 31.42 - 47.13: 160 47.13 - 62.84: 24 62.84 - 78.55: 20 Dihedral angle restraints: 18248 sinusoidal: 7272 harmonic: 10976 Sorted by residual: dihedral pdb=" CA PRO C 177 " pdb=" C PRO C 177 " pdb=" N LYS C 178 " pdb=" CA LYS C 178 " ideal model delta harmonic sigma weight residual -180.00 -128.51 -51.49 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PRO G 177 " pdb=" C PRO G 177 " pdb=" N LYS G 178 " pdb=" CA LYS G 178 " ideal model delta harmonic sigma weight residual -180.00 -128.56 -51.44 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA PRO E 177 " pdb=" C PRO E 177 " pdb=" N LYS E 178 " pdb=" CA LYS E 178 " ideal model delta harmonic sigma weight residual -180.00 -128.57 -51.43 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3038 0.054 - 0.108: 1192 0.108 - 0.162: 308 0.162 - 0.216: 38 0.216 - 0.270: 12 Chirality restraints: 4588 Sorted by residual: chirality pdb=" CG LEU C 134 " pdb=" CB LEU C 134 " pdb=" CD1 LEU C 134 " pdb=" CD2 LEU C 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU A 134 " pdb=" CB LEU A 134 " pdb=" CD1 LEU A 134 " pdb=" CD2 LEU A 134 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE C 266 " pdb=" CA ILE C 266 " pdb=" CG1 ILE C 266 " pdb=" CG2 ILE C 266 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4585 not shown) Planarity restraints: 5468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 36 " -0.059 2.00e-02 2.50e+03 3.11e-02 1.93e+01 pdb=" CG TYR R 36 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR R 36 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR R 36 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR R 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 36 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 36 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 36 " -0.059 2.00e-02 2.50e+03 3.10e-02 1.93e+01 pdb=" CG TYR S 36 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR S 36 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR S 36 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR S 36 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR S 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 36 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR S 36 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 36 " 0.059 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR T 36 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR T 36 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 36 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR T 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR T 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR T 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR T 36 " 0.027 2.00e-02 2.50e+03 ... (remaining 5465 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7411 2.79 - 3.32: 27813 3.32 - 3.84: 53731 3.84 - 4.37: 67628 4.37 - 4.90: 108305 Nonbonded interactions: 264888 Sorted by model distance: nonbonded pdb=" OD1 ASN G 206 " pdb=" OG SER H 120 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN A 206 " pdb=" OG SER B 120 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 191 " pdb=" OE1 GLU A 232 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR H 419 " pdb=" OE1 GLU H 455 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN C 206 " pdb=" OG SER D 120 " model vdw 2.266 3.040 ... (remaining 264883 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: 0.05 Found NCS groups: ncs_group { reference = chain 'T' selection = chain 'S' selection = chain 'R' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'E' selection = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'H' selection = chain 'F' selection = chain 'D' selection = chain 'B' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.810 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.006 0.089 30912 Z= 0.279 Angle : 1.038 9.417 42016 Z= 0.584 Chirality : 0.060 0.270 4588 Planarity : 0.007 0.054 5468 Dihedral : 10.049 75.320 11224 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.38 % Allowed : 2.01 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.10), residues: 3808 helix: -4.49 (0.06), residues: 1376 sheet: -3.47 (0.17), residues: 500 loop : -2.56 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 286 TYR 0.059 0.004 TYR R 36 PHE 0.045 0.005 PHE S 90 TRP 0.032 0.003 TRP R 53 HIS 0.023 0.004 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00643 (30904) covalent geometry : angle 1.03547 (42000) SS BOND : bond 0.01120 ( 8) SS BOND : angle 3.65948 ( 16) hydrogen bonds : bond 0.31207 ( 898) hydrogen bonds : angle 11.26257 ( 2568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 905 time to evaluate : 0.931 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: T 23 GLN cc_start: 0.7713 (mt0) cc_final: 0.7444 (mt0) REVERT: G 97 GLN cc_start: 0.7976 (tt0) cc_final: 0.7755 (tt0) REVERT: G 116 ASN cc_start: 0.8271 (t0) cc_final: 0.7549 (t0) REVERT: G 129 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7228 (mtmm) REVERT: G 156 ILE cc_start: 0.6691 (mt) cc_final: 0.6464 (mt) REVERT: G 214 ARG cc_start: 0.7756 (mmt180) cc_final: 0.7399 (mmt180) REVERT: G 253 LYS cc_start: 0.8001 (mttt) cc_final: 0.7796 (ttmm) REVERT: H 104 TYR cc_start: 0.8636 (m-80) cc_final: 0.8431 (m-80) REVERT: H 161 ASP cc_start: 0.7279 (m-30) cc_final: 0.6955 (m-30) REVERT: H 195 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7044 (ttt180) REVERT: H 295 HIS cc_start: 0.7250 (t-90) cc_final: 0.6868 (t70) REVERT: H 302 ILE cc_start: 0.7936 (mt) cc_final: 0.7732 (mt) REVERT: E 97 GLN cc_start: 0.7968 (tt0) cc_final: 0.7745 (tt0) REVERT: E 116 ASN cc_start: 0.8274 (t0) cc_final: 0.7543 (t0) REVERT: E 129 