Starting phenix.real_space_refine on Sun Feb 8 08:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.map" model { file = "/net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gev_51307/02_2026/9gev_51307.cif" } resolution = 3.47 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= 0.002 sd= 0.079 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: 5 Type Number sf(0) Gaussians P 285 5.49 5 S 170 5.16 5 C 26112 2.51 5 N 7674 2.21 5 O 8637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 348 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42878 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3412 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 17, 'TRANS': 425} Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 11, 'TRANS': 427} Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 845 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2787 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "L" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2748 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "M" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "N" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "O" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "T" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3344 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3453 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "D" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3317 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3376 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5608 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Chain: "H" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1153 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 13, 'TRANS': 133} Chain breaks: 3 Chain: "J" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3277 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.90, per 1000 atoms: 0.21 Number of scatterers: 42878 At special positions: 0 Unit cell: (135.321, 186.722, 206.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 170 16.00 P 285 15.00 O 8637 8.00 N 7674 7.00 C 26112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8776 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 36 sheets defined 50.6% alpha, 10.2% beta 131 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.608A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.674A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.781A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 4.308A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.579A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.582A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 removed outlier: 4.323A pdb=" N TYR C 454 " --> pdb=" O GLN C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 94 removed outlier: 4.104A pdb=" N GLN E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 109 removed outlier: 3.562A pdb=" N PHE E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.689A pdb=" N ALA E 212 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG E 213 " --> pdb=" O THR E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 213' Processing helix chain 'E' and resid 244 through 253 removed outlier: 4.296A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.553A pdb=" N GLN E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.907A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.708A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.957A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 199 through 207 Processing helix chain 'I' and resid 210 through 221 removed outlier: 3.509A pdb=" N GLY I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG I 221 " --> pdb=" O TYR I 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.811A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.575A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.893A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.699A pdb=" N GLN N 27 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 4.767A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 73 removed outlier: 3.891A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.533A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 Processing helix chain 'P' and resid 37 through 49 Processing helix chain 'P' and resid 55 through 85 Processing helix chain 'P' and resid 90 through 102 Processing helix chain 'P' and resid 103 through 125 Processing helix chain 'Q' and resid 44 through 57 removed outlier: 3.870A pdb=" N ARG Q 49 " --> pdb=" O THR Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 75 removed outlier: 3.964A pdb=" N PHE Q 67 " --> pdb=" O ARG Q 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA Q 75 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.673A pdb=" N MET Q 90 " --> pdb=" O SER Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 132 removed outlier: 3.639A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 removed outlier: 3.746A pdb=" N GLY R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.314A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 79 through 88 Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 83 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 122 removed outlier: 4.025A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.710A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.937A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 240 through 249 removed outlier: 4.042A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 272 through 288 removed outlier: 3.528A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.625A pdb=" N HIS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.835A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.883A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.642A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 451 through 454 removed outlier: 4.161A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.592A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.776A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.680A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.649A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.552A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.655A pdb=" N HIS B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 320 " --> pdb=" O HIS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.598A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.591A pdb=" N ILE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 454 removed outlier: 4.096A pdb=" N TYR B 454 " --> pdb=" O GLN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.520A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.544A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.583A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.957A pdb=" N SER D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.977A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.629A pdb=" N GLN D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.769A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 399 through 417 removed outlier: 3.805A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.687A pdb=" N GLN D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.759A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.210A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.959A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.759A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.701A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.782A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 447 through 450 Processing helix chain 'G' and resid 519 through 536 Processing helix chain 'G' and resid 550 through 555 removed outlier: 4.094A pdb=" N ALA G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 560 Processing helix chain 'G' and resid 563 through 568 Processing helix chain 'G' and resid 575 through 577 No H-bonds generated for 'chain 'G' and resid 575 through 577' Processing helix chain 'G' and resid 578 through 590 removed outlier: 4.328A pdb=" N HIS G 583 " --> pdb=" O LEU G 579 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN G 584 " --> pdb=" O ASN G 580 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE G 586 " --> pdb=" O TRP G 582 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR G 587 " --> pdb=" O HIS G 583 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG G 588 " --> pdb=" O GLN G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 610 Processing helix chain 'G' and resid 611 through 613 No H-bonds generated for 'chain 'G' and resid 611 through 613' Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 637 through 643 Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 662 through 669 Processing helix chain 'G' and resid 687 through 699 Processing helix chain 'G' and resid 707 through 712 removed outlier: 3.926A pdb=" N ASN G 710 " --> pdb=" O GLU G 707 " (cutoff:3.500A) Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 747 through 751 Processing helix chain 'G' and resid 768 through 780 Processing helix chain 'G' and resid 809 through 818 Processing helix chain 'G' and resid 819 through 822 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 Processing helix chain 'G' and resid 854 through 864 removed outlier: 4.370A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 861 " --> pdb=" O ARG G 857 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 877 Processing helix chain 'G' and resid 888 through 893 Processing helix chain 'G' and resid 897 through 907 Processing helix chain 'G' and resid 907 through 933 removed outlier: 3.940A pdb=" N ALA G 911 " --> pdb=" O GLN G 907 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 928 " --> pdb=" O TYR G 924 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU G 929 " --> pdb=" O ARG G 925 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP G 932 " --> pdb=" O GLN G 928 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 967 through 972 removed outlier: 3.978A pdb=" N LEU G 971 " --> pdb=" O LEU G 967 " (cutoff:3.500A) Processing helix chain 'G' and resid 992 through 994 No H-bonds generated for 'chain 'G' and resid 992 through 994' Processing helix chain 'G' and resid 1028 through 1041 Processing helix chain 'G' and resid 1043 through 1052 Processing helix chain 'G' and resid 1054 through 1065 removed outlier: 4.005A pdb=" N ASN G1063 " --> pdb=" O ALA G1059 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG G1065 " --> pdb=" O TRP G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1075 through 1079 Processing helix chain 'G' and resid 1093 through 1100 removed outlier: 4.284A pdb=" N ILE G1097 " --> pdb=" O LYS G1093 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER G1100 " --> pdb=" O LEU G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1100 through 1117 Processing helix chain 'G' and resid 1126 through 1140 Processing helix chain 'G' and resid 1152 through 1164 Processing helix chain 'G' and resid 1201 through 1209 Processing helix chain 'G' and resid 1230 through 1248 removed outlier: 3.701A pdb=" N MET G1247 " --> pdb=" O GLU G1243 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G1248 " --> pdb=" O ILE G1244 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 removed outlier: 4.197A pdb=" N GLU H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 Processing helix chain 'H' and resid 177 through 189 Processing helix chain 'H' and resid 212 through 234 removed outlier: 4.605A pdb=" N GLU H 218 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG H 224 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 225 " --> pdb=" O ARG H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 341 Processing helix chain 'J' and resid 108 through 121 Processing helix chain 'J' and resid 141 through 155 Processing helix chain 'J' and resid 166 through 175 Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 231 through 234 removed outlier: 3.842A pdb=" N LEU J 234 " --> pdb=" O PRO J 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 231 through 234' Processing helix chain 'J' and resid 238 through 249 removed outlier: 4.273A pdb=" N GLU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 263 removed outlier: 3.945A pdb=" N HIS J 261 " --> pdb=" O VAL J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'J' and resid 446 through 454 removed outlier: 3.678A pdb=" N ALA J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Proline residue: J 452 - end of helix Processing helix chain 'J' and resid 455 through 456 No H-bonds generated for 'chain 'J' and resid 455 through 456' Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 466 through 477 removed outlier: 4.031A pdb=" N GLU J 470 " --> pdb=" O ALA J 466 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 472 " --> pdb=" O ILE J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 489 removed outlier: 3.868A pdb=" N GLU J 485 " --> pdb=" O LYS J 481 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N MET J 486 " --> pdb=" O ASP J 482 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU J 487 " --> pdb=" O ILE J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 500 Processing helix chain 'J' and resid 502 through 513 Processing helix chain 'J' and resid 531 through 545 Processing helix chain 'J' and resid 555 through 559 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.116A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 142 removed outlier: 6.198A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 138 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE C 158 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N HIS C 156 " --> pdb=" O PRO C 140 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 142 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 154 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 161 " --> pdb=" O LYS C 168 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 172 current: chain 'C' and resid 200 through 205 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 200 through 205 current: chain 'E' and resid 158 through 164 removed outlier: 4.389A pdb=" N GLY E 159 " --> pdb=" O LEU E 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 174 current: chain 'E' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 204 through 207 current: chain 'G' and resid 996 through 1005 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 1005 current: chain 'H' and resid 282 through 286 Processing sheet with id=AA4, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.392A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AA7, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AA8, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.915A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'N' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'O' and resid 101 through 102 removed outlier: 6.756A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.746A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.813A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AB8, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.578A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 120 through 140 removed outlier: 5.676A pdb=" N VAL A 135 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 162 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 137 " --> pdb=" O GLY A 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 200 through 206 removed outlier: 5.556A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.842A pdb=" N ILE B 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR G 764 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET G1145 " --> pdb=" O LEU G1173 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.305A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 120 through 143 removed outlier: 8.487A pdb=" N GLY B 133 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 163 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 135 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 161 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 137 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 159 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR B 139 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL B 157 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS B 141 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 172 current: chain 'B' and resid 199 through 205 Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AC6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.253A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 127 through 148 removed outlier: 6.892A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE D 147 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 158 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 208 removed outlier: 5.167A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AC9, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AD1, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.444A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 146 removed outlier: 5.299A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 174 current: chain 'F' and resid 202 through 208 removed outlier: 6.066A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 224 through 225 current: chain 'H' and resid 328 through 329 Processing sheet with id=AD3, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AD4, first strand: chain 'G' and resid 539 through 540 removed outlier: 6.974A pdb=" N GLY G 539 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU G 571 " --> pdb=" O VAL G 650 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 838 through 840 Processing sheet with id=AD6, first strand: chain 'J' and resid 61 through 62 removed outlier: 4.091A pdb=" N ASN J 37 " --> pdb=" O THR J 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AD8, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AD9, first strand: chain 'J' and resid 183 through 188 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 203 current: chain 'J' and resid 523 through 525 1626 hydrogen bonds defined for protein. 4644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 668 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 16381 1.40 - 1.60: 26938 1.60 - 1.79: 554 1.79 - 1.99: 272 1.99 - 2.18: 5 Bond restraints: 44150 Sorted by residual: bond pdb=" O4' DC L -26 " pdb=" C1' DC L -26 " ideal model delta sigma weight residual 1.414 2.071 -0.657 2.00e-02 2.50e+03 1.08e+03 bond pdb=" C2' DC L -26 " pdb=" C1' DC L -26 " ideal model delta sigma weight residual 1.525 2.179 -0.654 2.00e-02 2.50e+03 1.07e+03 bond pdb=" C3' DC L -26 " pdb=" C2' DC L -26 " ideal model delta sigma weight residual 1.525 2.145 -0.620 2.00e-02 2.50e+03 9.61e+02 bond pdb=" C4' DC L -26 " pdb=" C3' DC L -26 " ideal model delta sigma weight residual 1.523 2.130 -0.607 2.00e-02 2.50e+03 9.20e+02 bond pdb=" C4' DC L -26 " pdb=" O4' DC L -26 " ideal model delta sigma weight residual 1.450 2.037 -0.587 2.00e-02 2.50e+03 8.61e+02 ... (remaining 44145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 57647 3.69 - 7.38: 3033 7.38 - 11.07: 59 11.07 - 14.76: 6 14.76 - 18.45: 9 Bond angle restraints: 60754 Sorted by residual: angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 118.38 18.45 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 121.98 17.89 1.00e+00 1.00e+00 3.20e+02 angle pdb=" CA ASP I 212 " pdb=" CB ASP I 212 " pdb=" CG ASP I 212 " ideal model delta sigma weight residual 112.60 119.53 -6.93 1.00e+00 1.00e+00 4.80e+01 angle pdb=" CA ASP C 244 " pdb=" CB ASP C 244 " pdb=" CG ASP C 244 " ideal model delta sigma weight residual 112.60 119.47 -6.87 1.00e+00 1.00e+00 4.73e+01 angle pdb=" N ASN F 329 " pdb=" CA ASN F 329 " pdb=" CB ASN F 329 " ideal model delta sigma weight residual 111.79 103.68 8.11 1.20e+00 6.94e-01 4.56e+01 ... (remaining 60749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 24644 33.85 - 67.70: 1533 67.70 - 101.55: 100 101.55 - 135.40: 6 135.40 - 169.25: 3 Dihedral angle restraints: 26286 sinusoidal: 12678 harmonic: 13608 Sorted by residual: dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 160.13 139.88 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 164.87 135.13 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" C MET F 320 " pdb=" N MET F 320 " pdb=" CA MET F 320 " pdb=" CB MET F 320 " ideal model delta harmonic sigma weight residual -122.60 -138.24 15.64 0 2.50e+00 1.60e-01 3.91e+01 ... (remaining 26283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 6866 0.329 - 0.658: 26 0.658 - 0.987: 0 0.987 - 1.316: 1 1.316 - 1.646: 2 Chirality restraints: 6895 Sorted by residual: chirality pdb=" C1' DC L -26 " pdb=" O4' DC L -26 " pdb=" C2' DC L -26 " pdb=" N1 DC L -26 " both_signs ideal model delta sigma weight residual False 2.47 4.11 -1.65 2.00e-01 2.50e+01 6.77e+01 chirality pdb=" C4' DC L -26 " pdb=" C5' DC L -26 " pdb=" O4' DC L -26 " pdb=" C3' DC L -26 " both_signs ideal model delta sigma weight residual False -2.53 -4.02 1.49 2.00e-01 2.50e+01 5.56e+01 chirality pdb=" C3' DC L -26 " pdb=" C4' DC L -26 " pdb=" O3' DC L -26 " pdb=" C2' DC L -26 " both_signs ideal model delta sigma weight residual False -2.66 -3.79 1.13 2.00e-01 2.50e+01 3.19e+01 ... (remaining 6892 not shown) Planarity restraints: 6829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 