Starting phenix.real_space_refine on Mon Aug 10 07:02:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gev_51307/08_2026/9gev_51307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gev_51307/08_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_51307/08_2026/9gev_51307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gev_51307/08_2026/9gev_51307.map" model { file = "/net/cci-nas-00/data/ceres_data/9gev_51307/08_2026/9gev_51307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gev_51307/08_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 8.67, per 1000 atoms: 0.20 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 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: 5.06 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: 13.31 Time building geometry restraints manager: 4.75 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=" C3' DC L -26 " pdb=" C2' DC L -26 " ideal model delta sigma weight residual 1.516 2.145 -0.629 8.00e-03 1.56e+04 6.18e+03 bond pdb=" C2' DC L -26 " pdb=" C1' DC L -26 " ideal model delta sigma weight residual 1.518 2.179 -0.661 1.00e-02 1.00e+04 4.37e+03 bond pdb=" C4' DC L -26 " pdb=" C3' DC L -26 " ideal model delta sigma weight residual 1.529 2.130 -0.601 1.00e-02 1.00e+04 3.61e+03 bond pdb=" O4' DC L -26 " pdb=" C1' DC L -26 " ideal model delta sigma weight residual 1.420 2.071 -0.651 1.10e-02 8.26e+03 3.50e+03 bond pdb=" C4' DC L -26 " pdb=" O4' DC L -26 " ideal model delta sigma weight residual 1.446 2.037 -0.591 1.00e-02 1.00e+04 3.49e+03 ... (remaining 44145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 57594 3.69 - 7.38: 3068 7.38 - 11.07: 76 11.07 - 14.76: 7 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=" O4' DC L -26 " pdb=" C1' DC L -26 " pdb=" N1 DC L -26 " ideal model delta sigma weight residual 108.00 118.26 -10.26 7.00e-01 2.04e+00 2.15e+02 angle pdb=" O5' DA L 24 " pdb=" C5' DA L 24 " pdb=" C4' DA L 24 " ideal model delta sigma weight residual 109.40 119.00 -9.60 8.00e-01 1.56e+00 1.44e+02 angle pdb=" O5' DA L 10 " pdb=" C5' DA L 10 " pdb=" C4' DA L 10 " ideal model delta sigma weight residual 109.40 118.90 -9.50 8.00e-01 1.56e+00 1.41e+02 ... (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 - 0.337: 6869 0.337 - 0.673: 23 0.673 - 1.010: 0 1.010 - 1.347: 1 1.347 - 1.683: 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 2.43 4.11 -1.68 2.00e-01 2.50e+01 7.08e+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 1.48 2.00e-01 2.50e+01 5.51e+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 -2.73 -3.79 1.06 2.00e-01 2.50e+01 2.81e+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: 4.830 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: 0.050 Extract box with map and model: 0.720 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 45.540 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.661 44150 Z= 1.160 Angle : 1.891 18.448 60754 Z= 1.492 Chirality : 0.101 1.683 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/Z covalent geometry : bond 0.01426 / 1.16 (44150) covalent geometry : angle 1.89108 / 1.49 (60754) hydrogen bonds : bond 0.15832 / 10.71 ( 1960) hydrogen bonds : angle 7.24316 / 5.08 ( 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 : 1.417 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: 0.8619 (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: 0.5308 (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: 0.7510 (t80) REVERT: M 76 GLN cc_start: 0.7895 (mt0) cc_final: 0.7632 (tp-100) REVERT: M 100 LEU cc_start: 0.9133 (mm) cc_final: 0.8780 (mm) REVERT: M 107 THR cc_start: 0.8552 (m) cc_final: 0.8305 (m) REVERT: M 113 HIS cc_start: 0.6171 (t70) cc_final: 0.5630 (t-90) REVERT: N 25 ASN cc_start: 0.7922 (m110) cc_final: 0.7537 (m110) REVERT: N 58 LEU cc_start: 0.8842 (tt) cc_final: 0.8548 (tt) REVERT: N 59 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8305 (mmtp) REVERT: N 80 THR cc_start: 0.7942 (m) cc_final: 0.7660 (m) 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: R 51 TYR cc_start: 0.5251 (m-80) cc_final: 0.4930 (m-80) 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: 0.6016 (t0) REVERT: S 92 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7136 (pt0) REVERT: S 100 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7589 (m) REVERT: S 101 THR cc_start: 0.7866 (m) cc_final: 0.7479 (p) REVERT: T 76 GLU cc_start: 0.7954 (tp30) cc_final: 0.7684 (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: 0.8492 (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: 0.8485 (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: 0.8028 (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: 0.7943 (t0) REVERT: J 128 VAL cc_start: 0.8752 (t) cc_final: 0.8520 (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: 0.2730 time to fit residues: 433.2355 Evaluate side-chains 615 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 595 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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: 5.9990 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... ** 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** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Q 93 GLN R 64 ASN T 82 HIS A 156 HIS A 247 ASN B 196 ASN B 392 ASN D 27 HIS D 92 GLN D 275 GLN F 49 GLN G 625 HIS G 954 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.133066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089472 restraints weight = 84608.194| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.42 r_work: 0.3047 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 44150 Z= 0.193 Angle : 0.847 12.231 60754 Z= 0.450 Chirality : 0.054 0.352 6895 Planarity : 0.005 0.055 6829 Dihedral : 22.486 175.008 8243 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.05 % Favored : 96.76 % Rotamer: Outliers : 2.64 % Allowed : 11.59 % Favored : 85.78 % 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: -0.80 (0.12), residues: 4661 helix: -0.24 (0.11), residues: 2201 sheet: -0.69 (0.19), residues: 631 loop : -0.61 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 17 TYR 0.035 0.003 TYR R 72 PHE 0.027 0.002 PHE D 311 TRP 0.049 0.003 TRP G 599 HIS 0.011 0.002 HIS P 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (44150) covalent geometry : angle 0.84677 / 0.45 (60754) hydrogen bonds : bond 0.05931 / 3.94 ( 1960) hydrogen bonds : angle 4.81207 / 3.40 ( 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 766 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 660 time to evaluate : 1.499 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: C 153 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8426 (p) REVERT: C 260 MET cc_start: 0.8620 (mmm) cc_final: 0.8173 (tpt) REVERT: E 148 ASP cc_start: 0.8005 (m-30) cc_final: 0.7697 (m-30) REVERT: E 168 MET cc_start: 0.8512 (tmm) cc_final: 0.7826 (tpp) REVERT: E 246 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: E 264 ASP cc_start: 0.8465 (t0) cc_final: 0.8186 (t0) REVERT: E 373 ILE cc_start: 0.9192 (tt) cc_final: 0.8911 (pt) REVERT: I 139 ARG cc_start: 0.6219 (mtt90) cc_final: 0.5969 (tpt170) REVERT: M 61 LEU cc_start: 0.7680 (mt) cc_final: 0.6572 (mt) REVERT: M 67 PHE cc_start: 0.7718 (t80) cc_final: 0.7515 (t80) REVERT: M 73 GLU cc_start: 0.7959 (tt0) cc_final: 0.6959 (tp30) REVERT: M 94 GLU cc_start: 0.8287 (tp30) cc_final: 0.7781 (tp30) REVERT: N 25 ASN cc_start: 0.7274 (m110) cc_final: 0.6391 (t0) REVERT: N 26 ILE cc_start: 0.8370 (mt) cc_final: 0.8143 (mt) REVERT: N 88 TYR cc_start: 0.8614 (m-80) cc_final: 0.8383 (m-80) REVERT: O 50 TYR cc_start: 0.8170 (m-80) cc_final: 0.7914 (m-80) REVERT: O 56 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8399 (tm-30) REVERT: O 73 ASN cc_start: 0.7352 (t0) cc_final: 0.6663 (p0) REVERT: O 95 LYS cc_start: 0.8550 (tttp) cc_final: 0.8315 (tmtt) REVERT: P 95 GLN cc_start: 0.8684 (mt0) cc_final: 0.8353 (mt0) REVERT: P 113 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7648 (pp20) REVERT: Q 50 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7171 (mt-10) REVERT: Q 105 GLU cc_start: 0.8783 (pt0) cc_final: 0.8526 (pp20) REVERT: R 44 LYS cc_start: 0.7070 (tttm) cc_final: 0.6378 (ttmt) REVERT: R 57 VAL cc_start: 0.7992 (t) cc_final: 0.7653 (m) REVERT: R 79 LYS cc_start: 0.6701 (mptt) cc_final: 0.6271 (mmtt) REVERT: S 78 ILE cc_start: 0.9051 (mm) cc_final: 0.8751 (pt) REVERT: S 90 ASP cc_start: 0.6974 (t0) cc_final: 0.6579 (t0) REVERT: S 101 THR cc_start: 0.7334 (m) cc_final: 0.6846 (p) REVERT: S 104 GLN cc_start: 0.8794 (mt0) cc_final: 0.8349 (mm-40) REVERT: T 45 LEU cc_start: 0.7747 (tp) cc_final: 0.7465 (tp) REVERT: T 69 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7561 (tp) REVERT: T 80 LEU cc_start: 0.8481 (mt) cc_final: 0.8168 (mt) REVERT: A 201 LYS cc_start: 0.8302 (mmpt) cc_final: 0.8011 (mtmm) REVERT: A 249 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8470 (mtm-85) REVERT: B 81 LEU cc_start: 0.9060 (mm) cc_final: 0.8855 (mt) REVERT: B 249 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8209 (tpp80) REVERT: B 259 MET cc_start: 0.8939 (ttm) cc_final: 0.8685 (ttm) REVERT: B 291 ILE cc_start: 0.9460 (mt) cc_final: 0.9101 (tt) REVERT: D 173 ASP cc_start: 0.8544 (m-30) cc_final: 0.8338 (m-30) REVERT: D 187 VAL cc_start: 0.9482 (t) cc_final: 0.9161 (p) REVERT: D 203 SER cc_start: 0.9038 (m) cc_final: 0.8621 (p) REVERT: F 231 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: F 264 ASP cc_start: 0.8169 (t0) cc_final: 0.7637 (t0) REVERT: F 392 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8423 (ttm110) REVERT: F 446 TYR cc_start: 0.7934 (m-10) cc_final: 0.7645 (m-80) REVERT: G 526 MET cc_start: 0.7952 (mmm) cc_final: 0.7726 (ptt) REVERT: G 653 GLU cc_start: 0.8402 (tp30) cc_final: 0.8035 (mm-30) REVERT: G 1194 TYR cc_start: 0.8387 (t80) cc_final: 0.8001 (t80) REVERT: H 173 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7455 (mm-30) REVERT: J 135 THR cc_start: 0.8813 (m) cc_final: 0.8590 (p) outliers start: 106 outliers final: 51 residues processed: 722 average time/residue: 0.2551 time to fit residues: 302.4552 Evaluate side-chains 584 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 529 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 ASP 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 71 THR 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 112 LEU Chi-restraints excluded: chain A residue 191 ILE 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 A residue 452 ASP 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 137 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 403 ILE 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 610 ARG 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 1138 VAL Chi-restraints excluded: chain G residue 1202 VAL 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: 30.0000 chunk 245 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 367 optimal weight: 8.9990 chunk 447 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 481 optimal weight: 3.9990 chunk 202 optimal weight: 0.4980 chunk 174 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 335 ASN ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 146 GLN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN G 832 HIS G 989 HIS H 234 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087210 restraints weight = 84670.005| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.39 r_work: 0.3001 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 44150 Z= 0.210 Angle : 0.768 9.739 60754 Z= 0.407 Chirality : 0.051 0.278 6895 Planarity : 0.005 0.048 6829 Dihedral : 22.547 176.050 8229 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Rotamer: Outliers : 3.11 % Allowed : 13.08 % Favored : 83.81 % 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: -0.51 (0.12), residues: 4661 helix: 0.09 (0.11), residues: 2207 sheet: -0.73 (0.19), residues: 622 loop : -0.53 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 851 TYR 0.036 0.002 TYR R 72 PHE 0.023 0.002 PHE M 78 TRP 0.027 0.002 TRP G 599 HIS 0.013 0.001 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (44150) covalent geometry : angle 0.76764 / 0.41 (60754) hydrogen bonds : bond 0.05135 / 3.40 ( 1960) hydrogen bonds : angle 4.53113 / 3.21 ( 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 689 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 564 time to evaluate : 1.831 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: 0.8706 (t) cc_final: 0.8470 (t) REVERT: C 153 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8498 (p) REVERT: C 218 GLU cc_start: 0.8127 (tp30) cc_final: 0.7916 (tt0) REVERT: C 260 MET cc_start: 0.8648 (mmm) cc_final: 0.8215 (tpt) REVERT: E 168 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8026 (tmm) REVERT: E 172 TYR cc_start: 0.8729 (m-80) cc_final: 0.8515 (m-80) REVERT: E 215 TYR cc_start: 0.6399 (t80) cc_final: 0.5965 (t80) REVERT: E 246 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: I 139 ARG cc_start: 0.6225 (mtt90) cc_final: 0.5969 (tpt170) REVERT: M 59 GLU cc_start: 0.7392 (pm20) cc_final: 0.7142 (mp0) REVERT: M 73 GLU cc_start: 0.7986 (tt0) cc_final: 0.6772 (tp30) REVERT: M 94 GLU cc_start: 0.8219 (tp30) cc_final: 0.7879 (tp30) REVERT: M 97 GLU cc_start: 0.8077 (pp20) cc_final: 0.7495 (pp20) REVERT: M 115 LYS cc_start: 0.7096 (tptt) cc_final: 0.6712 (pttm) REVERT: N 25 ASN cc_start: 0.7354 (m-40) cc_final: 0.6382 (t0) REVERT: N 26 ILE cc_start: 0.8352 (mt) cc_final: 0.8088 (mt) REVERT: O 50 TYR cc_start: 0.8025 (m-80) cc_final: 0.7045 (m-80) REVERT: O 56 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8060 (tm-30) REVERT: O 73 ASN cc_start: 0.7388 (t0) cc_final: 0.6692 (p0) REVERT: P 62 MET cc_start: 0.9092 (tpp) cc_final: 0.8862 (tmm) REVERT: P 95 GLN cc_start: 0.8677 (mt0) cc_final: 0.8043 (mt0) REVERT: P 109 HIS cc_start: 0.7714 (m90) cc_final: 0.7119 (m90) REVERT: P 113 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7678 (tt0) REVERT: P 118 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8162 (m) REVERT: Q 105 GLU cc_start: 0.8765 (pt0) cc_final: 0.8443 (pp20) REVERT: R 44 LYS cc_start: 0.7086 (tttm) cc_final: 0.6606 (ttmt) REVERT: R 79 LYS cc_start: 0.7187 (mptt) cc_final: 0.6656 (mmtt) REVERT: S 61 GLU cc_start: 0.8756 (tm-30) cc_final: 0.7884 (pt0) REVERT: S 90 ASP cc_start: 0.6732 (t0) cc_final: 0.6474 (t70) REVERT: S 92 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7000 (pt0) REVERT: S 101 THR cc_start: 0.7174 (m) cc_final: 0.6930 (p) REVERT: S 104 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8312 (mm-40) REVERT: T 69 ILE cc_start: 0.7761 (mm) cc_final: 0.7424 (tp) REVERT: A 214 ASP cc_start: 0.7836 (m-30) cc_final: 0.7046 (m-30) REVERT: A 249 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8513 (mtm-85) REVERT: A 271 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 397 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 259 MET cc_start: 0.8875 (ttm) cc_final: 0.8594 (ttm) REVERT: B 291 ILE cc_start: 0.9396 (mt) cc_final: 0.8986 (tt) REVERT: D 146 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7380 (tm-30) REVERT: D 173 ASP cc_start: 0.8737 (m-30) cc_final: 0.8413 (m-30) REVERT: D 203 SER cc_start: 0.9058 (m) cc_final: 0.8695 (p) REVERT: D 235 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8512 (tpp-160) REVERT: F 162 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8570 (p) REVERT: F 264 ASP cc_start: 0.8241 (t0) cc_final: 0.7675 (t0) REVERT: F 392 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8520 (ttm110) REVERT: G 545 MET cc_start: 0.8203 (mpp) cc_final: 0.7569 (mpp) REVERT: G 653 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8140 (mm-30) REVERT: G 823 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7114 (pt0) REVERT: G 1194 TYR cc_start: 0.8645 (t80) cc_final: 0.8163 (t80) REVERT: H 235 LYS cc_start: 0.8634 (ptpp) cc_final: 0.8174 (pttm) REVERT: J 99 ASP cc_start: 0.7960 (t0) cc_final: 0.7719 (t0) REVERT: J 101 ASN cc_start: 0.5079 (OUTLIER) cc_final: 0.4776 (t0) REVERT: J 135 THR cc_start: 0.8895 (m) cc_final: 0.8621 (p) outliers start: 125 outliers final: 66 residues processed: 642 average time/residue: 0.2486 time to fit residues: 266.2655 Evaluate side-chains 576 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 500 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 228 VAL 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 168 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 M residue 48 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR 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 