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7279 (mtmm) REVERT: E 156 ILE cc_start: 0.6690 (mt) cc_final: 0.6455 (mt) REVERT: E 214 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7424 (mmt180) REVERT: E 253 LYS cc_start: 0.8003 (mttt) cc_final: 0.7800 (ttmm) REVERT: E 267 MET cc_start: 0.7646 (ttp) cc_final: 0.7314 (ttp) REVERT: F 84 ARG cc_start: 0.7847 (ptp90) cc_final: 0.7589 (ptp-170) REVERT: F 161 ASP cc_start: 0.7328 (m-30) cc_final: 0.7100 (m-30) REVERT: F 195 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7081 (ttt180) REVERT: F 220 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mt) REVERT: F 295 HIS cc_start: 0.7246 (t-90) cc_final: 0.6895 (t70) REVERT: R 92 ASN cc_start: 0.5903 (m-40) cc_final: 0.5319 (p0) REVERT: C 116 ASN cc_start: 0.8268 (t0) cc_final: 0.7545 (t0) REVERT: C 129 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7224 (mtmm) REVERT: C 156 ILE cc_start: 0.6694 (mt) cc_final: 0.6460 (mt) REVERT: C 214 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7405 (mmt180) REVERT: C 253 LYS cc_start: 0.7998 (mttt) cc_final: 0.7792 (ttmm) REVERT: D 84 ARG cc_start: 0.7853 (ptp90) cc_final: 0.7651 (ptp-170) REVERT: D 104 TYR cc_start: 0.8623 (m-80) cc_final: 0.8419 (m-80) REVERT: D 161 ASP cc_start: 0.7281 (m-30) cc_final: 0.6945 (m-30) REVERT: D 195 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7087 (ttt180) REVERT: D 220 LEU cc_start: 0.8634 (mt) cc_final: 0.8416 (mt) REVERT: D 295 HIS cc_start: 0.7231 (t-90) cc_final: 0.6838 (t70) REVERT: Q 58 LEU cc_start: 0.6679 (mt) cc_final: 0.6478 (tt) REVERT: Q 88 VAL cc_start: 0.7058 (t) cc_final: 0.6751 (t) REVERT: A 97 GLN cc_start: 0.7973 (tt0) cc_final: 0.7750 (tt0) REVERT: A 116 ASN cc_start: 0.8268 (t0) cc_final: 0.7551 (t0) REVERT: A 129 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7210 (mtmm) REVERT: A 156 ILE cc_start: 0.6691 (mt) cc_final: 0.6457 (mt) REVERT: A 214 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7316 (mmt180) REVERT: A 253 LYS cc_start: 0.8000 (mttt) cc_final: 0.7786 (ttmm) REVERT: B 84 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7658 (ptp-170) REVERT: B 104 TYR cc_start: 0.8613 (m-80) cc_final: 0.8405 (m-80) REVERT: B 195 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7054 (ttt180) REVERT: B 220 LEU cc_start: 0.8660 (mt) cc_final: 0.8433 (mt) REVERT: B 295 HIS cc_start: 0.7235 (t-90) cc_final: 0.6848 (t70) outliers start: 12 outliers final: 4 residues processed: 909 average time/residue: 0.2229 time to fit residues: 306.9121 Evaluate side-chains 554 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 550 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 27 GLN ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 387 HIS G 402 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 239 HIS H 288 ASN ** H 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 HIS ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN S 27 GLN S 92 ASN ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 HIS ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN E 387 HIS E 402 GLN F 97 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 308 HIS ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 402 GLN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 308 HIS ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN Q 92 ASN Q 97 GLN A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 387 HIS A 402 GLN ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 308 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.188201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.156788 restraints weight = 32840.081| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.79 r_work: 0.3570 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30912 Z= 0.154 Angle : 0.697 15.663 42016 Z= 0.365 Chirality : 0.046 0.176 4588 Planarity : 0.005 0.050 5468 Dihedral : 6.661 43.264 4216 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.53 % Allowed : 9.36 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.11), residues: 3808 helix: -3.05 (0.10), residues: 1384 sheet: -3.09 (0.19), residues: 472 loop : -2.19 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 216 TYR 0.037 0.002 TYR S 36 PHE 0.022 0.002 PHE R 61 TRP 0.020 0.002 TRP H 284 HIS 0.009 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00350 (30904) covalent geometry : angle 0.69654 (42000) SS BOND : bond 0.00495 ( 8) SS BOND : angle 1.63347 ( 16) hydrogen bonds : bond 0.04733 ( 898) hydrogen bonds : angle 6.52260 ( 2568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 575 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 65 THR cc_start: 0.7157 (t) cc_final: 0.6887 (m) REVERT: G 129 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7458 (mtmm) REVERT: G 202 LYS cc_start: 0.7585 (ttpm) cc_final: 0.7272 (ttpt) REVERT: G 214 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7480 (mmt180) REVERT: H 198 LEU cc_start: 0.7997 (mt) cc_final: 0.7760 (mt) REVERT: H 302 ILE cc_start: 0.8148 (mt) cc_final: 0.7729 (mt) REVERT: S 65 THR cc_start: 0.7234 (t) cc_final: 0.6948 (m) REVERT: E 129 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7473 (mtmm) REVERT: E 214 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7499 (mmt180) REVERT: F 84 ARG cc_start: 0.8174 (ptp90) cc_final: 0.7815 (ptp-170) REVERT: F 198 LEU cc_start: 0.7843 (mt) cc_final: 0.7586 (mt) REVERT: R 65 THR cc_start: 0.7200 (t) cc_final: 0.6908 (m) REVERT: C 129 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7465 (mtmm) REVERT: C 202 LYS cc_start: 0.7606 (ttpm) cc_final: 0.7300 (ttpt) REVERT: C 214 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7501 (mmt180) REVERT: D 84 ARG cc_start: 0.8193 (ptp90) cc_final: 0.7823 (ptp-170) REVERT: D 198 LEU cc_start: 0.7958 (mt) cc_final: 0.7720 (mt) REVERT: Q 29 GLN cc_start: 0.6055 (mm-40) cc_final: 0.5853 (tp40) REVERT: A 129 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7436 (mtmm) REVERT: A 202 LYS cc_start: 0.7567 (ttpm) cc_final: 0.7263 (ttpt) REVERT: A 214 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7460 (mmt180) REVERT: B 84 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7797 (ptp-170) REVERT: B 198 LEU cc_start: 0.7806 (mt) cc_final: 0.7551 (mt) outliers start: 48 outliers final: 23 residues processed: 598 average time/residue: 0.1893 time to fit residues: 182.8756 Evaluate side-chains 487 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 464 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 217 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 205 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 34 GLN T 74 GLN T 97 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 230 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 ASN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 GLN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN S 97 GLN E 150 GLN E 230 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 ASN R 97 GLN C 150 GLN C 230 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN B 97 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS B 305 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.186573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156439 restraints weight = 32544.479| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.62 r_work: 0.3449 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30912 Z= 0.154 Angle : 0.634 12.367 42016 Z= 0.331 Chirality : 0.045 0.140 4588 Planarity : 0.004 0.037 5468 Dihedral : 6.122 41.584 4216 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.88 % Allowed : 12.39 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.12), residues: 3808 helix: -2.13 (0.12), residues: 1368 sheet: -2.98 (0.19), residues: 472 loop : -1.98 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 195 TYR 0.035 0.002 TYR R 36 PHE 0.027 0.002 PHE B 128 TRP 0.012 0.001 TRP Q 53 HIS 0.010 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00359 (30904) covalent geometry : angle 0.63328 (42000) SS BOND : bond 0.00462 ( 8) SS BOND : angle 1.29966 ( 16) hydrogen bonds : bond 0.04141 ( 898) hydrogen bonds : angle 5.78815 ( 2568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 536 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 65 THR cc_start: 0.7221 (t) cc_final: 0.6940 (m) REVERT: G 129 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7491 (mtmm) REVERT: G 202 LYS cc_start: 0.7878 (ttpm) cc_final: 0.7447 (ttpt) REVERT: G 214 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7656 (mmt180) REVERT: H 52 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7805 (mp0) REVERT: H 302 ILE cc_start: 0.8166 (mt) cc_final: 0.7726 (mt) REVERT: S 65 THR cc_start: 0.7304 (t) cc_final: 0.7017 (m) REVERT: E 129 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7503 (mttp) REVERT: E 150 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: E 202 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7717 (ttpp) REVERT: E 214 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7681 (mmt180) REVERT: E 354 TYR cc_start: 0.8473 (t80) cc_final: 0.8196 (t80) REVERT: E 428 CYS cc_start: 0.4821 (m) cc_final: 0.3877 (t) REVERT: F 52 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7868 (mp0) REVERT: F 94 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5740 (mm-30) REVERT: F 131 LEU cc_start: 0.8513 (mp) cc_final: 0.8250 (tt) REVERT: R 65 THR cc_start: 0.7234 (t) cc_final: 0.6945 (m) REVERT: C 129 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7499 (mtmm) REVERT: C 150 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: C 202 LYS cc_start: 0.7902 (ttpm) cc_final: 0.7468 (ttpt) REVERT: C 214 ARG cc_start: 0.7995 (mmt180) cc_final: 0.7646 (mmt180) REVERT: C 354 TYR cc_start: 0.8481 (t80) cc_final: 0.8218 (t80) REVERT: C 428 CYS cc_start: 0.4854 (m) cc_final: 0.3902 (t) REVERT: D 52 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7830 (mp0) REVERT: D 94 GLU cc_start: 0.6334 (mm-30) cc_final: 0.5802 (mm-30) REVERT: A 129 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7480 (mtmm) REVERT: A 150 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: A 202 LYS cc_start: 0.7852 (ttpm) cc_final: 0.7405 (ttpt) REVERT: A 214 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7662 (mmt180) REVERT: A 354 TYR cc_start: 0.8477 (t80) cc_final: 0.8209 (t80) REVERT: A 428 CYS cc_start: 0.4821 (m) cc_final: 0.3866 (t) REVERT: B 52 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7894 (mp0) REVERT: B 94 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5783 (mm-30) REVERT: B 131 LEU cc_start: 0.8478 (mp) cc_final: 0.8219 (tt) outliers start: 59 outliers final: 27 residues processed: 574 average time/residue: 0.1844 time to fit residues: 171.2692 Evaluate side-chains 493 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 463 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 324 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 336 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 295 optimal weight: 10.