47 " -0.305 2.00e-02 2.50e+03 1.54e-01 5.94e+02 pdb=" N1 DT K 47 " 0.010 2.00e-02 2.50e+03 pdb=" C2 DT K 47 " 0.070 2.00e-02 2.50e+03 pdb=" O2 DT K 47 " 0.199 2.00e-02 2.50e+03 pdb=" N3 DT K 47 " 0.040 2.00e-02 2.50e+03 pdb=" C4 DT K 47 " -0.063 2.00e-02 2.50e+03 pdb=" O4 DT K 47 " -0.249 2.00e-02 2.50e+03 pdb=" C5 DT K 47 " 0.064 2.00e-02 2.50e+03 pdb=" C7 DT K 47 " 0.138 2.00e-02 2.50e+03 pdb=" C6 DT K 47 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 15 " 0.299 2.00e-02 2.50e+03 1.21e-01 4.40e+02 pdb=" N9 DG K 15 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DG K 15 " -0.082 2.00e-02 2.50e+03 pdb=" N7 DG K 15 " -0.090 2.00e-02 2.50e+03 pdb=" C5 DG K 15 " -0.064 2.00e-02 2.50e+03 pdb=" C6 DG K 15 " 0.041 2.00e-02 2.50e+03 pdb=" O6 DG K 15 " 0.174 2.00e-02 2.50e+03 pdb=" N1 DG K 15 " 0.053 2.00e-02 2.50e+03 pdb=" C2 DG K 15 " -0.047 2.00e-02 2.50e+03 pdb=" N2 DG K 15 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG K 15 " -0.127 2.00e-02 2.50e+03 pdb=" C4 DG K 15 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 26 " -0.258 2.00e-02 2.50e+03 1.14e-01 3.93e+02 pdb=" N9 DG K 26 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG K 26 " 0.160 2.00e-02 2.50e+03 pdb=" N7 DG K 26 " 0.113 2.00e-02 2.50e+03 pdb=" C5 DG K 26 " 0.029 2.00e-02 2.50e+03 pdb=" C6 DG K 26 " -0.052 2.00e-02 2.50e+03 pdb=" O6 DG K 26 " -0.195 2.00e-02 2.50e+03 pdb=" N1 DG K 26 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DG K 26 " 0.025 2.00e-02 2.50e+03 pdb=" N2 DG K 26 " 0.091 2.00e-02 2.50e+03 pdb=" N3 DG K 26 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG K 26 " 0.034 2.00e-02 2.50e+03 ... (remaining 6826 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 20081 2.99 - 3.47: 44763 3.47 - 3.94: 74805 3.94 - 4.42: 84806 4.42 - 4.90: 132274 Nonbonded interactions: 356729 Sorted by model distance: nonbonded pdb=" OD1 ASP B 439 " pdb=" OG SER B 442 " model vdw 2.512 3.040 nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER A 29 " model vdw 2.516 3.040 nonbonded pdb=" OD1 ASP C 439 " pdb=" OG SER C 442 " model vdw 2.527 3.040 nonbonded pdb=" OG1 THR A 239 " pdb=" OD1 ASP A 242 " model vdw 2.527 3.040 nonbonded pdb=" OG SER O 40 " pdb=" O SER P 87 " model vdw 2.530 3.040 ... (remaining 356724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'B' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 42 through 134) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = chain 'O' selection = (chain 'S' and resid 13 through 118) } ncs_group { reference = (chain 'P' and resid 32 through 123) selection = (chain 'T' and resid 32 through 123) } 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=0.01 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: 4.250 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: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.200 Set scattering table: 0.200 Process input model: 42.310 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.657 44150 Z= 0.813 Angle : 1.881 18.448 60754 Z= 1.239 Chirality : 0.100 1.646 6895 Planarity : 0.020 0.238 6829 Dihedral : 19.337 169.245 17510 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.16 % Favored : 95.11 % Rotamer: Outliers : 1.14 % Allowed : 5.47 % Favored : 93.39 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.11), residues: 4661 helix: -1.51 (0.09), residues: 2186 sheet: -0.29 (0.21), residues: 556 loop : -0.85 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G1212 TYR 0.179 0.025 TYR C 150 PHE 0.078 0.013 PHE D 123 TRP 0.152 0.026 TRP I 141 HIS 0.018 0.004 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.01416 (44150) covalent geometry : angle 1.88116 (60754) hydrogen bonds : bond 0.15832 ( 1960) hydrogen bonds : angle 7.24316 ( 5312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 973 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 ILE cc_start: 0.9048 (tt) cc_final: 0.8655 (pt) REVERT: C 126 GLU cc_start: 0.8316 (tp30) cc_final: 0.8075 (tp30) REVERT: C 153 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8620 (p) REVERT: C 182 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8685 (tptt) REVERT: C 184 ARG cc_start: 0.8946 (mmt-90) cc_final: 0.8467 (mmt-90) REVERT: C 194 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8534 (mp0) REVERT: C 207 ASP cc_start: 0.9020 (t70) cc_final: 0.8714 (m-30) REVERT: C 218 GLU cc_start: 0.8877 (tt0) cc_final: 0.8469 (pm20) REVERT: C 219 GLU cc_start: 0.9008 (pt0) cc_final: 0.8608 (tm-30) REVERT: C 353 ASP cc_start: 0.9132 (p0) cc_final: 0.8696 (p0) REVERT: C 363 THR cc_start: 0.9283 (m) cc_final: 0.9032 (p) REVERT: E 15 ASP cc_start: 0.6928 (m-30) cc_final: 0.6635 (p0) REVERT: E 35 ASP cc_start: 0.9553 (m-30) cc_final: 0.9323 (p0) REVERT: E 47 VAL cc_start: 0.9139 (m) cc_final: 0.8765 (p) REVERT: E 148 ASP cc_start: 0.8371 (m-30) cc_final: 0.8075 (m-30) REVERT: E 167 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8846 (mp0) REVERT: E 168 MET cc_start: 0.8816 (tmm) cc_final: 0.8275 (tpp) REVERT: E 170 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8571 (t) REVERT: E 178 MET cc_start: 0.9029 (mmm) cc_final: 0.8543 (tpp) REVERT: E 274 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9007 (pt0) REVERT: E 377 GLU cc_start: 0.9138 (tp30) cc_final: 0.8937 (tp30) REVERT: I 133 VAL cc_start: 0.6473 (t) cc_final: 0.6259 (m) REVERT: I 139 ARG cc_start: 0.6230 (mtt90) cc_final: 0.5307 (tpt170) REVERT: I 157 GLN cc_start: 0.8867 (mt0) cc_final: 0.8640 (mp10) REVERT: I 201 GLU cc_start: 0.8670 (pm20) cc_final: 0.8449 (tm-30) REVERT: M 67 PHE cc_start: 0.7893 (t80) cc_final: 0.7509 (t80) REVERT: M 76 GLN cc_start: 0.7895 (mt0) cc_final: 0.7631 (tp-100) REVERT: M 100 LEU cc_start: 0.9133 (mm) cc_final: 0.8779 (mm) REVERT: M 107 THR cc_start: 0.8552 (m) cc_final: 0.8306 (m) REVERT: M 113 HIS cc_start: 0.6171 (t70) cc_final: 0.5634 (t-90) REVERT: N 25 ASN cc_start: 0.7922 (m110) cc_final: 0.7538 (m110) REVERT: N 58 LEU cc_start: 0.8842 (tt) cc_final: 0.8549 (tt) REVERT: N 59 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8305 (mmtp) REVERT: P 84 ASN cc_start: 0.7892 (m-40) cc_final: 0.7668 (m-40) REVERT: P 90 THR cc_start: 0.4942 (p) cc_final: 0.4157 (t) REVERT: P 96 THR cc_start: 0.8496 (m) cc_final: 0.8194 (m) REVERT: P 100 LEU cc_start: 0.8695 (mt) cc_final: 0.8465 (mt) REVERT: Q 89 VAL cc_start: 0.6342 (p) cc_final: 0.6081 (p) REVERT: S 27 VAL cc_start: 0.8800 (t) cc_final: 0.8417 (t) REVERT: S 87 ILE cc_start: 0.8338 (mp) cc_final: 0.8138 (pt) REVERT: S 90 ASP cc_start: 0.7188 (t0) cc_final: 0.6013 (t0) REVERT: S 92 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7137 (pt0) REVERT: S 100 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7590 (m) REVERT: S 101 THR cc_start: 0.7866 (m) cc_final: 0.7477 (p) REVERT: T 76 GLU cc_start: 0.7954 (tp30) cc_final: 0.7682 (tp30) REVERT: A 90 LYS cc_start: 0.8986 (mppt) cc_final: 0.8679 (tmtt) REVERT: A 123 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8043 (tpt90) REVERT: A 249 ARG cc_start: 0.9048 (mtp-110) cc_final: 0.8572 (mtm-85) REVERT: B 81 LEU cc_start: 0.8800 (mm) cc_final: 0.8573 (mm) REVERT: B 86 GLU cc_start: 0.9003 (tp30) cc_final: 0.8784 (mm-30) REVERT: B 244 ASP cc_start: 0.9339 (m-30) cc_final: 0.9011 (m-30) REVERT: B 249 ARG cc_start: 0.8899 (mtp-110) cc_final: 0.8376 (mmt90) REVERT: B 259 MET cc_start: 0.9016 (ttm) cc_final: 0.8709 (ttm) REVERT: B 291 ILE cc_start: 0.8861 (mt) cc_final: 0.8658 (tt) REVERT: B 377 ILE cc_start: 0.8593 (mt) cc_final: 0.8333 (tp) REVERT: D 34 ASP cc_start: 0.8806 (m-30) cc_final: 0.8573 (p0) REVERT: D 65 GLU cc_start: 0.9042 (tt0) cc_final: 0.8737 (mt-10) REVERT: D 97 ASP cc_start: 0.8880 (m-30) cc_final: 0.8644 (p0) REVERT: D 112 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8936 (tm-30) REVERT: D 146 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8493 (tm-30) REVERT: D 167 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8652 (mt-10) REVERT: D 196 ASP cc_start: 0.8211 (m-30) cc_final: 0.7655 (t0) REVERT: D 203 SER cc_start: 0.8731 (m) cc_final: 0.8486 (p) REVERT: D 375 CYS cc_start: 0.9214 (m) cc_final: 0.8965 (m) REVERT: D 401 TYR cc_start: 0.8651 (t80) cc_final: 0.8364 (t80) REVERT: F 29 ARG cc_start: 0.8479 (mtt90) cc_final: 0.8214 (mtm-85) REVERT: F 112 GLU cc_start: 0.9013 (pt0) cc_final: 0.8579 (tm-30) REVERT: F 178 MET cc_start: 0.9027 (tpt) cc_final: 0.8599 (tpt) REVERT: F 226 GLN cc_start: 0.8727 (pt0) cc_final: 0.8435 (tp-100) REVERT: F 231 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: F 264 ASP cc_start: 0.8885 (t0) cc_final: 0.8640 (t0) REVERT: F 274 GLU cc_start: 0.8833 (pt0) cc_final: 0.8616 (mm-30) REVERT: F 303 MET cc_start: 0.9116 (mmm) cc_final: 0.8800 (mmt) REVERT: F 365 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8701 (tttm) REVERT: G 526 MET cc_start: 0.8739 (mmm) cc_final: 0.7951 (ptt) REVERT: G 655 GLN cc_start: 0.8839 (pp30) cc_final: 0.8522 (tp40) REVERT: G 665 TRP cc_start: 0.8756 (t60) cc_final: 0.8554 (t60) REVERT: G 671 PHE cc_start: 0.8290 (m-80) cc_final: 0.8029 (m-80) REVERT: G 672 GLN cc_start: 0.7682 (mt0) cc_final: 0.7189 (pm20) REVERT: G 698 ILE cc_start: 0.8105 (mt) cc_final: 0.7866 (tp) REVERT: G 743 MET cc_start: 0.7880 (ttp) cc_final: 0.7660 (ttp) REVERT: G 775 TYR cc_start: 0.8247 (t80) cc_final: 0.7807 (t80) REVERT: G 992 ARG cc_start: 0.7617 (mtt180) cc_final: 0.6965 (mmp80) REVERT: G 1040 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7715 (tm-30) REVERT: G 1194 TYR cc_start: 0.8813 (t80) cc_final: 0.8439 (t80) REVERT: H 272 MET cc_start: 0.8776 (mmm) cc_final: 0.8316 (mmt) REVERT: H 298 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8460 (tp-100) REVERT: J 99 ASP cc_start: 0.8474 (t0) cc_final: 0.7942 (t0) REVERT: J 128 VAL cc_start: 0.8752 (t) cc_final: 0.8521 (m) REVERT: J 180 MET cc_start: 0.7680 (mmt) cc_final: 0.7452 (mmt) REVERT: J 190 TYR cc_start: 0.7607 (t80) cc_final: 0.7372 (t80) REVERT: J 200 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8568 (pm20) REVERT: J 242 MET cc_start: 0.8906 (mmp) cc_final: 0.8536 (mmm) REVERT: J 563 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6100 (pm20) outliers start: 46 outliers final: 15 residues processed: 1009 average time/residue: 0.2893 time to fit residues: 456.3198 Evaluate side-chains 610 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 590 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 1202 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 563 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 25 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Q 93 GLN R 64 ASN T 82 HIS T 84 ASN T 109 HIS A 34 GLN A 156 HIS A 247 ASN A 251 GLN A 373 