P residue 118 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 110 CYS Chi-restraints excluded: chain S residue 104 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain T residue 101 LEU 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 259 MET Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 364 MET 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 171 ILE Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 142 VAL 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 271 GLU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 403 ILE 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 606 LYS Chi-restraints excluded: chain G residue 610 ARG 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 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 G residue 1202 VAL Chi-restraints excluded: chain H residue 283 THR 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 152 LEU Chi-restraints excluded: chain J residue 233 HIS 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: 0.8980 chunk 469 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 403 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 264 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 146 GLN ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS T 95 GLN ** T 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN A 229 HIS A 247 ASN A 373 GLN B 156 HIS B 247 ASN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 559 HIS H 226 GLN H 333 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS ** 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 = 0.3990 r_free = 0.3990 target = 0.132885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088611 restraints weight = 84343.076| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.10 r_work: 0.3040 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 44150 Z= 0.154 Angle : 0.695 9.740 60754 Z= 0.369 Chirality : 0.048 0.301 6895 Planarity : 0.004 0.075 6829 Dihedral : 22.515 176.608 8223 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 3.21 % Allowed : 13.58 % Favored : 83.22 % 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: -0.31 (0.12), residues: 4661 helix: 0.34 (0.11), residues: 2210 sheet: -0.80 (0.19), residues: 617 loop : -0.48 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 152 TYR 0.043 0.002 TYR R 72 PHE 0.022 0.001 PHE G 853 TRP 0.022 0.002 TRP G 712 HIS 0.013 0.001 HIS J 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (44150) covalent geometry : angle 0.69521 / 0.37 (60754) hydrogen bonds : bond 0.04549 / 3.01 ( 1960) hydrogen bonds : angle 4.32402 / 3.06 ( 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 701 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 572 time to evaluate : 1.285 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: C 141 CYS cc_start: 0.8679 (t) cc_final: 0.8461 (t) REVERT: C 153 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 216 GLU cc_start: 0.7629 (tp30) cc_final: 0.6806 (tp30) REVERT: C 260 MET cc_start: 0.8580 (mmm) cc_final: 0.8190 (tpt) REVERT: E 168 MET cc_start: 0.8543 (tmm) cc_final: 0.8227 (ttt) REVERT: E 246 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: M 61 LEU cc_start: 0.6504 (mt) cc_final: 0.6129 (tp) REVERT: M 73 GLU cc_start: 0.7939 (tt0) cc_final: 0.6815 (tp30) REVERT: M 115 LYS cc_start: 0.7323 (tptt) cc_final: 0.6843 (ptpp) REVERT: N 25 ASN cc_start: 0.7402 (m-40) cc_final: 0.6371 (t0) REVERT: N 26 ILE cc_start: 0.8312 (mt) cc_final: 0.8057 (mt) REVERT: N 27 GLN cc_start: 0.8145 (pt0) cc_final: 0.7939 (tp-100) REVERT: N 40 ARG cc_start: 0.7018 (ttt180) cc_final: 0.6652 (mtt180) REVERT: N 98 TYR cc_start: 0.7118 (m-10) cc_final: 0.6867 (m-80) REVERT: O 73 ASN cc_start: 0.7463 (t0) cc_final: 0.6646 (p0) REVERT: P 62 MET cc_start: 0.9052 (tpp) cc_final: 0.8812 (tmm) REVERT: P 94 ILE cc_start: 0.8976 (tp) cc_final: 0.8569 (tp) REVERT: P 95 GLN cc_start: 0.8581 (mt0) cc_final: 0.8329 (mt0) REVERT: P 109 HIS cc_start: 0.7773 (m90) cc_final: 0.7203 (m90) REVERT: P 113 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7486 (tt0) REVERT: Q 56 LYS cc_start: 0.8353 (tppt) cc_final: 0.7893 (tppp) REVERT: Q 105 GLU cc_start: 0.8730 (pt0) cc_final: 0.8410 (pp20) REVERT: R 44 LYS cc_start: 0.7057 (tttm) cc_final: 0.6601 (ttmt) REVERT: R 64 ASN cc_start: 0.7856 (m-40) cc_final: 0.7468 (m-40) REVERT: S 61 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8001 (pt0) REVERT: S 90 ASP cc_start: 0.6745 (t0) cc_final: 0.6254 (t70) REVERT: S 93 LEU cc_start: 0.8218 (mp) cc_final: 0.7775 (mm) REVERT: S 94 ASN cc_start: 0.6908 (t0) cc_final: 0.6225 (m-40) REVERT: S 101 THR cc_start: 0.7285 (m) cc_final: 0.7072 (p) REVERT: S 104 GLN cc_start: 0.8820 (mt0) cc_final: 0.8278 (mm-40) REVERT: A 214 ASP cc_start: 0.7749 (m-30) cc_final: 0.7046 (m-30) REVERT: A 249 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8438 (mtm-85) REVERT: A 353 ASP cc_start: 0.8541 (p0) cc_final: 0.8151 (p0) REVERT: A 382 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: B 233 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8147 (mm-30) REVERT: B 259 MET cc_start: 0.8850 (ttm) cc_final: 0.8550 (ttm) REVERT: B 291 ILE cc_start: 0.9360 (mt) cc_final: 0.8936 (tt) REVERT: D 146 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 173 ASP cc_start: 0.8703 (m-30) cc_final: 0.8406 (m-30) REVERT: D 203 SER cc_start: 0.9032 (m) cc_final: 0.8682 (p) REVERT: D 235 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8476 (tpp-160) REVERT: F 162 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8505 (p) REVERT: F 264 ASP cc_start: 0.8334 (t0) cc_final: 0.7847 (t0) REVERT: F 303 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8772 (mpp) REVERT: G 526 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7176 (ptp) REVERT: G 599 TRP cc_start: 0.7600 (p-90) cc_final: 0.6722 (p-90) REVERT: G 653 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: G 1159 MET cc_start: 0.8180 (mmt) cc_final: 0.7778 (mtt) REVERT: G 1194 TYR cc_start: 0.8507 (t80) cc_final: 0.8161 (t80) REVERT: H 235 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8154 (pttm) REVERT: J 99 ASP cc_start: 0.7883 (t0) cc_final: 0.7628 (t0) REVERT: J 101 ASN cc_start: 0.4943 (OUTLIER) cc_final: 0.4647 (t0) REVERT: J 135 THR cc_start: 0.8886 (m) cc_final: 0.8615 (p) REVERT: J 139 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7917 (t) outliers start: 129 outliers final: 72 residues processed: 653 average time/residue: 0.2488 time to fit residues: 270.7007 Evaluate side-chains 587 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 505 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 228 VAL 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 232 LEU 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 159 ASN Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 73 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 56 SER 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 259 MET Chi-restraints excluded: chain A residue 323 ILE 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 139 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 171 ILE Chi-restraints excluded: chain D residue 243 SER 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 162 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 303 MET 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 526 MET Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 606 LYS Chi-restraints excluded: chain G residue 610 ARG 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 957 LEU Chi-restraints excluded: chain G residue 981 SER 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 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 139 CYS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 233 HIS 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: 0.2980 chunk 233 optimal weight: 3.9990 chunk 246 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 484 optimal weight: 5.9990 chunk 371 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 420 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN E 25 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 196 ASN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 ASN ** J 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089131 restraints weight = 