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 154 HIS ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 150 GLN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS H 410 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 154 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 154 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 150 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 154 HIS ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 150 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.173535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140345 restraints weight = 33754.492| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.80 r_work: 0.3497 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30912 Z= 0.142 Angle : 0.609 14.120 42016 Z= 0.315 Chirality : 0.045 0.161 4588 Planarity : 0.004 0.035 5468 Dihedral : 5.866 40.632 4216 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.36 % Allowed : 14.39 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.12), residues: 3808 helix: -1.65 (0.13), residues: 1372 sheet: -2.90 (0.18), residues: 504 loop : -1.84 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 351 TYR 0.033 0.002 TYR Q 36 PHE 0.020 0.002 PHE F 346 TRP 0.009 0.001 TRP G 369 HIS 0.009 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00331 (30904) covalent geometry : angle 0.60861 (42000) SS BOND : bond 0.00337 ( 8) SS BOND : angle 0.97759 ( 16) hydrogen bonds : bond 0.03571 ( 898) hydrogen bonds : angle 5.46942 ( 2568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 488 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 65 THR cc_start: 0.7257 (t) cc_final: 0.6965 (m) REVERT: G 129 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7443 (mtmm) REVERT: G 428 CYS cc_start: 0.5023 (m) cc_final: 0.4113 (t) REVERT: H 52 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7828 (mp0) REVERT: H 94 GLU cc_start: 0.6350 (mm-30) cc_final: 0.5849 (mm-30) REVERT: H 283 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7566 (mmm-85) REVERT: H 302 ILE cc_start: 0.8200 (mt) cc_final: 0.7734 (mt) REVERT: S 65 THR cc_start: 0.7239 (t) cc_final: 0.6959 (m) REVERT: E 202 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7759 (ttpt) REVERT: E 354 TYR cc_start: 0.8549 (t80) cc_final: 0.8295 (t80) REVERT: E 428 CYS cc_start: 0.4716 (m) cc_final: 0.3910 (t) REVERT: F 52 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7844 (mp0) REVERT: F 94 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5805 (mm-30) REVERT: F 283 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7680 (mmm-85) REVERT: R 65 THR cc_start: 0.7258 (t) cc_final: 0.6964 (m) REVERT: C 354 TYR cc_start: 0.8540 (t80) cc_final: 0.8288 (t80) REVERT: C 428 CYS cc_start: 0.4732 (m) cc_final: 0.3924 (t) REVERT: D 52 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7848 (mp0) REVERT: D 94 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5851 (mm-30) REVERT: D 283 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7650 (mmm-85) REVERT: A 129 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7495 (mtmm) REVERT: A 354 TYR cc_start: 0.8554 (t80) cc_final: 0.8298 (t80) REVERT: A 428 CYS cc_start: 0.4756 (m) cc_final: 0.3943 (t) REVERT: B 52 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7828 (mp0) REVERT: B 94 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5794 (mm-30) REVERT: B 283 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7607 (mmm-85) outliers start: 74 outliers final: 48 residues processed: 525 average time/residue: 0.1731 time to fit residues: 149.7812 Evaluate side-chains 499 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 451 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 339 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 330 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 402 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.177724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146565 restraints weight = 32625.132| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.65 r_work: 0.3382 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30912 Z= 0.242 Angle : 0.684 12.510 42016 Z= 0.353 Chirality : 0.048 0.179 4588 Planarity : 0.005 0.035 5468 Dihedral : 5.966 39.032 4216 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.15 % Allowed : 14.30 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.13), residues: 3808 helix: -1.52 (0.13), residues: 1372 sheet: -2.95 (0.19), residues: 484 loop : -1.73 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 188 TYR 0.038 0.002 TYR T 36 PHE 0.020 0.002 PHE F 346 TRP 0.013 0.002 TRP Q 53 HIS 0.010 0.002 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00580 (30904) covalent geometry : angle 0.68308 (42000) SS BOND : bond 0.00616 ( 8) SS BOND : angle 1.53524 ( 16) hydrogen bonds : bond 0.03858 ( 898) hydrogen bonds : angle 5.37501 ( 2568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 506 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: T 65 THR cc_start: 0.7232 (t) cc_final: 0.6917 (m) REVERT: G 298 MET cc_start: 0.8365 (mmm) cc_final: 0.8022 (ttm) REVERT: G 428 CYS cc_start: 0.4986 (m) cc_final: 0.4180 (t) REVERT: H 52 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7904 (mp0) REVERT: H 119 THR cc_start: 0.7371 (p) cc_final: 0.7083 (p) REVERT: H 302 ILE cc_start: 0.8509 (mt) cc_final: 0.8197 (mt) REVERT: S 65 THR cc_start: 0.7105 (t) cc_final: 0.6786 (m) REVERT: E 202 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7827 (ttpt) REVERT: E 298 MET cc_start: 0.8377 (mmm) cc_final: 0.8033 (ttm) REVERT: E 428 CYS cc_start: 0.4911 (m) cc_final: 0.4200 (t) REVERT: F 52 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7962 (mp0) REVERT: F 119 THR cc_start: 0.7339 (p) cc_final: 0.7081 (p) REVERT: R 1 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4934 (mmm) REVERT: R 65 THR cc_start: 0.7164 (t) cc_final: 0.6834 (m) REVERT: C 428 CYS cc_start: 0.4940 (m) cc_final: 0.4230 (t) REVERT: D 52 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7902 (mp0) REVERT: D 119 