GLN B 196 ASN B 247 ASN B 335 ASN B 392 ASN D 27 HIS D 92 GLN D 275 GLN F 49 GLN F 453 ASN G 954 ASN G 989 HIS ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089612 restraints weight = 84618.995| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.21 r_work: 0.3043 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44150 Z= 0.194 Angle : 0.767 12.156 60754 Z= 0.415 Chirality : 0.048 0.338 6895 Planarity : 0.005 0.050 6829 Dihedral : 22.324 174.553 8243 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.98 % Favored : 96.85 % Rotamer: Outliers : 2.76 % Allowed : 11.09 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4661 helix: -0.07 (0.11), residues: 2200 sheet: -0.55 (0.20), residues: 605 loop : -0.45 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 36 TYR 0.033 0.002 TYR R 72 PHE 0.027 0.002 PHE G 853 TRP 0.036 0.002 TRP G 599 HIS 0.011 0.001 HIS P 49 Details of bonding type rmsd covalent geometry : bond 0.00432 (44150) covalent geometry : angle 0.76746 (60754) hydrogen bonds : bond 0.05210 ( 1960) hydrogen bonds : angle 4.64171 ( 5312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 662 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 CYS cc_start: 0.8723 (t) cc_final: 0.8506 (t) REVERT: C 153 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8404 (p) REVERT: C 260 MET cc_start: 0.8662 (mmm) cc_final: 0.8316 (tpt) REVERT: C 286 TYR cc_start: 0.9069 (m-10) cc_final: 0.8864 (m-80) REVERT: C 363 THR cc_start: 0.9399 (m) cc_final: 0.9174 (p) REVERT: E 148 ASP cc_start: 0.8040 (m-30) cc_final: 0.7715 (m-30) REVERT: E 168 MET cc_start: 0.8520 (tmm) cc_final: 0.8062 (tpp) REVERT: E 246 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: I 139 ARG cc_start: 0.6218 (mtt90) cc_final: 0.5958 (tpt170) REVERT: M 61 LEU cc_start: 0.7725 (mt) cc_final: 0.6490 (tp) REVERT: M 67 PHE cc_start: 0.7759 (t80) cc_final: 0.7528 (t80) REVERT: M 73 GLU cc_start: 0.7842 (tt0) cc_final: 0.6816 (tp30) REVERT: M 94 GLU cc_start: 0.8287 (tp30) cc_final: 0.7752 (tp30) REVERT: N 25 ASN cc_start: 0.7328 (m110) cc_final: 0.6410 (t0) REVERT: N 26 ILE cc_start: 0.8264 (mt) cc_final: 0.8038 (mt) REVERT: N 74 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8708 (mm-30) REVERT: N 88 TYR cc_start: 0.8473 (m-80) cc_final: 0.8174 (m-80) REVERT: N 98 TYR cc_start: 0.7146 (m-10) cc_final: 0.6912 (m-80) REVERT: O 56 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8029 (tm-30) REVERT: O 73 ASN cc_start: 0.7383 (t0) cc_final: 0.6656 (p0) REVERT: O 95 LYS cc_start: 0.8574 (tttp) cc_final: 0.8372 (tmtt) REVERT: P 95 GLN cc_start: 0.8699 (mt0) cc_final: 0.8387 (mt0) REVERT: P 109 HIS cc_start: 0.7527 (m90) cc_final: 0.6927 (m90) REVERT: P 113 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7721 (tt0) REVERT: Q 94 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8133 (pt0) REVERT: Q 105 GLU cc_start: 0.8758 (pt0) cc_final: 0.8495 (pp20) REVERT: R 44 LYS cc_start: 0.6940 (tttm) cc_final: 0.6295 (ttmt) REVERT: R 79 LYS cc_start: 0.6871 (mptt) cc_final: 0.6334 (mmtt) REVERT: S 78 ILE cc_start: 0.9051 (mm) cc_final: 0.8770 (pt) REVERT: S 90 ASP cc_start: 0.6847 (t0) cc_final: 0.6507 (t0) REVERT: S 101 THR cc_start: 0.7406 (m) cc_final: 0.7065 (p) REVERT: S 104 GLN cc_start: 0.8822 (mt0) cc_final: 0.8392 (mm-40) REVERT: T 69 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7650 (tp) REVERT: T 80 LEU cc_start: 0.8607 (mt) cc_final: 0.8245 (mt) REVERT: A 201 LYS cc_start: 0.8395 (mmpt) cc_final: 0.8107 (mtmm) REVERT: A 249 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8484 (mtm-85) REVERT: B 249 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.8227 (tpp80) REVERT: B 259 MET cc_start: 0.8846 (ttm) cc_final: 0.8531 (ttm) REVERT: B 291 ILE cc_start: 0.9452 (mt) cc_final: 0.9222 (tt) REVERT: D 187 VAL cc_start: 0.9473 (t) cc_final: 0.9158 (p) REVERT: D 203 SER cc_start: 0.9048 (m) cc_final: 0.8640 (p) REVERT: F 162 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (p) REVERT: F 231 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: F 264 ASP cc_start: 0.8221 (t0) cc_final: 0.7732 (t0) REVERT: F 320 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: F 446 TYR cc_start: 0.7810 (m-10) cc_final: 0.7534 (m-80) REVERT: G 545 MET cc_start: 0.8091 (mpp) cc_final: 0.7788 (mpp) REVERT: G 599 TRP cc_start: 0.7323 (p-90) cc_final: 0.7023 (p-90) REVERT: G 653 GLU cc_start: 0.8408 (tp30) cc_final: 0.7991 (mm-30) REVERT: G 1194 TYR cc_start: 0.8552 (t80) cc_final: 0.7957 (t80) REVERT: H 173 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7420 (mm-30) REVERT: J 135 THR cc_start: 0.8906 (m) cc_final: 0.8621 (p) REVERT: J 242 MET cc_start: 0.8984 (mmp) cc_final: 0.8548 (mmm) outliers start: 111 outliers final: 46 residues processed: 729 average time/residue: 0.2800 time to fit residues: 332.6206 Evaluate side-chains 571 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 519 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 64 ASN Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 643 ARG Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1138 VAL Chi-restraints excluded: chain G residue 1202 VAL Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 161 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 chunk 363 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 447 optimal weight: 8.9990 chunk 361 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 481 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 335 ASN E 25 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS M 68 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN Q 68 GLN ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 HIS A 247 ASN B 156 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN G 559 HIS G 685 GLN G 832 HIS ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 GLN ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 572 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.132769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089732 restraints weight = 84844.518| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.40 r_work: 0.3039 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44150 Z= 0.169 Angle : 0.684 10.089 60754 Z= 0.366 Chirality : 0.045 0.261 6895 Planarity : 0.004 0.058 6829 Dihedral : 22.301 177.733 8225 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.48 % Rotamer: Outliers : 2.96 % Allowed : 13.28 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4661 helix: 0.30 (0.11), residues: 2214 sheet: -0.58 (0.19), residues: 612 loop : -0.37 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 92 TYR 0.040 0.002 TYR R 72 PHE 0.022 0.002 PHE G 853 TRP 0.023 0.002 TRP G 599 HIS 0.013 0.001 HIS J 440 Details of bonding type rmsd covalent geometry : bond 0.00382 (44150) covalent geometry : angle 0.68369 (60754) hydrogen bonds : bond 0.04459 ( 1960) hydrogen bonds : angle 4.31275 ( 5312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 587 time to evaluate : 1.608 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: C 141 CYS cc_start: 0.8689 (t) cc_final: 0.8455 (t) REVERT: C 153 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 216 GLU cc_start: 0.7755 (tp30) cc_final: 0.7233 (tp30) REVERT: C 260 MET cc_start: 0.8607 (mmm) cc_final: 0.8232 (tpt) REVERT: C 286 TYR cc_start: 0.9083 (m-10) cc_final: 0.8845 (m-80) REVERT: C 363 THR cc_start: 0.9304 (m) cc_final: 0.9098 (p) REVERT: E 168 MET cc_start: 0.8514 (tmm) cc_final: 0.8053 (tmm) REVERT: E 246 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: I 139 ARG cc_start: 0.6128 (mtt90) cc_final: 0.5898 (tpt170) REVERT: I 218 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8599 (mp) REVERT: M 61 LEU cc_start: 0.6309 (mt) cc_final: 0.6050 (tp) REVERT: M 67 PHE cc_start: 0.7928 (t80) cc_final: 0.7280 (t80) REVERT: M 73 GLU cc_start: 0.8024 (tt0) cc_final: 0.7001 (tp30) REVERT: M 93 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8527 (tp-100) REVERT: M 94 GLU cc_start: 0.8373 (tp30) cc_final: 0.7890 (tp30) REVERT: M 97 GLU cc_start: 0.8169 (pp20) cc_final: 0.7772 (pp20) REVERT: M 115 LYS cc_start: 0.7284 (tptt) cc_final: 0.6866 (ptpp) REVERT: N 25 ASN cc_start: 0.7403 (m-40) cc_final: 0.6302 (t0) REVERT: N 26 ILE cc_start: 0.8328 (mt) cc_final: 0.7534 (mt) REVERT: N 59 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8152 (mmtp) REVERT: O 73 ASN cc_start: 0.7424 (t0) cc_final: 0.6668 (p0) REVERT: P 54 ILE cc_start: 0.4751 (OUTLIER) cc_final: 0.4285 (tp) REVERT: P 62 MET cc_start: 0.9063 (tpp) cc_final: 0.8773 (tmm) REVERT: P 65 PHE cc_start: 0.8812 (t80) cc_final: 0.8574 (t80) REVERT: P 94 ILE cc_start: 0.9041 (tp) cc_final: 0.8560 (tp) REVERT: P 95 GLN cc_start: 0.8681 (mt0) cc_final: 0.8258 (mt0) REVERT: P 109 HIS cc_start: 0.7938 (m90) cc_final: 0.7351 (m90) REVERT: P 113 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7486 (tt0) REVERT: Q 105 GLU cc_start: 0.8748 (pt0) cc_final: 0.8420 (pp20) REVERT: R 44 LYS cc_start: 0.6991 (tttm) cc_final: 0.6556 (ttmt) REVERT: R 79 LYS cc_start: 0.7113 (mptt) cc_final: 0.6576 (mmtt) REVERT: S 61 GLU cc_start: 0.8794 (tm-30) cc_final: 0.7692 (pt0) REVERT: S 78 ILE cc_start: 0.9035 (mm) cc_final: 0.8809 (pt) REVERT: S 93 LEU cc_start: 0.8359 (mp) cc_final: 0.7937 (mm) REVERT: S 101 THR cc_start: 0.7180 (m) cc_final: 0.6973 (p) REVERT: S 104 GLN cc_start: 0.8909 (mt0) cc_final: 0.8238 (mm-40) REVERT: T 45 LEU cc_start: 0.7809 (tp) cc_final: 0.7577 (tp) REVERT: A 249 ARG cc_start: 0.8769 (mtp-110) cc_final: 0.8433 (mtm-85) REVERT: A 271 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9054 (mm) REVERT: A 397 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 259 MET cc_start: 0.8803 (ttm) cc_final: 0.8488 (ttm) REVERT: B 291 ILE cc_start: 0.9380 (mt) cc_final: 0.8963 (tt) REVERT: D 146 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 203 SER cc_start: 0.9046 (m) cc_final: 0.8659 (p) REVERT: D 235 ARG cc_start: 0.8730 (tpp80) cc_final: 0.8389 (tpp-160) REVERT: F 264 ASP cc_start: 0.8250 (t0) cc_final: 0.7722 (t0) REVERT: F 392 ARG cc_start: 0.8717 (ttm110) cc_final: 0.8394 (ttm110) REVERT: G 549 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5769 (mttp) REVERT: G 653 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: G 1086 SER cc_start: 0.8695 (t) cc_final: 0.8484 (m) REVERT: G 1194 TYR cc_start: 0.8472 (t80) cc_final: 0.8135 (t80) REVERT: H 223 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7485 (ptp-170) REVERT: H 234 HIS cc_start: 0.5909 (m170) cc_final: 0.5675 (m170) REVERT: H 235 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8350 (pttm) REVERT: J 99 ASP cc_start: 0.7902 (t0) cc_final: 0.7631 (t0) REVERT: J 101 ASN cc_start: 0.5090 (OUTLIER) cc_final: 0.4796 (t0) REVERT: J 135 THR cc_start: 0.8913 (m) cc_final: 0.8635 (p) outliers start: 119 outliers final: 52 residues processed: 661 average time/residue: 0.2664 time to fit residues: 291.7327 Evaluate side-chains 573 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 510 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 549 LYS Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 643 ARG Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain H residue 235 LYS Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 359 optimal weight: 0.6980 chunk 469 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 228 optimal weight: 0.2980 chunk 403 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN R 75 HIS T 84 ASN T 95 GLN ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS B 156 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 GLN J 37 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 GLN J 212 ASN J 249 HIS ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.133436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089068 restraints weight = 84877.431| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.99 r_work: 0.3066 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 44150 Z= 0.145 Angle : 0.645 10.990 60754 Z= 0.343 Chirality : 0.043 0.216 6895 Planarity : 0.004 0.049 6829 Dihedral : 22.178 179.870 8221 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 2.69 % Allowed : 14.22 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4661 helix: 0.51 (0.11), residues: 2219 sheet: -0.61 (0.19), residues: 613 loop : -0.35 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1209 TYR 0.042 0.002 TYR R 72 PHE 0.022 0.001 PHE G 853 TRP 0.024 0.002 TRP G 712 HIS 0.012 0.001 HIS J 440 Details of bonding type rmsd covalent geometry : bond 0.00321 (44150) covalent geometry : angle 0.64495 (60754) hydrogen bonds : bond 0.04024 ( 1960) hydrogen bonds : angle 4.14544 ( 5312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 561 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.8802 (mmm) cc_final: 0.8115 (mmm) REVERT: C 102 TYR cc_start: 0.8992 (m-80) cc_final: 0.8613 (m-80) REVERT: C 141 CYS cc_start: 0.8429 (t) cc_final: 0.8169 (t) REVERT: C 260 MET cc_start: 0.8585 (mmm) cc_final: 0.8164 (tpt) REVERT: C 286 TYR cc_start: 0.9063 (m-10) cc_final: 0.8736 (m-80) REVERT: C 363 THR cc_start: 0.9327 (m) cc_final: 0.9078 (p) REVERT: E 168 MET cc_start: 0.8553 (tmm) cc_final: 0.8193 (ttt) REVERT: I 139 ARG cc_start: 0.6057 (mtt90) cc_final: 0.5809 (tpt170) REVERT: M 67 PHE cc_start: 0.7772 (t80) cc_final: 0.7218 (t80) REVERT: M 115 LYS cc_start: 0.7421 (tptt) cc_final: 0.7028 (ptpp) REVERT: N 25 ASN cc_start: 0.7425 (m-40) cc_final: 0.6835 (t0) REVERT: N 59 LYS cc_start: 0.8813 (pttp) cc_final: 0.8446 (pptt) REVERT: N 96 THR cc_start: 0.8586 (t) cc_final: 0.8306 (p) REVERT: O 95 LYS cc_start: 0.7571 (tmtt) cc_final: 0.7077 (mmtt) REVERT: P 62 MET cc_start: 0.8984 (tpp) cc_final: 0.8779 (tmm) REVERT: P 92 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8178 (ttt180) REVERT: P 95 GLN cc_start: 0.8655 (mt0) cc_final: 0.8317 (mt0) REVERT: P 101 LEU cc_start: 0.7020 (mp) cc_final: 0.6234 (mp) REVERT: P 109 HIS cc_start: 0.8004 (m90) cc_final: 0.7457 (m90) REVERT: P 113 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7499 (tt0) REVERT: Q 105 GLU cc_start: 0.8742 (pt0) cc_final: 0.8473 (pp20) REVERT: R 44 LYS cc_start: 0.6934 (tttm) cc_final: 0.6508 (ttmt) REVERT: R 79 LYS cc_start: 0.7025 (mptt) cc_final: 0.6586 (mmtt) REVERT: R 88 TYR cc_start: 0.8485 (m-10) cc_final: 0.7957 (m-10) REVERT: S 56 GLU cc_start: 0.8960 (tp30) cc_final: 0.8758 (tp30) REVERT: S 61 GLU cc_start: 0.8870 (tm-30) cc_final: 0.7985 (pt0) REVERT: S 90 ASP cc_start: 0.6431 (t70) cc_final: 0.6202 (t70) REVERT: S 93 LEU cc_start: 0.8196 (mp) cc_final: 0.7961 (mm) REVERT: S 104 GLN cc_start: 0.8858 (mt0) cc_final: 0.8625 (mm-40) REVERT: T 120 LYS cc_start: 0.8646 (mmtp) cc_final: 0.8445 (mmtp) REVERT: A 249 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8361 (mtm-85) REVERT: A 271 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9021 (mm) REVERT: A 382 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: B 186 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: B 233 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8218 (mm-30) REVERT: B 259 MET cc_start: 0.8791 (ttm) cc_final: 0.8492 (ttm) REVERT: B 291 ILE cc_start: 0.9362 (mt) cc_final: 0.8923 (tt) REVERT: D 203 SER cc_start: 0.9074 (m) cc_final: 0.8693 (p) REVERT: F 264 ASP cc_start: 0.8516 (t0) cc_final: 0.7980 (t0) REVERT: F 303 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (mpp) REVERT: F 392 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8416 (ttm110) REVERT: F 443 MET cc_start: 0.8714 (ttp) cc_final: 0.8489 (ttt) REVERT: G 643 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6057 (ptm-80) REVERT: G 653 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: G 823 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7238 (pt0) REVERT: G 1123 TYR cc_start: 0.9105 (m-80) cc_final: 0.8738 (m-10) REVERT: J 99 ASP cc_start: 0.7930 (t0) cc_final: 0.7683 (t0) REVERT: J 101 ASN cc_start: 0.5185 (OUTLIER) cc_final: 0.4924 (t0) REVERT: J 135 THR cc_start: 0.8842 (m) cc_final: 0.8575 (p) outliers start: 108 outliers final: 56 residues processed: 628 average time/residue: 0.2559 time to fit residues: 265.7404 Evaluate side-chains 559 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 496 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 110 CYS Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 643 ARG Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 418 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 484 optimal weight: 6.9990 chunk 371 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 420 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 417 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 565 ASN G 625 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087071 restraints weight = 84466.641| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.34 r_work: 0.3001 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 44150 Z= 0.210 Angle : 0.659 8.909 60754 Z= 0.348 Chirality : 0.044 0.213 6895 Planarity : 0.004 0.049 6829 Dihedral : 22.071 177.980 8220 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.39 % Favored : 96.46 % Rotamer: Outliers : 3.28 % Allowed : 15.07 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4661 helix: 0.54 (0.11), residues: 2227 sheet: -0.71 (0.19), residues: 625 loop : -0.38 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 353 TYR 0.038 0.002 TYR R 72 PHE 0.024 0.002 PHE D 311 TRP 0.023 0.002 TRP G 712 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00490 (44150) covalent geometry : angle 0.65852 (60754) hydrogen bonds : bond 0.04145 ( 1960) hydrogen bonds : angle 4.18125 ( 5312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 517 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.8895 (mmm) cc_final: 0.8170 (mmm) REVERT: C 141 CYS cc_start: 0.8468 (t) cc_final: 0.8239 (t) REVERT: C 259 MET cc_start: 0.8521 (mtm) cc_final: 0.8246 (mtm) REVERT: C 260 MET cc_start: 0.8651 (mmm) cc_final: 0.8284 (tpt) REVERT: E 168 MET cc_start: 0.8542 (tmm) cc_final: 0.8269 (ttt) REVERT: E 246 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: I 139 ARG cc_start: 0.6003 (mtt90) cc_final: 0.5712 (tpt170) REVERT: M 76 GLN cc_start: 0.8315 (pp30) cc_final: 0.7857 (tp-100) REVERT: M 99 TYR cc_start: 0.7804 (t80) cc_final: 0.7286 (t80) REVERT: M 115 LYS cc_start: 0.7538 (tptt) cc_final: 0.7172 (ptpp) REVERT: N 25 ASN cc_start: 0.7618 (m-40) cc_final: 0.6917 (t0) REVERT: N 59 LYS cc_start: 0.8845 (pttp) cc_final: 0.8539 (pptt) REVERT: N 96 THR cc_start: 0.8619 (t) cc_final: 0.8376 (p) REVERT: O 50 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7211 (t80) REVERT: O 95 LYS cc_start: 0.7543 (tmtt) cc_final: 0.7097 (mmtt) REVERT: P 92 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8191 (ttt-90) REVERT: P 95 GLN cc_start: 0.8731 (mt0) cc_final: 0.8180 (mt0) REVERT: P 101 LEU cc_start: 0.6832 (mp) cc_final: 0.6208 (mp) REVERT: P 109 HIS cc_start: 0.8050 (m90) cc_final: 0.7524 (m-70) REVERT: P 113 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7397 (tp30) REVERT: Q 105 GLU cc_start: 0.8751 (pt0) cc_final: 0.8486 (pp20) REVERT: R 44 LYS cc_start: 0.6708 (tttm) cc_final: 0.6086 (ttpt) REVERT: R 53 GLU cc_start: 0.5935 (tp30) cc_final: 0.5269 (tt0) REVERT: R 57 VAL cc_start: 0.8076 (t) cc_final: 0.7825 (m) REVERT: R 79 LYS cc_start: 0.7057 (mptt) cc_final: 0.6766 (mmtt) REVERT: S 56 GLU cc_start: 0.8995 (tp30) cc_final: 0.8694 (tt0) REVERT: S 61 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8090 (pt0) REVERT: S 93 LEU cc_start: 0.8199 (mp) cc_final: 0.7961 (mt) REVERT: S 104 GLN cc_start: 0.8823 (mt0) cc_final: 0.8298 (mm-40) REVERT: A 178 GLU cc_start: 0.8027 (tp30) cc_final: 0.7798 (tp30) REVERT: A 244 ASP cc_start: 0.8297 (m-30) cc_final: 0.8054 (m-30) REVERT: A 249 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8460 (mtm-85) REVERT: A 271 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9031 (mm) REVERT: A 382 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 397 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8840 (tt) REVERT: B 233 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 291 ILE cc_start: 0.9350 (mt) cc_final: 0.8941 (tt) REVERT: B 310 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: D 146 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 203 SER cc_start: 0.9106 (m) cc_final: 0.8771 (p) REVERT: F 264 ASP cc_start: 0.8588 (t0) cc_final: 0.8086 (t0) REVERT: F 303 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8761 (mpp) REVERT: F 392 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8418 (ttm110) REVERT: F 443 MET cc_start: 0.8821 (ttp) cc_final: 0.8592 (ttt) REVERT: G 545 MET cc_start: 0.8296 (mpp) cc_final: 0.7451 (mpp) REVERT: G 640 TYR cc_start: 0.7203 (m-80) cc_final: 0.6898 (m-10) REVERT: G 653 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: G 823 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7305 (pt0) REVERT: G 976 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8372 (t-90) REVERT: G 1064 ARG cc_start: 0.8530 (ppt170) cc_final: 0.8165 (ptm160) REVERT: J 65 CYS cc_start: 0.4718 (m) cc_final: 0.4355 (m) REVERT: J 99 ASP cc_start: 0.8030 (t0) cc_final: 0.7733 (t0) REVERT: J 101 ASN cc_start: 0.5080 (OUTLIER) cc_final: 0.4737 (t0) REVERT: J 135 THR cc_start: 0.8915 (m) cc_final: 0.8640 (p) outliers start: 132 outliers final: 80 residues processed: 610 average time/residue: 