Starting phenix.real_space_refine on Thu Jan 16 06:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgz_40474/01_2025/8sgz_40474.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 354 5.16 5 C 33684 2.51 5 N 9342 2.21 5 O 10050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 53430 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "C" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: S, V, Y, X, Z, E, D, G, F, H Time building chain proxies: 15.10, per 1000 atoms: 0.28 Number of scatterers: 53430 At special positions: 0 Unit cell: (182.6, 199.1, 183.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 354 16.00 O 10050 8.00 N 9342 7.00 C 33684 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: 10.05 Conformation dependent library (CDL) restraints added in 5.3 seconds 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12660 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 90 sheets defined 37.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'B' and resid 15 through 29 removed outlier: 3.503A pdb=" N CYS B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG B 26 " --> pdb=" O MET B 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.806A pdb=" N LYS B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.540A pdb=" N ALA B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.929A pdb=" N ALA B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.855A pdb=" N ILE B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 removed outlier: 4.056A pdb=" N ALA B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 4.257A pdb=" N THR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.631A pdb=" N ASP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.227A pdb=" N GLY B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 459 through 482 removed outlier: 3.630A pdb=" N LEU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 584 Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.574A pdb=" N SER C 113 " --> pdb=" O PHE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.923A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 151 through 168 Processing helix chain 'C' and resid 182 through 185 removed outlier: 3.761A pdb=" N ALA C 185 " --> pdb=" O ALA C 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 185' Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.548A pdb=" N ALA C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.528A pdb=" N VAL C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 244 through 257 removed outlier: 3.567A pdb=" N ARG C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.621A pdb=" N VAL C 286 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 348 through 365 removed outlier: 3.556A pdb=" N PHE C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.584A pdb=" N GLU C 385 " --> pdb=" O GLY C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 403 removed outlier: 3.573A pdb=" N ALA C 394 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 396 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 423 removed outlier: 3.762A pdb=" N ASP C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 460 through 474 removed outlier: 4.391A pdb=" N GLN C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.488A pdb=" N ALA C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 493 through 505 Processing helix chain 'C' and resid 506 through 508 No H-bonds generated for 'chain 'C' and resid 506 through 508' Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.575A pdb=" N SER D 113 " --> pdb=" O PHE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 removed outlier: 3.922A pdb=" N LYS D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 151 through 168 Processing helix chain 'D' and resid 182 through 185 removed outlier: 3.761A pdb=" N ALA D 185 " --> pdb=" O ALA D 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 182 through 185' Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.549A pdb=" N ALA D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.528A pdb=" N VAL D 212 " --> pdb=" O GLY D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 244 through 257 removed outlier: 3.568A pdb=" N ARG D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.621A pdb=" N VAL D 286 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 348 through 365 removed outlier: 3.555A pdb=" N PHE D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 387 removed outlier: 3.583A pdb=" N GLU D 385 " --> pdb=" O GLY D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 403 removed outlier: 3.574A pdb=" N ALA D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D 396 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 397 " --> pdb=" O GLY D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 423 removed outlier: 3.762A pdb=" N ASP D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 454 Processing helix chain 'D' and resid 460 through 474 removed outlier: 4.392A pdb=" N GLN D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP D 468 " --> pdb=" O GLN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 4.488A pdb=" N ALA D 479 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 493 through 505 Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.575A pdb=" N SER E 113 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.923A pdb=" N LYS E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 151 through 168 Processing helix chain 'E' and resid 182 through 185 removed outlier: 3.761A pdb=" N ALA E 185 " --> pdb=" O ALA E 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 182 through 185' Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.549A pdb=" N ALA E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.527A pdb=" N VAL E 212 " --> pdb=" O GLY E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 244 through 257 removed outlier: 3.567A pdb=" N ARG E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.620A pdb=" N VAL E 286 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 305 Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 348 through 365 removed outlier: 3.556A pdb=" N PHE E 365 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 removed outlier: 3.583A pdb=" N GLU E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 403 removed outlier: 3.573A pdb=" N ALA E 394 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU E 396 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 397 " --> pdb=" O GLY E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 423 removed outlier: 3.761A pdb=" N ASP E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 454 Processing helix chain 'E' and resid 460 through 474 removed outlier: 4.391A pdb=" N GLN E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 483 removed outlier: 4.487A pdb=" N ALA E 479 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 493 through 505 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.575A pdb=" N SER F 113 " --> pdb=" O PHE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 132 removed outlier: 3.922A pdb=" N LYS F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 151 through 168 Processing helix chain 'F' and resid 182 through 185 removed outlier: 3.760A pdb=" N ALA F 185 " --> pdb=" O ALA F 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 182 through 185' Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.548A pdb=" N ALA F 190 " --> pdb=" O VAL F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 216 removed outlier: 3.529A pdb=" N VAL F 212 " --> pdb=" O GLY F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 227 Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 244 through 257 removed outlier: 3.568A pdb=" N ARG F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.620A pdb=" N VAL F 286 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 