THR cc_start: 0.7442 (p) cc_final: 0.7199 (p) REVERT: A 298 MET cc_start: 0.8393 (mmm) cc_final: 0.7996 (ttm) REVERT: A 428 CYS cc_start: 0.4931 (m) cc_final: 0.4238 (t) REVERT: B 52 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7948 (mp0) REVERT: B 119 THR cc_start: 0.7356 (p) cc_final: 0.7044 (p) outliers start: 99 outliers final: 70 residues processed: 566 average time/residue: 0.1752 time to fit residues: 163.4614 Evaluate side-chains 520 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 449 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 304 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN G 97 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN E 97 GLN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.174944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142661 restraints weight = 32812.899| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.91 r_work: 0.3314 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30912 Z= 0.171 Angle : 0.628 13.523 42016 Z= 0.323 Chirality : 0.046 0.176 4588 Planarity : 0.004 0.034 5468 Dihedral : 5.765 39.748 4216 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.96 % Allowed : 15.99 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.13), residues: 3808 helix: -1.32 (0.13), residues: 1376 sheet: -2.74 (0.19), residues: 496 loop : -1.69 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 42 TYR 0.035 0.002 TYR T 36 PHE 0.019 0.002 PHE B 346 TRP 0.008 0.001 TRP Q 56 HIS 0.008 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00410 (30904) covalent geometry : angle 0.62773 (42000) SS BOND : bond 0.00508 ( 8) SS BOND : angle 1.13638 ( 16) hydrogen bonds : bond 0.03463 ( 898) hydrogen bonds : angle 5.19260 ( 2568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 504 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: T 65 THR cc_start: 0.7093 (t) cc_final: 0.6747 (m) REVERT: G 129 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7503 (mttp) REVERT: G 202 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7453 (ttpt) REVERT: G 298 MET cc_start: 0.8376 (mmm) cc_final: 0.8022 (ttm) REVERT: G 428 CYS cc_start: 0.5173 (m) cc_final: 0.4301 (t) REVERT: H 52 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7877 (mp0) REVERT: H 94 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6291 (mm-30) REVERT: H 119 THR cc_start: 0.7375 (p) cc_final: 0.7121 (p) REVERT: H 204 ASP cc_start: 0.7169 (t0) cc_final: 0.6907 (m-30) REVERT: H 283 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7857 (mmm-85) REVERT: H 302 ILE cc_start: 0.8593 (mt) cc_final: 0.8212 (mt) REVERT: S 65 THR cc_start: 0.7158 (t) cc_final: 0.6831 (m) REVERT: E 129 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7597 (mttp) REVERT: E 202 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7829 (ttpt) REVERT: E 298 MET cc_start: 0.8464 (mmm) cc_final: 0.8104 (ttm) REVERT: E 428 CYS cc_start: 0.4792 (m) cc_final: 0.4143 (t) REVERT: F 52 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7881 (mp0) REVERT: F 119 THR cc_start: 0.7330 (p) cc_final: 0.7082 (p) REVERT: F 283 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7817 (mmm-85) REVERT: F 335 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7160 (mtpp) REVERT: R 65 THR cc_start: 0.7118 (t) cc_final: 0.6757 (m) REVERT: C 129 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7540 (mttp) REVERT: C 428 CYS cc_start: 0.4887 (m) cc_final: 0.4210 (t) REVERT: D 52 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7930 (mp0) REVERT: D 119 THR cc_start: 0.7453 (p) cc_final: 0.7249 (p) REVERT: D 283 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7833 (mmm-85) REVERT: A 129 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7572 (mttp) REVERT: A 202 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7540 (ttpt) REVERT: A 249 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 298 MET cc_start: 0.8393 (mmm) cc_final: 0.8083 (ttm) REVERT: A 339 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 428 CYS cc_start: 0.4890 (m) cc_final: 0.4226 (t) REVERT: B 52 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7882 (mp0) REVERT: B 119 THR cc_start: 0.7398 (p) cc_final: 0.7148 (p) REVERT: B 283 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7782 (mmm-85) REVERT: B 335 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7205 (mtpp) outliers start: 93 outliers final: 65 residues processed: 554 average time/residue: 0.1723 time to fit residues: 160.0042 Evaluate side-chains 538 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 471 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 88 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 99 optimal weight: 0.6980 chunk 358 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN A 116 ASN A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.139246 restraints weight = 33588.066| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.02 r_work: 0.3434 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30912 Z= 0.123 Angle : 0.587 12.822 42016 Z= 0.301 Chirality : 0.044 0.161 4588 Planarity : 0.004 0.034 5468 Dihedral : 5.493 39.184 4216 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.61 % Allowed : 16.66 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 3808 helix: -0.99 (0.14), residues: 1376 sheet: -2.55 (0.20), residues: 512 loop : -1.54 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.030 0.002 TYR T 36 PHE 0.018 0.002 PHE B 346 TRP 0.009 0.001 TRP T 56 HIS 0.007 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00289 (30904) covalent geometry : angle 0.58651 (42000) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.73374 ( 16) hydrogen bonds : bond 