0.2584 time to fit residues: 262.9291 Evaluate side-chains 561 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 64 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 580 ASN Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1109 LEU Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 422 optimal weight: 1.9990 chunk 345 optimal weight: 0.9980 chunk 366 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 396 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 163 optimal weight: 0.2980 chunk 217 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.132345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088782 restraints weight = 84582.061| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.20 r_work: 0.3029 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44150 Z= 0.153 Angle : 0.631 10.103 60754 Z= 0.332 Chirality : 0.042 0.296 6895 Planarity : 0.004 0.050 6829 Dihedral : 21.932 179.241 8220 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.78 % Rotamer: Outliers : 3.08 % Allowed : 15.51 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4661 helix: 0.65 (0.11), residues: 2233 sheet: -0.72 (0.19), residues: 633 loop : -0.36 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 353 TYR 0.046 0.002 TYR T 83 PHE 0.021 0.001 PHE G 853 TRP 0.023 0.002 TRP G 599 HIS 0.007 0.001 HIS J 247 Details of bonding type rmsd covalent geometry : bond 0.00348 (44150) covalent geometry : angle 0.63107 (60754) hydrogen bonds : bond 0.03825 ( 1960) hydrogen bonds : angle 4.08578 ( 5312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 525 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.8814 (mmm) cc_final: 0.8135 (mmm) REVERT: C 259 MET cc_start: 0.8534 (mtm) cc_final: 0.8289 (mtm) REVERT: C 260 MET cc_start: 0.8620 (mmm) cc_final: 0.8253 (tpt) REVERT: C 409 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8797 (mp) REVERT: E 168 MET cc_start: 0.8526 (tmm) cc_final: 0.8285 (ttt) REVERT: E 246 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: I 139 ARG cc_start: 0.6028 (mtt90) cc_final: 0.5691 (tpt170) REVERT: M 50 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: M 76 GLN cc_start: 0.8199 (pp30) cc_final: 0.7775 (tp-100) REVERT: M 99 TYR cc_start: 0.7638 (t80) cc_final: 0.7037 (t80) REVERT: M 104 PHE cc_start: 0.7659 (m-10) cc_final: 0.7386 (m-10) REVERT: M 115 LYS cc_start: 0.7537 (tptt) cc_final: 0.7207 (ptpp) REVERT: N 25 ASN cc_start: 0.7498 (m-40) cc_final: 0.6971 (t0) REVERT: N 27 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6876 (tp-100) REVERT: N 59 LYS cc_start: 0.8851 (pttp) cc_final: 0.8562 (pptt) REVERT: O 50 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7150 (t80) REVERT: O 95 LYS cc_start: 0.7527 (tmtt) cc_final: 0.7076 (mmtt) REVERT: P 92 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8078 (ttt-90) REVERT: P 95 GLN cc_start: 0.8779 (tt0) cc_final: 0.8199 (mt0) REVERT: P 101 LEU cc_start: 0.6647 (mp) cc_final: 0.6113 (mp) REVERT: P 109 HIS cc_start: 0.8049 (m90) cc_final: 0.7592 (m-70) REVERT: P 113 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7322 (tp30) REVERT: Q 105 GLU cc_start: 0.8751 (pt0) cc_final: 0.8485 (pp20) REVERT: R 44 LYS cc_start: 0.6673 (tttm) cc_final: 0.6094 (ttpt) REVERT: R 79 LYS cc_start: 0.6984 (mptt) cc_final: 0.6733 (mmtt) REVERT: R 95 ARG cc_start: 0.5663 (ttm-80) cc_final: 0.5462 (ttm-80) REVERT: S 61 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8130 (pt0) REVERT: S 78 ILE cc_start: 0.8900 (mm) cc_final: 0.8466 (tp) REVERT: S 93 LEU cc_start: 0.8246 (mp) cc_final: 0.7461 (mt) REVERT: S 104 GLN cc_start: 0.8774 (mt0) cc_final: 0.8537 (mm-40) REVERT: A 244 ASP cc_start: 0.8322 (m-30) cc_final: 0.8099 (m-30) REVERT: A 249 ARG cc_start: 0.8773 (mtp-110) cc_final: 0.8443 (mtm-85) REVERT: A 271 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8997 (mm) REVERT: A 382 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: D 203 SER cc_start: 0.9018 (m) cc_final: 0.8713 (p) REVERT: F 264 ASP cc_start: 0.8588 (t0) cc_final: 0.8154 (p0) REVERT: F 392 ARG cc_start: 0.8693 (ttm110) cc_final: 0.8436 (ttm170) REVERT: G 610 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: G 640 TYR cc_start: 0.7104 (m-80) cc_final: 0.6864 (m-10) REVERT: G 745 ARG cc_start: 0.4473 (OUTLIER) cc_final: 0.3503 (mmm160) REVERT: G 823 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7385 (pt0) REVERT: G 976 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.8296 (t-90) REVERT: G 1064 ARG cc_start: 0.8520 (ppt170) cc_final: 0.8174 (ptm160) REVERT: G 1123 TYR cc_start: 0.9070 (m-80) cc_final: 0.8799 (m-10) REVERT: G 1166 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7980 (mtp180) REVERT: J 65 CYS cc_start: 0.4881 (m) cc_final: 0.4635 (m) REVERT: J 99 ASP cc_start: 0.7994 (t0) cc_final: 0.7672 (t0) REVERT: J 101 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.5227 (t0) REVERT: J 135 THR cc_start: 0.8924 (m) cc_final: 0.8643 (p) outliers start: 124 outliers final: 73 residues processed: 609 average time/residue: 0.2467 time to fit residues: 246.7310 Evaluate side-chains 567 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 482 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 110 CYS Chi-restraints excluded: chain R residue 64 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 580 ASN Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 610 ARG Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1044 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1166 ARG Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 295 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 62 optimal weight: 0.0570 chunk 436 optimal weight: 0.0470 chunk 326 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 398 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 245 optimal weight: 0.0000 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS N 27 GLN R 64 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN T 95 GLN A 20 HIS ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 686 ASN G1027 ASN G1082 GLN G1142 HIS H 226 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 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 = 0.4014 r_free = 0.4014 target = 0.133875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.083222 restraints weight = 85572.209| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.29 r_work: 0.3016 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44150 Z= 0.128 Angle : 0.615 9.856 60754 Z= 0.323 Chirality : 0.041 0.299 6895 Planarity : 0.004 0.054 6829 Dihedral : 21.731 179.515 8220 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.92 % Favored : 96.93 % Rotamer: Outliers : 2.54 % Allowed : 16.24 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4661 helix: 0.78 (0.11), residues: 2228 sheet: -0.64 (0.20), residues: 624 loop : -0.31 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 353 TYR 0.049 0.001 TYR T 83 PHE 0.028 0.001 PHE M 67 TRP 0.023 0.001 TRP G 599 HIS 0.008 0.001 HIS J 247 Details of bonding type rmsd covalent geometry : bond 0.00279 (44150) covalent geometry : angle 0.61488 (60754) hydrogen bonds : bond 0.03569 ( 1960) hydrogen bonds : angle 3.95778 ( 5312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 547 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.8710 (mtm) cc_final: 0.8421 (mtm) REVERT: C 260 MET cc_start: 0.8670 (mmm) cc_final: 0.8329 (tpt) REVERT: C 267 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8862 (ttpp) REVERT: C 278 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8715 (mp0) REVERT: C 409 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 168 MET cc_start: 0.8504 (tmm) cc_final: 0.8151 (ttt) REVERT: E 317 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8569 (mt-10) REVERT: I 139 ARG cc_start: 0.6192 (mtt90) cc_final: 0.5655 (tpt170) REVERT: I 152 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.7626 (mmm-85) REVERT: M 50 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: M 76 GLN cc_start: 0.8551 (pp30) cc_final: 0.8098 (tp-100) REVERT: M 99 TYR cc_start: 0.7737 (t80) cc_final: 0.6958 (t80) REVERT: M 115 LYS cc_start: 0.7567 (tptt) cc_final: 0.7297 (ptpp) REVERT: N 25 ASN cc_start: 0.7743 (m-40) cc_final: 0.7066 (t0) REVERT: N 59 LYS cc_start: 0.8814 (pttp) cc_final: 0.8514 (pptt) REVERT: O 50 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7381 (t80) REVERT: O 95 LYS cc_start: 0.7553 (tmtt) cc_final: 0.7143 (mmtt) REVERT: P 92 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8291 (ttt-90) REVERT: P 95 GLN cc_start: 0.8739 (tt0) cc_final: 0.8208 (mt0) REVERT: P 101 LEU cc_start: 0.6672 (mp) cc_final: 0.6064 (mp) REVERT: P 109 HIS cc_start: 0.8142 (m90) cc_final: 0.7726 (m-70) REVERT: P 113 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7311 (tp30) REVERT: Q 54 TYR cc_start: 0.8157 (m-10) cc_final: 0.7875 (m-10) REVERT: Q 73 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: Q 85 GLN cc_start: 0.6653 (mm-40) cc_final: 0.6007 (tp40) REVERT: Q 105 GLU cc_start: 0.8753 (pt0) cc_final: 0.8505 (pp20) REVERT: R 35 ARG cc_start: 0.7033 (mtp-110) cc_final: 0.6521 (tmm160) REVERT: R 44 LYS cc_start: 0.6690 (tttm) cc_final: 0.6155 (ttmt) REVERT: R 53 GLU cc_start: 0.5874 (tp30) cc_final: 0.5463 (tp30) REVERT: R 79 LYS cc_start: 0.7213 (mptt) cc_final: 0.6954 (mmtt) REVERT: R 95 ARG cc_start: 0.5169 (ttm-80) cc_final: 0.4884 (ttm-80) REVERT: S 61 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8003 (pt0) REVERT: S 78 ILE cc_start: 0.8866 (mm) cc_final: 0.8444 (tp) REVERT: S 104 GLN cc_start: 0.8924 (mt0) cc_final: 0.8539 (mm-40) REVERT: T 35 GLU cc_start: 0.7954 (mp0) cc_final: 0.7720 (mp0) REVERT: A 244 ASP cc_start: 0.8699 (m-30) cc_final: 0.8356 (m-30) REVERT: A 249 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8244 (mtm-85) REVERT: A 346 SER cc_start: 0.9387 (t) cc_final: 0.9057 (p) REVERT: D 139 GLU cc_start: 0.8703 (pt0) cc_final: 0.8147 (pm20) REVERT: D 146 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7316 (tm-30) REVERT: D 203 SER cc_start: 0.9077 (m) cc_final: 0.8628 (p) REVERT: D 257 PHE cc_start: 0.8968 (p90) cc_final: 0.8751 (p90) REVERT: F 264 ASP cc_start: 0.8718 (t0) cc_final: 0.8069 (p0) REVERT: F 392 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8516 (ttm170) REVERT: G 526 MET cc_start: 0.6868 (ptt) cc_final: 0.5819 (mmt) REVERT: G 823 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7390 (pt0) REVERT: G 976 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8241 (t-90) REVERT: G 1008 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8521 (t) REVERT: G 1028 ASP cc_start: 0.8449 (t0) cc_final: 0.8086 (t0) REVERT: G 1064 ARG cc_start: 0.8481 (ppt170) cc_final: 