84112.272| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.32 r_work: 0.3043 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44150 Z= 0.142 Angle : 0.674 9.687 60754 Z= 0.355 Chirality : 0.047 0.477 6895 Planarity : 0.004 0.099 6829 Dihedral : 22.379 177.056 8221 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.33 % Favored : 96.52 % Rotamer: Outliers : 2.76 % Allowed : 14.69 % Favored : 82.55 % 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: 0.46 (0.11), residues: 2213 sheet: -0.72 (0.19), residues: 605 loop : -0.45 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1209 TYR 0.042 0.002 TYR R 72 PHE 0.026 0.001 PHE M 104 TRP 0.024 0.002 TRP G 712 HIS 0.018 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (44150) covalent geometry : angle 0.67446 / 0.36 (60754) hydrogen bonds : bond 0.04324 / 2.87 ( 1960) hydrogen bonds : angle 4.24464 / 3.00 ( 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 646 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 535 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 61 MET cc_start: 0.8753 (mmm) cc_final: 0.8004 (mmm) REVERT: C 141 CYS cc_start: 0.8535 (t) cc_final: 0.8301 (t) REVERT: C 153 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 259 MET cc_start: 0.8528 (mtm) cc_final: 0.8291 (mtm) REVERT: C 260 MET cc_start: 0.8617 (mmm) cc_final: 0.8250 (tpt) REVERT: C 409 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8755 (mp) REVERT: E 168 MET cc_start: 0.8487 (tmm) cc_final: 0.8191 (ttt) REVERT: E 215 TYR cc_start: 0.6398 (t80) cc_final: 0.5752 (t80) REVERT: E 246 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: I 157 GLN cc_start: 0.8012 (mp10) cc_final: 0.7727 (pm20) REVERT: M 50 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: M 61 LEU cc_start: 0.6377 (mt) cc_final: 0.6167 (tp) REVERT: M 73 GLU cc_start: 0.7792 (tt0) cc_final: 0.6897 (tp30) REVERT: M 115 LYS cc_start: 0.7446 (tptt) cc_final: 0.6984 (ptpp) REVERT: N 25 ASN cc_start: 0.7489 (m-40) cc_final: 0.6365 (t0) REVERT: N 26 ILE cc_start: 0.8327 (mt) cc_final: 0.8058 (mt) REVERT: N 27 GLN cc_start: 0.8176 (pt0) cc_final: 0.7963 (tp-100) REVERT: N 98 TYR cc_start: 0.7216 (m-10) cc_final: 0.7011 (m-80) REVERT: O 73 ASN cc_start: 0.7409 (t0) cc_final: 0.6627 (p0) REVERT: P 62 MET cc_start: 0.8974 (tpp) cc_final: 0.8760 (tmm) REVERT: P 95 GLN cc_start: 0.8573 (mt0) cc_final: 0.8327 (mt0) REVERT: P 109 HIS cc_start: 0.7920 (m90) cc_final: 0.7376 (m90) REVERT: P 113 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7259 (tp30) REVERT: Q 105 GLU cc_start: 0.8708 (pt0) cc_final: 0.8375 (pp20) REVERT: R 31 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7908 (mmtp) REVERT: R 44 LYS cc_start: 0.7026 (tttm) cc_final: 0.6356 (ttpt) REVERT: R 64 ASN cc_start: 0.7857 (m-40) cc_final: 0.7571 (m-40) REVERT: R 79 LYS cc_start: 0.6616 (mptt) cc_final: 0.6278 (tptp) REVERT: S 61 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8027 (pt0) REVERT: S 78 ILE cc_start: 0.9049 (mm) cc_final: 0.8823 (mm) REVERT: S 90 ASP cc_start: 0.6658 (t0) cc_final: 0.6249 (t70) REVERT: S 93 LEU cc_start: 0.8033 (mp) cc_final: 0.7580 (mm) REVERT: S 94 ASN cc_start: 0.6909 (t0) cc_final: 0.6187 (m-40) REVERT: S 101 THR cc_start: 0.7199 (m) cc_final: 0.6954 (p) REVERT: S 104 GLN cc_start: 0.8890 (mt0) cc_final: 0.8354 (mm-40) REVERT: A 214 ASP cc_start: 0.7830 (m-30) cc_final: 0.7030 (m-30) REVERT: A 244 ASP cc_start: 0.8308 (m-30) cc_final: 0.7984 (m-30) REVERT: A 249 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.8417 (mtm-85) REVERT: A 271 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.9011 (mm) REVERT: A 382 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 233 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 259 MET cc_start: 0.8842 (ttm) cc_final: 0.8536 (ttm) REVERT: B 291 ILE cc_start: 0.9356 (mt) cc_final: 0.8899 (tt) REVERT: B 310 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: D 173 ASP cc_start: 0.8742 (m-30) cc_final: 0.8387 (m-30) REVERT: D 203 SER cc_start: 0.9073 (m) cc_final: 0.8716 (p) REVERT: D 235 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8491 (tpp-160) REVERT: F 162 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8529 (p) REVERT: F 264 ASP cc_start: 0.8465 (t0) cc_final: 0.7900 (t0) REVERT: F 303 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8724 (mpp) REVERT: G 545 MET cc_start: 0.8198 (mpp) cc_final: 0.7940 (mpp) REVERT: G 653 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: G 690 GLU cc_start: 0.8211 (mp0) cc_final: 0.7909 (mp0) REVERT: G 823 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7149 (pt0) REVERT: H 235 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8124 (pttm) REVERT: J 99 ASP cc_start: 0.7956 (t0) cc_final: 0.7639 (t0) REVERT: J 101 ASN cc_start: 0.4915 (OUTLIER) cc_final: 0.4643 (t0) REVERT: J 135 THR cc_start: 0.8856 (m) cc_final: 0.8558 (p) REVERT: J 139 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7757 (t) outliers start: 111 outliers final: 70 residues processed: 603 average time/residue: 0.2626 time to fit residues: 263.5547 Evaluate side-chains 575 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 492 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 295 VAL 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 E residue 370 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 M residue 65 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 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 P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU 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 T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 139 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 310 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 73 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 243 SER 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 162 THR 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 316 LEU 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 580 ASN Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 606 LYS Chi-restraints excluded: chain G residue 610 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 957 LEU Chi-restraints excluded: chain G residue 1008 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1130 ILE Chi-restraints excluded: chain G residue 1136 TYR 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 139 CYS 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: 4.9990 chunk 345 optimal weight: 0.6980 chunk 366 optimal weight: 8.9990 chunk 196 optimal weight: 0.4980 chunk 187 optimal weight: 9.9990 chunk 396 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 270 optimal weight: 0.0670 chunk 163 optimal weight: 0.3980 chunk 217 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 348 HIS 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** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS B 156 HIS D 313 ASN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088636 restraints weight = 84529.943| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.22 r_work: 0.3067 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44150 Z= 0.131 Angle : 0.657 10.484 60754 Z= 0.346 Chirality : 0.046 0.324 6895 Planarity : 0.004 0.053 6829 Dihedral : 22.201 176.231 8221 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.78 % Rotamer: Outliers : 3.16 % Allowed : 15.09 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.12), residues: 4661 helix: 0.57 (0.11), residues: 2227 sheet: -0.63 (0.20), residues: 590 loop : -0.47 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 179 TYR 0.049 0.002 TYR R 72 PHE 0.024 0.001 PHE M 104 TRP 0.024 0.002 TRP G 712 HIS 0.021 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (44150) covalent geometry : angle 0.65719 / 0.35 (60754) hydrogen bonds : bond 0.04102 / 2.72 ( 1960) hydrogen bonds : angle 4.15296 / 2.93 ( 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 681 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 554 time to evaluate : 1.582 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: 0.8729 (mmm) cc_final: 0.7945 (mmm) REVERT: C 141 CYS cc_start: 0.8481 (t) cc_final: 0.8256 (t) REVERT: C 153 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 259 MET cc_start: 0.8447 (mtm) cc_final: 0.8201 (mtm) REVERT: C 260 MET cc_start: 0.8593 (mmm) cc_final: 0.8177 (tpt) REVERT: C 278 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8491 (mp0) REVERT: C 409 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8728 (mp) REVERT: E 168 MET cc_start: 0.8421 (tmm) cc_final: 0.8194 (ttt) REVERT: E 317 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8247 (mt-10) REVERT: M 73 GLU cc_start: 0.8062 (tt0) cc_final: 0.7412 (tp30) REVERT: M 76 GLN cc_start: 0.8407 (pp30) cc_final: 0.7781 (tp-100) REVERT: M 94 GLU cc_start: 0.8462 (tp30) cc_final: 0.7979 (tp30) REVERT: M 99 TYR cc_start: 0.7689 (t80) cc_final: 0.7213 (t80) REVERT: M 104 PHE cc_start: 0.7832 (m-10) cc_final: 0.7431 (m-10) REVERT: M 115 LYS cc_start: 0.7506 (tptt) cc_final: 0.7137 (ptpp) REVERT: N 25 ASN cc_start: 0.7449 (m-40) cc_final: 0.6331 (t0) REVERT: N 26 ILE cc_start: 0.8381 (mt) cc_final: 0.8141 (mt) REVERT: N 27 GLN cc_start: 0.8196 (pt0) cc_final: 0.7992 (tp-100) REVERT: P 73 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8006 (tt) REVERT: P 95 GLN cc_start: 0.8630 (mt0) cc_final: 0.8393 (mt0) REVERT: P 109 HIS cc_start: 0.7991 (m90) cc_final: 0.7248 (m90) REVERT: P 113 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7468 (tt0) REVERT: Q 105 GLU cc_start: 0.8720 (pt0) cc_final: 0.8435 (pp20) REVERT: R 31 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7780 (mmtp) REVERT: R 35 ARG cc_start: 0.6688 (mtp-110) cc_final: 0.6212 (tmm160) REVERT: R 44 LYS cc_start: 0.6981 (tttm) cc_final: 0.6516 (ttmt) REVERT: R 79 LYS cc_start: 0.6490 (mptt) cc_final: 0.5764 (mmtt) REVERT: S 61 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8058 (pt0) REVERT: S 93 LEU cc_start: 0.7903 (mp) cc_final: 0.7495 (mt) REVERT: S 94 ASN cc_start: 0.6906 (t0) cc_final: 0.6162 (m-40) REVERT: S 101 THR cc_start: 0.7169 (m) cc_final: 0.6861 (p) REVERT: S 104 GLN cc_start: 0.8905 (mt0) cc_final: 0.8479 (mm-40) REVERT: A 214 ASP cc_start: 0.7752 (m-30) cc_final: 0.6953 (m-30) REVERT: A 244 ASP cc_start: 0.8214 (m-30) cc_final: 0.7876 (m-30) REVERT: A 249 ARG cc_start: 0.8731 (mtp-110) cc_final: 0.8393 (mtm-85) REVERT: A 271 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8980 (mm) REVERT: A 397 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8703 (tt) REVERT: B 291 ILE cc_start: 0.9339 (mt) cc_final: 0.8894 (tt) REVERT: B 310 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: D 146 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7376 (tm-30) REVERT: D 173 ASP cc_start: 0.8660 (m-30) cc_final: 0.8308 (m-30) REVERT: D 203 SER cc_start: 0.9056 (m) cc_final: 0.8693 (p) REVERT: F 162 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8471 (p) REVERT: F 264 ASP cc_start: 0.8426 (t0) cc_final: 0.7892 (t0) REVERT: F 303 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: G 545 MET cc_start: 0.8193 (mpp) cc_final: 0.7573 (mpp) REVERT: G 690 GLU cc_start: 0.8235 (mp0) cc_final: 0.7866 (mp0) REVERT: G 823 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7213 (pt0) REVERT: G 1230 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8389 (tp) REVERT: H 235 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8103 (pttm) REVERT: H 325 THR cc_start: 0.8951 (p) cc_final: 0.8594 (t) REVERT: J 99 ASP cc_start: 0.7947 (t0) cc_final: 0.7615 (t0) REVERT: J 101 ASN cc_start: 0.5238 (OUTLIER) cc_final: 0.4963 (t0) REVERT: J 135 THR cc_start: 0.8854 (m) cc_final: 0.8592 (p) REVERT: J 139 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7730 (t) outliers start: 127 outliers final: 66 residues processed: 641 average time/residue: 0.2711 time to fit residues: 287.3351 Evaluate side-chains 586 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 508 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 409 LEU 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 I residue 159 ASN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 73 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 82 LEU 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 T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 310 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 73 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER 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 142 VAL Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 162 THR 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 316 LEU 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 580 ASN 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 712 TRP Chi-restraints excluded: chain G residue 767 LEU Chi-restraints excluded: chain G residue 905 MET 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 1130 ILE Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain G residue 1230 ILE Chi-restraints excluded: chain H residue 235 LYS 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 139 CYS Chi-restraints excluded: chain J residue 233 HIS 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: 0.9980 chunk 230 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 436 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 398 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN T 82 HIS ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS F 447 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.132082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086940 restraints weight = 84173.604| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.10 r_work: 0.3031 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 44150 Z= 0.175 Angle : 0.681 15.201 60754 Z= 0.355 Chirality : 0.046 0.325 6895 Planarity : 0.004 0.054 6829 Dihedral : 22.081 176.121 8221 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 2.76 % Allowed : 16.14 % Favored : 81.10 % 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: -0.09 (0.12), residues: 4661 helix: 0.57 (0.11), residues: 2238 sheet: -0.72 (0.19), residues: 641 loop : -0.43 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 205 TYR 0.045 0.002 TYR R 72 PHE 0.027 0.002 PHE D 311 TRP 0.020 0.001 TRP G 712 HIS 0.012 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (44150) covalent geometry : angle 0.68072 / 0.35 (60754) hydrogen bonds : bond 0.04217 / 2.79 ( 1960) hydrogen bonds : angle 4.17214 / 2.95 ( 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 647 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 536 time to evaluate : 1.724 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: 0.8824 (mmm) cc_final: 0.8001 (mmm) REVERT: C 141 CYS cc_start: 0.8401 (t) cc_final: 0.8165 (t) REVERT: C 259 MET cc_start: 0.8543 (mtm) cc_final: 0.8274 (mtm) REVERT: C 260 MET cc_start: 0.8615 (mmm) cc_final: 0.8195 (tpt) REVERT: C 409 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8789 (mp) REVERT: E 246 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: I 218 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8272 (mp) REVERT: M 50 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: M 94 GLU cc_start: 0.8408 (tp30) cc_final: 0.7865 (tp30) REVERT: M 99 TYR cc_start: 0.7683 (t80) cc_final: 0.7240 (t80) REVERT: M 115 LYS cc_start: 0.7537 (tptt) cc_final: 0.7169 (ptpp) REVERT: N 25 ASN cc_start: 0.7337 (m-40) cc_final: 0.6615 (t0) REVERT: N 27 GLN cc_start: 0.8227 (pt0) cc_final: 0.7946 (tp-100) REVERT: P 65 PHE cc_start: 0.8730 (t80) cc_final: 0.8502 (t80) REVERT: P 73 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8017 (tt) REVERT: P 95 GLN cc_start: 0.8706 (mt0) cc_final: 0.8439 (mt0) REVERT: P 105 GLU cc_start: 0.7111 (pp20) cc_final: 0.6838 (pp20) REVERT: P 109 HIS cc_start: 0.8030 (m90) cc_final: 0.7483 (m-70) REVERT: P 113 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7483 (tt0) REVERT: Q 105 GLU cc_start: 0.8736 (pt0) cc_final: 0.8489 (pp20) REVERT: R 31 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7786 (mmtp) REVERT: R 35 ARG cc_start: 0.6770 (mtp-110) cc_final: 0.6168 (tmm160) REVERT: R 44 LYS cc_start: 0.6886 (tttm) cc_final: 0.6273 (ttpt) REVERT: R 64 ASN cc_start: 0.7832 (m-40) cc_final: 0.7613 (m-40) REVERT: R 79 LYS cc_start: 0.6520 (mptt) cc_final: 0.5817 (mmtt) REVERT: R 88 TYR cc_start: 0.8573 (m-10) cc_final: 0.8337 (m-10) REVERT: S 61 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8200 (pt0) REVERT: S 78 ILE cc_start: 0.8889 (mm) cc_final: 0.8462 (tp) REVERT: S 93 LEU cc_start: 