0.03176 ( 898) hydrogen bonds : angle 4.98901 ( 2568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 510 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: T 43 ASN cc_start: 0.7465 (t0) cc_final: 0.7148 (t0) REVERT: T 65 THR cc_start: 0.7159 (t) cc_final: 0.6831 (m) REVERT: G 129 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7392 (mttp) REVERT: G 202 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7517 (ttpt) REVERT: G 298 MET cc_start: 0.8197 (mmm) cc_final: 0.7946 (ttm) REVERT: G 428 CYS cc_start: 0.5209 (m) cc_final: 0.4437 (t) REVERT: H 52 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7856 (mp0) REVERT: H 94 GLU cc_start: 0.6470 (mm-30) cc_final: 0.5966 (mm-30) REVERT: H 119 THR cc_start: 0.7261 (p) cc_final: 0.7034 (p) REVERT: H 131 LEU cc_start: 0.8551 (mp) cc_final: 0.8284 (tt) REVERT: H 204 ASP cc_start: 0.7035 (t0) cc_final: 0.6783 (m-30) REVERT: H 283 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7724 (mmm-85) REVERT: H 302 ILE cc_start: 0.8484 (mt) cc_final: 0.8069 (mt) REVERT: S 65 THR cc_start: 0.7146 (t) cc_final: 0.6814 (m) REVERT: E 129 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7445 (mttp) REVERT: E 205 GLU cc_start: 0.6029 (mt-10) cc_final: 0.5796 (mt-10) REVERT: E 270 TYR cc_start: 0.8639 (p90) cc_final: 0.8354 (p90) REVERT: E 298 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8048 (ttm) REVERT: E 428 CYS cc_start: 0.4926 (m) cc_final: 0.4386 (t) REVERT: F 52 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7886 (mp0) REVERT: F 119 THR cc_start: 0.7187 (p) cc_final: 0.6920 (p) REVERT: F 283 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7723 (mmm-85) REVERT: F 302 ILE cc_start: 0.8061 (mt) cc_final: 0.7805 (mt) REVERT: R 43 ASN cc_start: 0.7464 (t0) cc_final: 0.7149 (t0) REVERT: R 65 THR cc_start: 0.7016 (t) cc_final: 0.6652 (m) REVERT: C 81 TYR cc_start: 0.8012 (m-80) cc_final: 0.7794 (m-80) REVERT: C 96 ASN cc_start: 0.8159 (t0) cc_final: 0.7903 (t0) REVERT: C 129 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7407 (mttp) REVERT: C 202 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7763 (ttpp) REVERT: C 428 CYS cc_start: 0.4935 (m) cc_final: 0.4363 (t) REVERT: D 52 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7871 (mp0) REVERT: D 283 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7744 (mmm-85) REVERT: D 335 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7152 (mtpp) REVERT: A 129 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7483 (mttp) REVERT: A 202 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7447 (ttpt) REVERT: A 298 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8020 (ttm) REVERT: A 428 CYS cc_start: 0.4980 (m) cc_final: 0.4410 (t) REVERT: B 52 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7857 (mp0) REVERT: B 119 THR cc_start: 0.7282 (p) cc_final: 0.7055 (p) REVERT: B 131 LEU cc_start: 0.8489 (mp) cc_final: 0.8210 (tt) REVERT: B 145 TYR cc_start: 0.8899 (t80) cc_final: 0.8540 (t80) REVERT: B 283 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7715 (mmm-85) REVERT: B 302 ILE cc_start: 0.8073 (mt) cc_final: 0.7812 (mt) outliers start: 82 outliers final: 57 residues processed: 556 average time/residue: 0.1789 time to fit residues: 162.8815 Evaluate side-chains 520 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 461 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 147 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 317 optimal weight: 0.7980 chunk 340 optimal weight: 0.2980 chunk 232 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 96 ASN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140213 restraints weight = 33498.365| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.04 r_work: 0.3471 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30912 Z= 0.131 Angle : 0.598 13.298 42016 Z= 0.305 Chirality : 0.044 0.140 4588 Planarity : 0.004 0.040 5468 Dihedral : 5.402 38.632 4216 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.83 % Allowed : 16.72 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.13), residues: 3808 helix: -0.89 (0.14), residues: 1396 sheet: -2.31 (0.21), residues: 472 loop : -1.53 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 351 TYR 0.028 0.002 TYR Q 36 PHE 0.016 0.002 PHE D 109 TRP 0.008 0.001 TRP S 56 HIS 0.007 0.001 HIS Q 104 Details of bonding type rmsd covalent geometry : bond 0.00309 (30904) covalent geometry : angle 0.59770 (42000) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.70932 ( 16) hydrogen bonds : bond 0.03180 ( 898) hydrogen bonds : angle 4.88990 ( 2568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 497 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 43 ASN cc_start: 0.7299 (t0) cc_final: 0.7048 (t0) REVERT: T 65 THR cc_start: 0.7151 (t) cc_final: 0.6823 (m) REVERT: G 298 MET cc_start: 0.8277 (mmm) cc_final: 0.7981 (ttm) REVERT: G 428 CYS cc_start: 0.4786 (m) cc_final: 0.4283 (t) REVERT: H 94 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6215 (mm-30) REVERT: H 119 THR cc_start: 0.7261 (p) cc_final: 0.7061 (p) REVERT: H 283 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7699 (mmm-85) REVERT: H 302 ILE cc_start: 0.8431 (mt) cc_final: 0.7803 (mt) REVERT: H 304 ARG cc_start: 0.7817 (tpt-90) cc_final: 0.7492 (ttm-80) REVERT: S 65 THR cc_start: 0.7174 (t) cc_final: 0.6857 (m) REVERT: E 129 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7465 (mttp) REVERT: E 270 TYR cc_start: 0.8639 (p90) cc_final: 0.8389 (p90) REVERT: E 298 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: E 428 CYS cc_start: 0.5114 (m) cc_final: 0.4591 (t) REVERT: F 94 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6013 (mm-30) REVERT: F 119 THR cc_start: 0.7188 (p) cc_final: 0.6949 (p) REVERT: F 131 LEU cc_start: 0.8636 (mp) cc_final: 0.8086 (tt) REVERT: F 145 TYR cc_start: 0.8775 (t80) cc_final: 0.8372 (t80) REVERT: F 283 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7721 (mmm-85) REVERT: R 65 THR cc_start: 0.7024 (t) cc_final: 0.6656 (m) REVERT: C 96 ASN cc_start: 0.8028 (t0) cc_final: 0.7737 (t0) REVERT: C 129 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7428 (mttp) REVERT: C 176 LYS cc_start: 0.5275 (tttp) cc_final: 0.5057 (tttp) REVERT: C 202 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7828 (ttpp) REVERT: C 270 TYR cc_start: 0.8585 (p90) cc_final: 0.8341 (p90) REVERT: C 344 MET cc_start: 0.7750 (tpp) cc_final: 0.7528 (tpp) REVERT: C 428 CYS cc_start: 0.5137 (m) cc_final: 0.4591 (t) REVERT: D 52 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7943 (mp0) REVERT: D 94 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6014 (mm-30) REVERT: D 145 TYR cc_start: 0.8840 (t80) cc_final: 0.8418 (t80) REVERT: D 283 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7701 (mmm-85) REVERT: A 129 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7502 (mttp) REVERT: A 202 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7389 (ttpt) REVERT: A 298 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (ttm) REVERT: A 428 CYS cc_start: 0.4960 (m) cc_final: 0.4382 (t) REVERT: B 119 THR cc_start: 0.7198 (p) cc_final: 0.6989 (p) REVERT: B 198 LEU cc_start: 0.7727 (mt) cc_final: 0.7460 (mt) REVERT: B 283 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7624 (mmm-85) outliers start: 89 outliers final: 62 residues processed: 553 average time/residue: 0.1784 time to fit residues: 161.2194 Evaluate side-chains 528 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 464 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 217 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 256 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN ** Q 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142488 restraints weight = 32758.411| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.76 r_work: 0.3312 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30912 Z= 0.196 Angle : 0.650 12.619 42016 Z= 0.332 Chirality : 0.047 0.185 4588 Planarity : 0.004 0.036 5468 Dihedral : 5.559 38.032 4216 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.68 % Allowed : 16.75 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.13), residues: 3808 helix: -0.86 (0.14), residues: 1372 sheet: -2.35 (0.21), residues: 472 loop : -1.51 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 304 TYR 0.032 0.002 TYR T 36 PHE 0.017 0.002 PHE F 346 TRP 0.010 0.001 TRP C 369 HIS 0.007 0.001 HIS H 239 Details of bonding type rmsd covalent geometry : bond 0.00471 (30904) covalent geometry : angle 0.64965 (42000) SS BOND : bond 0.00494 ( 8) SS BOND : angle 1.19714 ( 16) hydrogen bonds : bond 0.03476 ( 898) hydrogen bonds : angle 4.97189 ( 2568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 468 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 65 THR cc_start: 0.7130 (t) cc_final: 0.6787 (m) REVERT: G 89 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7554 (mm-30) REVERT: G 298 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8098 (ttm) REVERT: G 428 CYS cc_start: 0.4832 (m) cc_final: 0.4291 (t) REVERT: H 94 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6143 (mm-30) REVERT: H 119 THR cc_start: 0.7403 (p) cc_final: 0.7178 (p) REVERT: H 302 ILE cc_start: 0.8217 (mt) cc_final: 0.7764 (mt) REVERT: S 65 THR cc_start: 0.7171 (t) cc_final: 0.6837 (m) REVERT: E 129 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7520 (mttp) REVERT: E 270 TYR cc_start: 0.8713 (p90) cc_final: 0.8444 (p90) REVERT: E 298 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8086 (ttm) REVERT: E 428 CYS cc_start: 0.5197 (m) cc_final: 0.4654 (t) REVERT: F 119 THR cc_start: 0.7407 (p) cc_final: 0.7146 (p) REVERT: F 384 HIS cc_start: 0.4321 (OUTLIER) cc_final: 0.3447 (t-90) REVERT: R 65 THR cc_start: 0.7238 (t) cc_final: 0.6888 (m) REVERT: C 129 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7508 (mttp) REVERT: C 202 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7863 (ttpp) REVERT: C 344 MET cc_start: 0.7878 (tpp) cc_final: 0.7672 (tpp) REVERT: C 428 CYS cc_start: 0.5189 (m) cc_final: 0.4635 (t) REVERT: D 52 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7950 (mp0) REVERT: D 335 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7080 (mtpp) REVERT: Q 43 ASN cc_start: 0.7363 (t0) cc_final: 0.7152 (t0) REVERT: A 298 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8052 (ttm) REVERT: A 428 CYS cc_start: 0.4993 (m) cc_final: 0.4393 (t) REVERT: B 52 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7883 (mp0) REVERT: B 119 THR cc_start: 0.7419 (p) cc_final: 0.7183 (p) REVERT: B 131 LEU cc_start: 0.8561 (mp) cc_final: 0.8245 (tt) outliers start: 84 outliers final: 69 residues processed: 518 average time/residue: 0.1696 time to fit residues: 146.9819 Evaluate side-chains 525 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 451 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 166 TYR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 230 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 103 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 288 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 230 GLN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 230 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 150 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 230 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 230 