0.7796 (ptm160) REVERT: G 1123 TYR cc_start: 0.9074 (m-80) cc_final: 0.8773 (m-10) REVERT: H 325 THR cc_start: 0.8968 (p) cc_final: 0.8576 (t) REVERT: J 65 CYS cc_start: 0.4815 (m) cc_final: 0.4493 (m) REVERT: J 99 ASP cc_start: 0.8022 (t0) cc_final: 0.7655 (t0) REVERT: J 101 ASN cc_start: 0.5214 (OUTLIER) cc_final: 0.4951 (t0) REVERT: J 135 THR cc_start: 0.8556 (m) cc_final: 0.8286 (p) outliers start: 102 outliers final: 53 residues processed: 614 average time/residue: 0.2478 time to fit residues: 250.1848 Evaluate side-chains 552 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 492 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 110 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 325 optimal weight: 0.7980 chunk 411 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 224 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS T 95 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.133232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082564 restraints weight = 85900.170| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.28 r_work: 0.3006 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44150 Z= 0.139 Angle : 0.625 11.750 60754 Z= 0.326 Chirality : 0.042 0.294 6895 Planarity : 0.004 0.053 6829 Dihedral : 21.610 179.742 8220 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.36 % Allowed : 17.01 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4661 helix: 0.80 (0.11), residues: 2235 sheet: -0.61 (0.19), residues: 626 loop : -0.31 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 353 TYR 0.067 0.002 TYR T 83 PHE 0.023 0.001 PHE M 104 TRP 0.022 0.001 TRP G 599 HIS 0.013 0.001 HIS T 109 Details of bonding type rmsd covalent geometry : bond 0.00313 (44150) covalent geometry : angle 0.62502 (60754) hydrogen bonds : bond 0.03602 ( 1960) hydrogen bonds : angle 3.92789 ( 5312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 518 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.8705 (mtm) cc_final: 0.8444 (mtm) REVERT: C 260 MET cc_start: 0.8648 (mmm) cc_final: 0.8195 (tpt) REVERT: C 267 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8860 (ttpp) REVERT: C 278 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8700 (mp0) REVERT: C 404 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7438 (mpp80) REVERT: C 409 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8705 (mp) REVERT: E 168 MET cc_start: 0.8490 (tmm) cc_final: 0.8169 (ttt) REVERT: E 317 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8569 (mt-10) REVERT: I 139 ARG cc_start: 0.6160 (mtt90) cc_final: 0.5641 (tpt170) REVERT: I 152 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: M 50 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: M 76 GLN cc_start: 0.8549 (pp30) cc_final: 0.8105 (tp-100) REVERT: M 94 GLU cc_start: 0.8583 (tp30) cc_final: 0.8305 (tp30) REVERT: M 99 TYR cc_start: 0.7645 (t80) cc_final: 0.6919 (t80) REVERT: M 115 LYS cc_start: 0.7625 (tptt) cc_final: 0.7351 (ptpp) REVERT: N 25 ASN cc_start: 0.7638 (m-40) cc_final: 0.7035 (t0) REVERT: N 59 LYS cc_start: 0.8832 (pttp) cc_final: 0.8516 (pptt) REVERT: O 50 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7318 (t80) REVERT: O 95 LYS cc_start: 0.7515 (tmtt) cc_final: 0.7139 (mmtt) REVERT: P 92 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8391 (ttt90) REVERT: P 95 GLN cc_start: 0.8749 (tt0) cc_final: 0.8208 (mt0) REVERT: P 101 LEU cc_start: 0.6661 (mp) cc_final: 0.6087 (mp) REVERT: P 105 GLU cc_start: 0.8264 (tp30) cc_final: 0.8033 (tt0) REVERT: P 109 HIS cc_start: 0.8166 (m90) cc_final: 0.7622 (m-70) REVERT: P 113 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7315 (tp30) REVERT: Q 54 TYR cc_start: 0.8088 (m-10) cc_final: 0.7761 (m-10) REVERT: Q 73 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: Q 85 GLN cc_start: 0.6626 (mm-40) cc_final: 0.5989 (tp40) REVERT: Q 93 GLN cc_start: 0.8461 (tt0) cc_final: 0.7208 (tp-100) REVERT: Q 105 GLU cc_start: 0.8751 (pt0) cc_final: 0.8496 (pp20) REVERT: R 35 ARG cc_start: 0.7096 (mtp-110) cc_final: 0.6564 (tmm160) REVERT: R 44 LYS cc_start: 0.6724 (tttm) cc_final: 0.6118 (ttpt) REVERT: R 53 GLU cc_start: 0.5934 (tp30) cc_final: 0.5435 (tt0) REVERT: R 79 LYS cc_start: 0.7208 (mptt) cc_final: 0.6961 (mmtt) REVERT: R 95 ARG cc_start: 0.5188 (ttm-80) cc_final: 0.4939 (ttm-80) REVERT: S 25 PHE cc_start: 0.7772 (m-80) cc_final: 0.7157 (m-10) REVERT: S 56 GLU cc_start: 0.8885 (tp30) cc_final: 0.8670 (tp30) REVERT: S 61 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8050 (pt0) REVERT: S 78 ILE cc_start: 0.8876 (mm) cc_final: 0.8483 (tp) REVERT: S 104 GLN cc_start: 0.8926 (mt0) cc_final: 0.8523 (mm-40) REVERT: T 35 GLU cc_start: 0.7996 (mp0) cc_final: 0.7763 (mp0) REVERT: T 46 LYS cc_start: 0.6776 (mmtt) cc_final: 0.6538 (mmtt) REVERT: A 178 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8418 (tp30) REVERT: A 244 ASP cc_start: 0.8690 (m-30) cc_final: 0.8383 (m-30) REVERT: A 249 ARG cc_start: 0.8954 (mtp-110) cc_final: 0.8304 (mtm-85) REVERT: A 346 SER cc_start: 0.9392 (t) cc_final: 0.9086 (p) REVERT: B 129 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: D 139 GLU cc_start: 0.8718 (pt0) cc_final: 0.8136 (pm20) REVERT: D 146 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7301 (tm-30) REVERT: D 203 SER cc_start: 0.9086 (m) cc_final: 0.8625 (p) REVERT: F 264 ASP cc_start: 0.8736 (t0) cc_final: 0.8131 (p0) REVERT: F 303 MET cc_start: 0.8630 (tpp) cc_final: 0.8383 (mpp) REVERT: F 392 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8507 (ttm170) REVERT: G 639 LYS cc_start: 0.8215 (mttm) cc_final: 0.7917 (ptpp) REVERT: G 655 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: G 745 ARG cc_start: 0.4511 (OUTLIER) cc_final: 0.4037 (mmm160) REVERT: G 823 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7419 (pt0) REVERT: G 976 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8267 (t-90) REVERT: G 1008 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8390 (t) REVERT: G 1010 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8661 (mp) REVERT: G 1028 ASP cc_start: 0.8526 (t0) cc_final: 0.8150 (t0) REVERT: G 1064 ARG cc_start: 0.8545 (ppt170) cc_final: 0.7791 (ptm160) REVERT: G 1123 TYR cc_start: 0.9110 (m-80) cc_final: 0.8655 (m-10) REVERT: H 325 THR cc_start: 0.8961 (p) cc_final: 0.8572 (t) REVERT: J 99 ASP cc_start: 0.8051 (t0) cc_final: 0.7664 (t0) REVERT: J 135 THR cc_start: 0.8551 (m) cc_final: 0.8295 (p) outliers start: 95 outliers final: 58 residues processed: 585 average time/residue: 0.2511 time to fit residues: 243.1137 Evaluate side-chains 557 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 488 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 962 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1010 LEU Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 114 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 226 optimal weight: 0.2980 chunk 347 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 432 optimal weight: 4.9990 chunk 419 optimal weight: 1.9990 chunk 263 optimal weight: 0.0970 chunk 381 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 636 GLN ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.081809 restraints weight = 85511.107| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.26 r_work: 0.2990 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 44150 Z= 0.155 Angle : 0.633 12.098 60754 Z= 0.329 Chirality : 0.042 0.327 6895 Planarity : 0.004 0.053 6829 Dihedral : 21.487 179.912 8220 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.04 % Allowed : 17.55 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4661 helix: 0.82 (0.11), residues: 2229 sheet: -0.72 (0.19), residues: 636 loop : -0.29 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 353 TYR 0.060 0.002 TYR T 83 PHE 0.025 0.001 PHE J 434 TRP 0.018 0.001 TRP G 712 HIS 0.012 0.001 HIS T 109 Details of bonding type rmsd covalent geometry : bond 0.00357 (44150) covalent geometry : angle 0.63254 (60754) hydrogen bonds : bond 0.03690 ( 1960) hydrogen bonds : angle 3.96112 ( 5312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 516 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 MET cc_start: 0.8673 (mtm) cc_final: 0.8410 (mtm) REVERT: C 260 MET cc_start: 0.8612 (mmm) cc_final: 0.8126 (tpt) REVERT: C 267 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8879 (ttpp) REVERT: C 404 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7342 (mpp80) REVERT: C 409 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8859 (mp) REVERT: E 147 ILE cc_start: 0.9403 (mm) cc_final: 0.9194 (mm) REVERT: E 168 MET cc_start: 0.8521 (tmm) cc_final: 0.8215 (ttt) REVERT: E 317 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8556 (mt-10) REVERT: I 139 ARG cc_start: 0.5823 (mtt90) cc_final: 0.5454 (tpt170) REVERT: I 152 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: M 50 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: M 97 GLU cc_start: 0.8857 (tp30) cc_final: 0.8577 (tp30) REVERT: M 99 TYR cc_start: 0.7386 (t80) cc_final: 0.6634 (t80) REVERT: M 115 LYS cc_start: 0.7708 (tptt) cc_final: 0.7426 (ptpp) REVERT: N 25 ASN cc_start: 0.7687 (m-40) cc_final: 0.7014 (t0) REVERT: N 57 VAL cc_start: 0.8451 (p) cc_final: 0.8207 (p) REVERT: N 59 LYS cc_start: 0.8778 (pttp) cc_final: 0.8441 (pptt) REVERT: O 50 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7328 (t80) REVERT: O 95 LYS cc_start: 0.7554 (tmtt) cc_final: 0.7188 (mmtt) REVERT: P 92 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8420 (ttt90) REVERT: P 95 GLN cc_start: 0.8713 (tt0) cc_final: 0.8184 (mt0) REVERT: P 101 LEU cc_start: 0.6623 (mp) cc_final: 0.6077 (mp) REVERT: P 105 GLU cc_start: 0.8252 (tp30) cc_final: 0.8004 (tt0) REVERT: P 109 HIS cc_start: 0.8156 (m90) cc_final: 0.7597 (m-70) REVERT: P 113 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7363 (tp30) REVERT: Q 54 TYR cc_start: 0.7954 (m-10) cc_final: 0.7540 (m-10) REVERT: Q 85 GLN cc_start: 0.6637 (mm-40) cc_final: 0.5934 (tp40) REVERT: Q 93 GLN cc_start: 0.8424 (tt0) cc_final: 0.7229 (tp-100) REVERT: Q 105 GLU cc_start: 0.8778 (pt0) cc_final: 0.8575 (pp20) REVERT: Q 122 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7727 (pttt) REVERT: R 35 ARG cc_start: 0.7073 (mtp-110) cc_final: 0.6395 (tmm160) REVERT: R 44 LYS cc_start: 0.6687 (tttm) cc_final: 0.6045 (ttpt) REVERT: R 72 TYR cc_start: 0.8293 (m-80) cc_final: 0.7010 (t80) REVERT: R 79 LYS cc_start: 0.7199 (mptt) cc_final: 0.6955 (mmtt) REVERT: R 95 ARG cc_start: 0.5105 (ttm-80) cc_final: 0.4855 (ttm-80) REVERT: S 25 PHE cc_start: 0.7839 (m-80) cc_final: 0.7132 (m-10) REVERT: S 56 GLU cc_start: 0.8945 (tp30) cc_final: 0.8541 (tp30) REVERT: S 61 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8071 (pt0) REVERT: S 78 ILE cc_start: 0.8914 (mm) cc_final: 0.8536 (tp) REVERT: S 104 GLN cc_start: 0.8816 (mt0) cc_final: 0.8497 (mm-40) REVERT: T 35 GLU cc_start: 0.7991 (mp0) cc_final: 0.7749 (mp0) REVERT: T 83 TYR cc_start: 0.6982 (m-80) cc_final: 0.6157 (m-80) REVERT: A 178 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8337 (tp30) REVERT: A 244 ASP cc_start: 0.8678 (m-30) cc_final: 0.8376 (m-30) REVERT: A 249 ARG cc_start: 0.8994 (mtp-110) cc_final: 0.8301 (mtm-85) REVERT: A 259 MET cc_start: 0.8015 (ttm) cc_final: 0.7747 (ttm) REVERT: A 346 SER cc_start: 0.9409 (t) cc_final: 0.9120 (p) REVERT: D 139 GLU cc_start: 0.8659 (pt0) cc_final: 0.8197 (pm20) REVERT: D 146 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7265 (tm-30) REVERT: D 203 SER cc_start: 0.9090 (m) cc_final: 0.8632 (p) REVERT: F 213 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8449 (tpp80) REVERT: F 264 ASP cc_start: 0.8753 (t0) cc_final: 0.8252 (p0) REVERT: F 303 MET cc_start: 0.8642 (tpp) cc_final: 0.8373 (mpp) REVERT: F 392 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8508 (ttm170) REVERT: G 639 LYS cc_start: 0.8229 (mttm) cc_final: 0.7981 (ptpp) REVERT: G 655 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: G 745 ARG cc_start: 0.4403 (OUTLIER) cc_final: 0.3943 (mmm160) REVERT: G 823 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7460 (pt0) REVERT: G 976 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8310 (t-90) REVERT: G 1010 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8693 (mp) REVERT: G 1028 ASP cc_start: 0.8571 (t0) cc_final: 0.8196 (t0) REVERT: G 1064 ARG cc_start: 0.8484 (ppt170) cc_final: 0.7738 (ptm160) REVERT: G 1123 TYR cc_start: 0.9148 (m-80) cc_final: 0.8640 (m-10) REVERT: H 272 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8271 (tpt) REVERT: H 325 THR cc_start: 0.8958 (p) cc_final: 0.8542 (t) REVERT: J 99 ASP cc_start: 0.8063 (t0) cc_final: 0.7747 (t0) REVERT: J 135 THR cc_start: 0.8578 (m) cc_final: 0.8315 (p) outliers start: 82 outliers final: 62 residues processed: 575 average time/residue: 0.2405 time to fit residues: 228.6359 Evaluate side-chains 557 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 485 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 122 LYS Chi-restraints excluded: chain R residue 64 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1010 LEU Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 151 optimal weight: 6.9990 chunk 467 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 474 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079998 restraints weight = 85478.445| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.24 r_work: 0.2952 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 44150 Z= 0.204 Angle : 0.668 12.396 60754 Z= 0.346 Chirality : 0.043 0.299 6895 Planarity : 0.004 0.051 6829 Dihedral : 21.473 179.805 8220 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 2.19 % Allowed : 17.60 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 4661 helix: 0.71 (0.11), residues: 2231 sheet: -0.74 (0.19), residues: 626 loop : -0.38 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 353 TYR 0.073 0.002 TYR T 83 PHE 0.026 0.002 PHE D 311 TRP 0.023 0.002 TRP G 599 HIS 0.008 0.001 HIS J 247 Details of bonding type rmsd covalent geometry : bond 0.00478 (44150) covalent geometry : angle 0.66812 (60754) hydrogen bonds : bond 0.03952 ( 1960) hydrogen bonds : angle 4.07038 ( 5312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9322 Ramachandran restraints generated. 4661 Oldfield, 0 Emsley, 4661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 492 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.9041 (mmm) cc_final: 0.8257 (mmm) REVERT: C 259 MET cc_start: 0.8676 (mtm) cc_final: 0.8421 (mtm) REVERT: C 260 MET cc_start: 0.8652 (mmm) cc_final: 0.8199 (tpt) REVERT: C 267 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8904 (ttpp) REVERT: C 404 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7474 (mpp80) REVERT: C 409 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8733 (mp) REVERT: E 168 MET cc_start: 0.8596 (tmm) cc_final: 0.8309 (ttt) REVERT: I 139 ARG cc_start: 0.5747 (mtt90) cc_final: 0.5386 (tpt170) REVERT: I 142 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7550 (mptt) REVERT: M 50 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: M 84 PHE cc_start: 0.7315 (m-80) cc_final: 0.6503 (m-10) REVERT: M 97 GLU cc_start: 0.8810 (tp30) cc_final: 0.8537 (tp30) REVERT: M 115 LYS cc_start: 0.7664 (tptt) cc_final: 0.7339 (ptpp) REVERT: N 25 ASN cc_start: 0.7697 (m-40) cc_final: 0.7034 (t0) REVERT: N 57 VAL cc_start: 0.8454 (p) cc_final: 0.8211 (p) REVERT: N 59 LYS cc_start: 0.8789 (pttp) cc_final: 0.8429 (pptt) REVERT: O 50 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7330 (t80) REVERT: O 95 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7137 (mmtt) REVERT: P 59 MET cc_start: 0.5783 (mmm) cc_final: 0.5204 (mmm) REVERT: P 92 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8422 (ttt90) REVERT: P 95 GLN cc_start: 0.8764 (tt0) cc_final: 0.8223 (mt0) REVERT: P 101 LEU cc_start: 0.6599 (mp) cc_final: 0.6050 (mp) REVERT: P 105 GLU cc_start: 0.8298 (tp30) cc_final: 0.8064 (tt0) REVERT: P 109 HIS cc_start: 0.8181 (m90) cc_final: 0.7676 (m-70) REVERT: P 113 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7491 (tt0) REVERT: Q 55 GLN cc_start: 0.6254 (mp10) cc_final: 0.6015 (mp10) REVERT: Q 93 GLN cc_start: 0.8300 (tt0) cc_final: 0.7094 (tp-100) REVERT: Q 105 GLU cc_start: 0.8781 (pt0) cc_final: 0.8573 (pp20) REVERT: R 35 ARG cc_start: 0.7166 (mtp-110) cc_final: 0.6814 (ttp80) REVERT: R 44 LYS cc_start: 0.6628 (tttm) cc_final: 0.6108 (ttmt) REVERT: R 53 GLU cc_start: 0.5829 (tp30) cc_final: 0.5296 (tt0) REVERT: R 57 VAL cc_start: 0.8032 (m) cc_final: 0.7822 (m) REVERT: R 72 TYR cc_start: 0.8351 (m-80) cc_final: 0.7028 (t80) REVERT: R 84 MET cc_start: 0.8908 (mmm) cc_final: 0.8136 (tmm) REVERT: R 88 TYR cc_start: 0.8506 (m-10) cc_final: 0.8003 (m-10) REVERT: R 95 ARG cc_start: 0.5207 (ttm-80) cc_final: 0.4945 (ttm-80) REVERT: S 56 GLU cc_start: 0.8875 (tp30) cc_final: 0.8476 (tp30) REVERT: S 61 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8079 (pt0) REVERT: S 78 ILE cc_start: 0.8921 (mm) cc_final: 0.8525 (tp) REVERT: T 35 GLU cc_start: 0.8038 (mp0) cc_final: 0.7768 (mp0) REVERT: T 105 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7648 (mm-30) REVERT: T 108 LYS cc_start: 0.8227 (pptt) cc_final: 0.7643 (ttpp) REVERT: A 178 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8317 (tp30) REVERT: A 207 ASP cc_start: 0.8997 (p0) cc_final: 0.8265 (t0) REVERT: A 244 ASP cc_start: 0.8716 (m-30) cc_final: 0.8422 (m-30) REVERT: A 249 ARG cc_start: 0.9020 (mtp-110) cc_final: 0.8352 (mtm-85) REVERT: A 346 SER cc_start: 0.9430 (t) cc_final: 0.9154 (p) REVERT: D 146 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7317 (tm-30) REVERT: D 203 SER cc_start: 0.9125 (m) cc_final: 0.8650 (p) REVERT: D 243 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8987 (p) REVERT: F 264 ASP cc_start: 0.8757 (t0) cc_final: 0.8305 (p0) REVERT: F 303 MET cc_start: 0.8726 (tpp) cc_final: 0.8315 (mpp) REVERT: F 392 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8528 (ttm170) REVERT: G 526 MET cc_start: 0.6939 (ptt) cc_final: 0.6566 (ppp) REVERT: G 639 LYS cc_start: 0.8223 (mttm) cc_final: 0.7968 (ptpp) REVERT: G 655 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: G 745 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.3917 (mmm160) REVERT: G 767 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8081 (pp) REVERT: G 823 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7468 (pt0) REVERT: G 976 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8430 (t-90) REVERT: G 1010 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8795 (mp) REVERT: G 1028 ASP cc_start: 0.8634 (t0) cc_final: 0.8300 (t0) REVERT: G 1064 ARG cc_start: 0.8526 (ppt170) cc_final: 0.7701 (ptm160) REVERT: H 235 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7787 (pttp) REVERT: J 65 CYS cc_start: 0.4992 (m) cc_final: 0.4617 (m) REVERT: J 94 LEU cc_start: 0.8170 (mt) cc_final: 0.7870 (mm) REVERT: J 99 ASP cc_start: 0.8140 (t0) cc_final: 0.7806 (t0) REVERT: J 135 THR cc_start: 0.8619 (m) cc_final: 0.8359 (p) REVERT: J 148 MET cc_start: 0.8942 (tpt) cc_final: 0.8731 (tpp) outliers start: 88 outliers final: 64 residues processed: 554 average time/residue: 0.2581 time to fit residues: 235.4941 Evaluate side-chains 549 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 475 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 64 ASN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 413 CYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 687 THR Chi-restraints excluded: chain G residue 712 TRP Chi-restraints excluded: chain G residue 743 MET Chi-restraints excluded: chain G residue 745 ARG Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 1010 LEU Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain H residue 325 THR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 233 HIS Chi-restraints excluded: chain J residue 488 VAL Chi-restraints excluded: chain J residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 271 optimal weight: 0.6980 chunk 404 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 442 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 419 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 334 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS D 121 GLN F 240 HIS ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082085 restraints weight = 85990.724| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.47 r_work: 0.2976 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44150 Z= 0.151 Angle : 0.637 12.514 60754 Z= 0.330 Chirality : 0.042 0.284 6895 Planarity : 0.004 0.052 6829 Dihedral : 21.385 179.208 8220 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 1.86 % Allowed : 18.05 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 4661 helix: 0.77 (0.11), residues: 2234 sheet: -0.74 (0.20), residues: 611 loop : -0.38 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 353 TYR 0.054 0.002 TYR T 83 PHE 0.026 0.001 PHE J 434 TRP 0.026 0.002 TRP G 599 HIS 0.007 0.001 HIS J 247 Details of bonding type rmsd covalent geometry : bond 0.00346 (44150) covalent geometry : angle 0.63650 (60754) hydrogen bonds : bond 0.03644 ( 1960) hydrogen bonds : angle 3.99644 ( 5312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15194.99 seconds wall clock time: 259 minutes 23.08 seconds (15563.08 seconds total)