0.7966 (mp) cc_final: 0.7710 (mt) REVERT: S 101 THR cc_start: 0.7234 (m) cc_final: 0.6845 (p) REVERT: S 104 GLN cc_start: 0.8870 (mt0) cc_final: 0.8495 (mm-40) REVERT: A 214 ASP cc_start: 0.7805 (m-30) cc_final: 0.7067 (m-30) REVERT: A 244 ASP cc_start: 0.8300 (m-30) cc_final: 0.7981 (m-30) REVERT: A 249 ARG cc_start: 0.8829 (mtp-110) cc_final: 0.8437 (mtm-85) REVERT: A 271 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 397 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8760 (tt) REVERT: B 81 LEU cc_start: 0.9181 (mt) cc_final: 0.8975 (mt) REVERT: B 259 MET cc_start: 0.8975 (mtp) cc_final: 0.8750 (ttm) REVERT: B 291 ILE cc_start: 0.9362 (mt) cc_final: 0.8908 (tt) REVERT: B 310 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: D 146 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 173 ASP cc_start: 0.8737 (m-30) cc_final: 0.8325 (m-30) REVERT: D 203 SER cc_start: 0.9106 (m) cc_final: 0.8767 (p) REVERT: F 162 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8536 (p) REVERT: F 264 ASP cc_start: 0.8506 (t0) cc_final: 0.7968 (t0) REVERT: F 303 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: F 392 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8405 (ttm170) REVERT: G 823 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7240 (pt0) REVERT: G 976 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8261 (t-90) REVERT: H 235 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8011 (pttm) REVERT: H 325 THR cc_start: 0.9019 (p) cc_final: 0.8660 (t) REVERT: J 65 CYS cc_start: 0.4742 (m) cc_final: 0.4396 (m) REVERT: J 101 ASN cc_start: 0.5077 (OUTLIER) cc_final: 0.4751 (t0) REVERT: J 135 THR cc_start: 0.8856 (m) cc_final: 0.8589 (p) outliers start: 111 outliers final: 73 residues processed: 608 average time/residue: 0.2467 time to fit residues: 250.9139 Evaluate side-chains 574 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 488 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 194 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE 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 E residue 370 ILE 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 M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 73 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 68 ASP Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 139 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 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 171 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER 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 162 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 421 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 580 ASN Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 655 GLN Chi-restraints excluded: chain G residue 657 LEU 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 905 MET Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 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 G residue 1136 TYR Chi-restraints excluded: chain H residue 235 LYS 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 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 325 optimal weight: 0.8980 chunk 411 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 224 optimal weight: 0.9990 chunk 119 optimal weight: 50.0000 chunk 313 optimal weight: 0.6980 chunk 277 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 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 = 0.3997 r_free = 0.3997 target = 0.132670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082675 restraints weight = 84539.455| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.21 r_work: 0.3002 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44150 Z= 0.138 Angle : 0.657 12.026 60754 Z= 0.344 Chirality : 0.045 0.378 6895 Planarity : 0.004 0.054 6829 Dihedral : 21.960 175.949 8220 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % Rotamer: Outliers : 2.61 % Allowed : 16.53 % Favored : 80.86 % 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: -0.03 (0.12), residues: 4661 helix: 0.62 (0.11), residues: 2238 sheet: -0.69 (0.19), residues: 621 loop : -0.41 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 67 TYR 0.046 0.002 TYR T 83 PHE 0.022 0.001 PHE D 311 TRP 0.021 0.001 TRP G 712 HIS 0.011 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (44150) covalent geometry : angle 0.65691 / 0.34 (60754) hydrogen bonds : bond 0.04009 / 2.65 ( 1960) hydrogen bonds : angle 4.15078 / 2.93 ( 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 622 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 517 time to evaluate : 1.576 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: C 61 MET cc_start: 0.9029 (mmm) cc_final: 0.8153 (mmm) REVERT: C 141 CYS cc_start: 0.8281 (t) cc_final: 0.7878 (t) REVERT: C 259 MET cc_start: 0.8700 (mtm) cc_final: 0.8411 (mtm) REVERT: C 260 MET cc_start: 0.8658 (mmm) cc_final: 0.8290 (tpt) REVERT: C 409 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8726 (mp) REVERT: E 172 TYR cc_start: 0.8950 (m-80) cc_final: 0.8572 (m-80) REVERT: I 218 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7962 (mp) REVERT: M 50 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: M 94 GLU cc_start: 0.8481 (tp30) cc_final: 0.7861 (tp30) REVERT: M 99 TYR cc_start: 0.7682 (t80) cc_final: 0.7109 (t80) REVERT: M 115 LYS cc_start: 0.7505 (tptt) cc_final: 0.7194 (ptpp) REVERT: N 25 ASN cc_start: 0.7448 (m-40) cc_final: 0.6701 (t0) REVERT: N 27 GLN cc_start: 0.8374 (pt0) cc_final: 0.8008 (tp-100) REVERT: N 59 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7927 (mmtp) REVERT: P 65 PHE cc_start: 0.8733 (t80) cc_final: 0.8510 (t80) REVERT: P 73 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8176 (tt) REVERT: P 95 GLN cc_start: 0.8683 (mt0) cc_final: 0.8423 (mt0) REVERT: P 105 GLU cc_start: 0.7229 (pp20) cc_final: 0.6957 (pp20) REVERT: P 109 HIS cc_start: 0.8051 (m90) cc_final: 0.7489 (m-70) REVERT: P 113 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7341 (tp30) REVERT: Q 105 GLU cc_start: 0.8741 (pt0) cc_final: 0.8505 (pp20) REVERT: R 31 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7697 (mmtp) REVERT: R 35 ARG cc_start: 0.6949 (mtp-110) cc_final: 0.6396 (tmm160) REVERT: R 44 LYS cc_start: 0.6890 (tttm) cc_final: 0.6436 (ttpt) REVERT: R 64 ASN cc_start: 0.7886 (m-40) cc_final: 0.7646 (m-40) REVERT: R 79 LYS cc_start: 0.6726 (mptt) cc_final: 0.6084 (mmtt) REVERT: S 48 PRO cc_start: 0.8441 (Cg_exo) cc_final: 0.8232 (Cg_endo) REVERT: S 61 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8149 (pt0) REVERT: S 78 ILE cc_start: 0.8814 (mm) cc_final: 0.8405 (tp) REVERT: S 93 LEU cc_start: 0.7955 (mp) cc_final: 0.7740 (mt) REVERT: S 101 THR cc_start: 0.7049 (m) cc_final: 0.6696 (p) REVERT: S 104 GLN cc_start: 0.9038 (mt0) cc_final: 0.8513 (mm-40) REVERT: A 211 THR cc_start: 0.9301 (m) cc_final: 0.9041 (m) REVERT: A 214 ASP cc_start: 0.8083 (m-30) cc_final: 0.7122 (m-30) REVERT: A 244 ASP cc_start: 0.8671 (m-30) cc_final: 0.8220 (m-30) REVERT: A 249 ARG cc_start: 0.8972 (mtp-110) cc_final: 0.8272 (mtm-85) REVERT: A 271 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8914 (mm) REVERT: A 397 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8308 (tt) REVERT: B 310 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: D 173 ASP cc_start: 0.8763 (m-30) cc_final: 0.8065 (m-30) REVERT: D 203 SER cc_start: 0.9106 (m) cc_final: 0.8660 (p) REVERT: F 162 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8421 (p) REVERT: F 264 ASP cc_start: 0.8665 (t0) cc_final: 0.8064 (t0) REVERT: G 640 TYR cc_start: 0.7201 (m-80) cc_final: 0.6925 (m-10) REVERT: G 823 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7248 (pt0) REVERT: G 976 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8243 (t-90) REVERT: H 223 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7705 (ptp-170) REVERT: H 235 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8092 (pttm) REVERT: H 325 THR cc_start: 0.8993 (p) cc_final: 0.8639 (t) REVERT: J 65 CYS cc_start: 0.4655 (m) cc_final: 0.4225 (m) REVERT: J 101 ASN cc_start: 0.5163 (OUTLIER) cc_final: 0.4933 (t0) REVERT: J 135 THR cc_start: 0.8583 (m) cc_final: 0.8343 (p) outliers start: 105 outliers final: 70 residues processed: 582 average time/residue: 0.2606 time to