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.178793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.146108 restraints weight = 32327.067| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.75 r_work: 0.3447 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30912 Z= 0.148 Angle : 0.615 13.109 42016 Z= 0.315 Chirality : 0.045 0.153 4588 Planarity : 0.004 0.041 5468 Dihedral : 5.459 38.760 4216 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.58 % Allowed : 16.75 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3808 helix: -0.76 (0.14), residues: 1372 sheet: -2.27 (0.22), residues: 468 loop : -1.50 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 304 TYR 0.029 0.002 TYR T 36 PHE 0.016 0.002 PHE D 346 TRP 0.008 0.001 TRP Q 56 HIS 0.007 0.001 HIS Q 104 Details of bonding type rmsd covalent geometry : bond 0.00352 (30904) covalent geometry : angle 0.61444 (42000) SS BOND : bond 0.00369 ( 8) SS BOND : angle 0.83553 ( 16) hydrogen bonds : bond 0.03262 ( 898) hydrogen bonds : angle 4.91566 ( 2568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7616 Ramachandran restraints generated. 3808 Oldfield, 0 Emsley, 3808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 456 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 9 ARG cc_start: 0.6193 (mtt180) cc_final: 0.5419 (mmm-85) REVERT: T 65 THR cc_start: 0.7176 (t) cc_final: 0.6846 (m) REVERT: G 298 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8026 (ttm) REVERT: G 428 CYS cc_start: 0.4763 (m) cc_final: 0.4292 (t) REVERT: H 94 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6086 (mm-30) REVERT: H 119 THR cc_start: 0.7314 (p) cc_final: 0.7096 (p) REVERT: H 131 LEU cc_start: 0.8526 (mp) cc_final: 0.8288 (tt) REVERT: H 283 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7676 (mmm-85) REVERT: H 302 ILE cc_start: 0.8212 (mt) cc_final: 0.7742 (mt) REVERT: S 65 THR cc_start: 0.7198 (t) cc_final: 0.6876 (m) REVERT: E 129 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7490 (mttp) REVERT: E 270 TYR cc_start: 0.8649 (p90) cc_final: 0.8410 (p90) REVERT: E 298 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7994 (ttm) REVERT: E 428 CYS cc_start: 0.5137 (m) cc_final: 0.4641 (t) REVERT: F 119 THR cc_start: 0.7279 (p) cc_final: 0.7044 (p) REVERT: F 283 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7680 (mmm-85) REVERT: F 384 HIS cc_start: 0.4321 (OUTLIER) cc_final: 0.3621 (t-90) REVERT: R 9 ARG cc_start: 0.6232 (mtt180) cc_final: 0.5484 (mmm-85) REVERT: R 43 ASN cc_start: 0.7425 (t0) cc_final: 0.7179 (t0) REVERT: R 65 THR cc_start: 0.7198 (t) cc_final: 0.6872 (m) REVERT: C 96 ASN cc_start: 0.8110 (t0) cc_final: 0.7825 (t0) REVERT: C 129 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7739 (mttp) REVERT: C 202 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7895 (ttpp) REVERT: C 428 CYS cc_start: 0.5120 (m) cc_final: 0.4612 (t) REVERT: D 94 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6047 (mm-30) REVERT: D 283 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7713 (mmm-85) REVERT: A 298 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7996 (ttm) REVERT: A 428 CYS cc_start: 0.5143 (m) cc_final: 0.4633 (t) REVERT: B 119 THR cc_start: 0.7309 (p) cc_final: 0.7101 (p) REVERT: B 131 LEU cc_start: 0.8480 (mp) cc_final: 0.8237 (tt) REVERT: B 198 LEU cc_start: 0.7863 (mt) cc_final: 0.7599 (mt) REVERT: B 283 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7644 (mmm-85) REVERT: B 335 LYS cc_start: 0.7441 (mttp) cc_final: 0.7230 (mtpp) outliers start: 81 outliers final: 66 residues processed: 509 average time/residue: 0.1795 time to fit residues: 153.1923 Evaluate side-chains 515 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 445 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 230 GLN Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain F residue 230 GLN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 112 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 340 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 368 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 285 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 359 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 43 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 230 GLN ** H 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN E 150 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 230 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN D 230 GLN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN A 150 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.180652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148031 restraints weight = 32661.885| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.76 r_work: 0.3470 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30912 Z= 0.131 Angle : 0.602 13.066 42016 Z= 0.308 Chirality : 0.044 0.144 4588 Planarity : 0.004 0.055 5468 Dihedral : 5.363 38.353 4216 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 16.97 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 3808 helix: -0.61 (0.14), residues: 1376 sheet: -2.25 (0.22), residues: 468 loop : -1.41 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 132 TYR 0.028 0.002 TYR T 36 PHE 0.016 0.002 PHE F 346 TRP 0.009 0.001 TRP Q 56 HIS 0.007 0.001 HIS D 295 Details of bonding type rmsd covalent geometry : bond 0.00308 (30904) covalent geometry : angle 0.60151 (42000) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.69460 ( 16) hydrogen bonds : bond 0.03171 ( 898) hydrogen bonds : angle 4.84969 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7398.31 seconds wall clock time: 127 minutes 50.87 seconds (7670.87 seconds total)