fit residues: 254.7641 Evaluate side-chains 571 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 489 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 194 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE 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 I residue 218 LEU Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 73 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 R residue 96 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 364 MET 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 171 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER 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 162 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 F residue 451 LEU Chi-restraints excluded: chain G residue 573 ILE Chi-restraints excluded: chain G residue 580 ASN Chi-restraints excluded: chain G residue 649 MET Chi-restraints excluded: chain G residue 657 LEU 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 905 MET Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain H residue 235 LYS 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 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 114 optimal weight: 50.0000 chunk 169 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 347 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 432 optimal weight: 6.9990 chunk 419 optimal weight: 0.9990 chunk 263 optimal weight: 0.0670 chunk 381 optimal weight: 0.4980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 313 ASN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS A 20 HIS B 156 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.133103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083220 restraints weight = 84291.093| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.21 r_work: 0.3013 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- 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 = 0.61 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 = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 44150 Z= 0.135 Angle : 0.660 13.980 60754 Z= 0.344 Chirality : 0.045 0.304 6895 Planarity : 0.004 0.057 6829 Dihedral : 21.839 176.294 8220 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 2.34 % Allowed : 17.23 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4661 helix: 0.69 (0.11), residues: 2227 sheet: -0.65 (0.19), residues: 629 loop : -0.40 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 95 TYR 0.059 0.002 TYR T 83 PHE 0.040 0.001 PHE M 104 TRP 0.020 0.001 TRP G 712 HIS 0.006 0.001 HIS T 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (44150) covalent geometry : angle 0.65989 / 0.34 (60754) hydrogen bonds : bond 0.03952 / 2.60 ( 1960) hydrogen bonds : angle 4.09616 / 2.88 ( 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 615 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 521 time to evaluate : 1.563 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: 0.8299 (t) cc_final: 0.7906 (t) REVERT: C 259 MET cc_start: 0.8627 (mtm) cc_final: 0.8337 (mtm) REVERT: C 260 MET cc_start: 0.8644 (mmm) cc_final: 0.8258 (tpt) REVERT: C 409 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8707 (mp) REVERT: E 172 TYR cc_start: 0.9000 (m-80) cc_final: 0.8685 (m-80) REVERT: E 317 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 354 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9002 (pp) REVERT: I 218 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7943 (mp) REVERT: M 50 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: M 99 TYR cc_start: 0.7773 (t80) cc_final: 0.7183 (t80) REVERT: M 115 LYS cc_start: 0.7589 (tptt) cc_final: 0.7321 (ptpp) REVERT: N 25 ASN cc_start: 0.7506 (m-40) cc_final: 0.6700 (t0) REVERT: N 27 GLN cc_start: 0.8495 (pt0) cc_final: 0.8179 (tp-100) REVERT: N 59 LYS cc_start: 0.8613 (ptmm) cc_final: 0.8101 (mmtp) REVERT: N 64 ASN cc_start: 0.9220 (m110) cc_final: 0.8959 (m-40) REVERT: N 74 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8616 (mt-10) REVERT: N 96 THR cc_start: 0.8445 (t) cc_final: 0.8035 (m) REVERT: P 95 GLN cc_start: 0.8676 (mt0) cc_final: 0.8425 (mt0) REVERT: P 105 GLU cc_start: 0.7202 (pp20) cc_final: 0.6909 (pp20) REVERT: P 109 HIS cc_start: 0.8082 (m90) cc_final: 0.7476 (m-70) REVERT: P 113 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7404 (tt0) REVERT: Q 54 TYR cc_start: 0.8451 (m-10) cc_final: 0.8208 (m-10) REVERT: R 31 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7656 (mmtp) REVERT: R 35 ARG cc_start: 0.6945 (mtp-110) cc_final: 0.6468 (tmm160) REVERT: R 36 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.6995 (mtm-85) REVERT: R 44 LYS cc_start: 0.7178 (tttm) cc_final: 0.6483 (ttpt) REVERT: R 53 GLU cc_start: 0.5800 (tp30) cc_final: 0.5253 (tt0) REVERT: R 64 ASN cc_start: 0.7787 (m-40) cc_final: 0.7509 (m-40) REVERT: R 95 ARG cc_start: 0.5288 (ttm-80) cc_final: 0.4881 (ttm-80) REVERT: S 48 PRO cc_start: 0.8396 (Cg_exo) cc_final: 0.8188 (Cg_endo) REVERT: S 61 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8151 (pt0) REVERT: S 93 LEU cc_start: 0.7926 (mp) cc_final: 0.7692 (mt) REVERT: S 104 GLN cc_start: 0.9102 (mt0) cc_final: 0.8559 (mm-40) REVERT: T 46 LYS cc_start: 0.8134 (tptm) cc_final: 0.7838 (tppt) REVERT: A 214 ASP cc_start: 0.8028 (m-30) cc_final: 0.7091 (m-30) REVERT: A 244 ASP cc_start: 0.8676 (m-30) cc_final: 0.8266 (m-30) REVERT: A 249 ARG cc_start: 0.8972 (mtp-110) cc_final: 0.8268 (mtm-85) REVERT: A 271 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 346 SER cc_start: 0.9411 (t) cc_final: 0.9067 (p) REVERT: B 129 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: B 260 MET cc_start: 0.9202 (ttm) cc_final: 0.8863 (mmm) REVERT: B 310 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: D 173 ASP cc_start: 0.8789 (m-30) cc_final: 0.8061 (m-30) REVERT: D 203 SER cc_start: 0.9104 (m) cc_final: 0.8647 (p) REVERT: F 162 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8407 (p) REVERT: F 264 ASP cc_start: 0.8696 (t0) cc_final: 0.8055 (p0) REVERT: F 303 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8356 (mpp) REVERT: G 526 MET cc_start: 0.6999 (ptt) cc_final: 0.5964 (mmt) REVERT: G 545 MET cc_start: 0.8159 (mpp) cc_final: 0.7861 (mpp) REVERT: G 640 TYR cc_start: 0.7263 (m-80) cc_final: 0.7008 (m-10) REVERT: G 823 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7340 (pt0) REVERT: G 976 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8219 (t-90) REVERT: H 223 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7671 (ptp-170) REVERT: H 235 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8059 (pttm) REVERT: H 325 THR cc_start: 0.8977 (p) cc_final: 0.8606 (t) REVERT: J 65 CYS cc_start: 0.4638 (m) cc_final: 0.4231 (m) REVERT: J 101 ASN cc_start: 0.5073 (OUTLIER) cc_final: 0.4784 (t0) REVERT: J 135 THR cc_start: 0.8597 (m) cc_final: 0.8327 (p) outliers start: 94 outliers final: 65 residues processed: 583 average time/residue: 0.2302 time to fit residues: 225.7869 Evaluate side-chains 572 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 495 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 194 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE 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 E residue 354 LEU 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 M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain Q residue 64 LYS Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 402 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 364 MET 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 171 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER 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 162 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 238 VAL 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 649 MET 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 905 MET Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain H residue 235 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 151 optimal weight: 4.9990 chunk 467 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 474 optimal weight: 10.0000 chunk 106 optimal weight: 40.0000 chunk 300 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 340 optimal weight: 0.9980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 565 ASN ** G1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081750 restraints weight = 84448.477| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.19 r_work: 0.2980 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 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 = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44150 Z= 0.181 Angle : 0.685 13.336 60754 Z= 0.356 Chirality : 0.046 0.345 6895 Planarity : 0.004 0.056 6829 Dihedral : 21.809 176.129 8220 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.14 % Allowed : 17.70 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4661 helix: 0.70 (0.11), residues: 2232 sheet: -0.64 (0.20), residues: 625 loop : -0.41 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 353 TYR 0.043 0.002 TYR R 72 PHE 0.026 0.001 PHE D 311 TRP 0.020 0.002 TRP G 712 HIS 0.023 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (44150) covalent geometry : angle 0.68456 / 0.36 (60754) hydrogen bonds : bond 0.04102 / 2.70 ( 1960) hydrogen bonds : angle 4.12951 / 2.90 ( 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 587 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 501 time to evaluate : 1.369 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 61 MET cc_start: 0.9071 (mmm) cc_final: 0.8226 (mmm) REVERT: C 126 GLU cc_start: 0.7063 (tp30) cc_final: 0.6722 (tp30) REVERT: C 141 CYS cc_start: 0.8299 (t) cc_final: 0.7903 (t) REVERT: C 255 ASP cc_start: 0.8073 (t0) cc_final: 0.7828 (t0) REVERT: C 259 MET cc_start: 0.8652 (mtm) cc_final: 0.8370 (mtm) REVERT: C 267 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8898 (ttpp) REVERT: C 409 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8730 (mp) REVERT: E 172 TYR cc_start: 0.8969 (m-80) cc_final: 0.8633 (m-80) REVERT: E 317 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8553 (mt-10) REVERT: E 354 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9001 (pp) REVERT: M 94 GLU cc_start: 0.8639 (tp30) cc_final: 0.7732 (tp30) REVERT: M 99 TYR cc_start: 0.7695 (t80) cc_final: 0.6978 (t80) REVERT: M 115 LYS cc_start: 0.7647 (tptt) cc_final: 0.7312 (ptpp) REVERT: N 25 ASN cc_start: 0.7528 (m-40) cc_final: 0.7226 (m110) REVERT: N 27 GLN cc_start: 0.8509 (pt0) cc_final: 0.8235 (tp-100) REVERT: N 29 ILE cc_start: 0.8157 (mm) cc_final: 0.7952 (mp) REVERT: N 74 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8582 (mt-10) REVERT: P 105 GLU cc_start: 0.7205 (pp20) cc_final: 0.6939 (pp20) REVERT: P 109 HIS cc_start: 0.8119 (m90) cc_final: 0.7504 (m-70) REVERT: P 113 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7382 (tt0) REVERT: Q 54 TYR cc_start: 0.8457 (m-10) cc_final: 0.8195 (m-10) REVERT: R 31 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7754 (mmtp) REVERT: R 35 ARG cc_start: 0.6958 (mtp-110) cc_final: 0.6476 (tmm160) REVERT: R 36 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.6924 (mtm-85) REVERT: R 44 LYS cc_start: 0.7197 (tttm) cc_final: 0.6539 (ttpt) REVERT: R 53 GLU cc_start: 0.5958 (tp30) cc_final: 0.5384 (tt0) REVERT: R 64 ASN cc_start: 0.7787 (m-40) cc_final: 0.7514 (m-40) REVERT: R 84 MET cc_start: 0.8749 (mmm) cc_final: 0.8252 (mpp) REVERT: R 95 ARG cc_start: 0.5252 (ttm-80) cc_final: 0.4857 (ttm-80) REVERT: S 48 PRO cc_start: 0.8397 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: S 61 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8192 (pt0) REVERT: S 93 LEU cc_start: 0.7970 (mp) cc_final: 0.7724 (mt) REVERT: S 104 GLN cc_start: 0.9077 (mt0) cc_final: 0.8580 (mm-40) REVERT: T 46 LYS cc_start: 0.8141 (tptm) cc_final: 0.7839 (tppt) REVERT: A 178 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8375 (tp30) REVERT: A 214 ASP cc_start: 0.8095 (m-30) cc_final: 0.7117 (m-30) REVERT: A 244 ASP cc_start: 0.8709 (m-30) cc_final: 0.8301 (m-30) REVERT: A 249 ARG cc_start: 0.9018 (mtp-110) cc_final: 0.8308 (mtm-85) REVERT: A 271 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8941 (mm) REVERT: A 346 SER cc_start: 0.9409 (t) cc_final: 0.9077 (p) REVERT: B 129 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8603 (pm20) REVERT: B 310 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: D 173 ASP cc_start: 0.8862 (m-30) cc_final: 0.8104 (m-30) REVERT: D 203 SER cc_start: 0.9160 (m) cc_final: 0.8703 (p) REVERT: F 162 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8456 (p) REVERT: F 264 ASP cc_start: 0.8738 (t0) cc_final: 0.8118 (p0) REVERT: F 303 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8471 (mpp) REVERT: F 392 ARG cc_start: 0.8742 (ttm110) cc_final: 0.8500 (ttm170) REVERT: F 443 MET cc_start: 0.8724 (ttp) cc_final: 0.8431 (ttt) REVERT: G 823 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7325 (pt0) REVERT: G 976 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8290 (t-90) REVERT: G 1064 ARG cc_start: 0.8727 (ppt170) cc_final: 0.7936 (ptm160) REVERT: H 223 ARG cc_start: 0.7979 (ptp-170) cc_final: 0.7748 (ptp-170) REVERT: H 325 THR cc_start: 0.8982 (p) cc_final: 0.8600 (t) REVERT: J 65 CYS cc_start: 0.4716 (m) cc_final: 0.4329 (m) REVERT: J 135 THR cc_start: 0.8623 (m) cc_final: 0.8344 (p) outliers start: 86 outliers final: 73 residues processed: 555 average time/residue: 0.2211 time to fit residues: 206.4480 Evaluate side-chains 562 residues out of total 4024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 481 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 194 GLU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 291 ILE 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 E residue 354 LEU Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 64 LYS 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 S residue 100 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE 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 397 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 364 MET 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 171 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 243 SER 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 112 GLU 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 162 THR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 ILE 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 649 MET 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 905 MET Chi-restraints excluded: chain G residue 957 LEU Chi-restraints excluded: chain G residue 976 HIS Chi-restraints excluded: chain G residue 981 SER Chi-restraints excluded: chain G residue 1038 LEU Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1136 TYR Chi-restraints excluded: chain H residue 235 LYS 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 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 271 optimal weight: 1.9990 chunk 404 optimal weight: 0.8980 chunk 114 optimal weight: 40.0000 chunk 336 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 442 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 419 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 334 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN T 95 GLN B 156 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 = 0.3992 r_free = 0.3992 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081674 restraints weight = 86375.767| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.46 r_work: 0.2971 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- 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 = 0.67 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 = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44150 Z= 0.157 Angle : 0.671 11.700 60754 Z= 0.348 Chirality : 0.045 0.355 6895 Planarity : 0.004 0.058 6829 Dihedral : 21.745 176.377 8220 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 17.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4661 helix: 0.69 (0.11), residues: 2228 sheet: -0.59 (0.20), residues: 603 loop : -0.43 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 353 TYR 0.119 0.002 TYR T 83 PHE 0.023 0.001 PHE J 434 TRP 0.020 0.001 TRP G 712 HIS 0.005 0.001 HIS J 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (44150) covalent geometry : angle 0.67100 / 0.35 (60754) hydrogen bonds : bond 0.03986 / 2.62 ( 1960) hydrogen bonds : angle 4.11058 / 2.88 ( 5312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14147.75 seconds wall clock time: 241 minutes 51.56 seconds (14511.56 seconds total)