305 Proline residue: F 303 - end of helix Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 348 through 365 removed outlier: 3.555A pdb=" N PHE F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 387 removed outlier: 3.583A pdb=" N GLU F 385 " --> pdb=" O GLY F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 403 removed outlier: 3.573A pdb=" N ALA F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU F 396 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 397 " --> pdb=" O GLY F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 423 removed outlier: 3.762A pdb=" N ASP F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 460 through 474 removed outlier: 4.392A pdb=" N GLN F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA F 467 " --> pdb=" O ALA F 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP F 468 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 483 removed outlier: 4.487A pdb=" N ALA F 479 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 493 through 505 Processing helix chain 'F' and resid 506 through 508 No H-bonds generated for 'chain 'F' and resid 506 through 508' Processing helix chain 'G' and resid 38 through 43 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.574A pdb=" N SER G 113 " --> pdb=" O PHE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 132 removed outlier: 3.922A pdb=" N LYS G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL G 122 " --> pdb=" O ASN G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 Processing helix chain 'G' and resid 151 through 168 Processing helix chain 'G' and resid 182 through 185 removed outlier: 3.761A pdb=" N ALA G 185 " --> pdb=" O ALA G 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 182 through 185' Processing helix chain 'G' and resid 186 through 192 removed outlier: 3.549A pdb=" N ALA G 190 " --> pdb=" O VAL G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 216 removed outlier: 3.527A pdb=" N VAL G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 244 through 257 removed outlier: 3.567A pdb=" N ARG G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 removed outlier: 3.620A pdb=" N VAL G 286 " --> pdb=" O LEU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 Proline residue: G 303 - end of helix Processing helix chain 'G' and resid 342 through 346 Processing helix chain 'G' and resid 348 through 365 removed outlier: 3.554A pdb=" N PHE G 365 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 387 removed outlier: 3.583A pdb=" N GLU G 385 " --> pdb=" O GLY G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 403 removed outlier: 3.573A pdb=" N ALA G 394 " --> pdb=" O ILE G 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS G 395 " --> pdb=" O ARG G 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU G 396 " --> pdb=" O HIS G 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 397 " --> pdb=" O GLY G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 removed outlier: 3.763A pdb=" N ASP G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 454 Processing helix chain 'G' and resid 460 through 474 removed outlier: 4.392A pdb=" N GLN G 464 " --> pdb=" O GLU G 460 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA G 467 " --> pdb=" O ALA G 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP G 468 " --> pdb=" O GLN G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 removed outlier: 4.488A pdb=" N ALA G 479 " --> pdb=" O THR G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 492 No H-bonds generated for 'chain 'G' and resid 490 through 492' Processing helix chain 'G' and resid 493 through 505 Processing helix chain 'G' and resid 506 through 508 No H-bonds generated for 'chain 'G' and resid 506 through 508' Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.574A pdb=" N SER H 113 " --> pdb=" O PHE H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 removed outlier: 3.923A pdb=" N LYS H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL H 122 " --> pdb=" O ASN H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 151 through 168 Processing helix chain 'H' and resid 182 through 185 removed outlier: 3.761A pdb=" N ALA H 185 " --> pdb=" O ALA H 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 182 through 185' Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.549A pdb=" N ALA H 190 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 216 removed outlier: 3.528A pdb=" N VAL H 212 " --> pdb=" O GLY H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'H' and resid 244 through 257 removed outlier: 3.567A pdb=" N ARG H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 removed outlier: 3.621A pdb=" N VAL H 286 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 Proline residue: H 303 - end of helix Processing helix chain 'H' and resid 342 through 346 Processing helix chain 'H' and resid 348 through 365 removed outlier: 3.555A pdb=" N PHE H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 387 removed outlier: 3.583A pdb=" N GLU H 385 " --> pdb=" O GLY H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 403 removed outlier: 3.573A pdb=" N ALA H 394 " --> pdb=" O ILE H 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 396 " --> pdb=" O HIS H 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU H 397 " --> pdb=" O GLY H 393 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 423 removed outlier: 3.762A pdb=" N ASP H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 454 Processing helix chain 'H' and resid 460 through 474 removed outlier: 4.391A pdb=" N GLN H 464 " --> pdb=" O GLU H 460 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA H 467 " --> pdb=" O ALA H 463 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP H 468 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 483 removed outlier: 4.488A pdb=" N ALA H 479 " --> pdb=" O THR H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 492 No H-bonds generated for 'chain 'H' and resid 490 through 492' Processing helix chain 'H' and resid 493 through 505 Processing helix chain 'H' and resid 506 through 508 No H-bonds generated for 'chain 'H' and resid 506 through 508' Processing helix chain 'S' and resid 15 through 29 removed outlier: 3.503A pdb=" N CYS S 19 " --> pdb=" O GLY S 15 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG S 26 " --> pdb=" O MET S 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 49 removed outlier: 3.806A pdb=" N LYS S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 74 Processing helix chain 'S' and resid 92 through 102 removed outlier: 3.541A pdb=" N ALA S 98 " --> pdb=" O GLU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 118 Processing helix chain 'S' and resid 122 through 130 removed outlier: 3.928A pdb=" N ALA S 130 " --> pdb=" O LEU S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 156 removed outlier: 3.855A pdb=" N ILE S 155 " --> pdb=" O PHE S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA S 194 " --> pdb=" O GLU S 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS S 197 " --> pdb=" O LYS S 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 252 through 270 removed outlier: 4.056A pdb=" N ALA S 258 " --> pdb=" O THR S 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL S 270 " --> pdb=" O MET S 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 300 through 308 removed outlier: 4.256A pdb=" N THR S 304 " --> pdb=" O GLU S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 320 Processing helix chain 'S' and resid 399 through 413 removed outlier: 3.630A pdb=" N ASP S 412 " --> pdb=" O GLU S 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU S 413 " --> pdb=" O LYS S 409 " (cutoff:3.500A) Processing helix chain 'S' and resid 422 through 432 Processing helix chain 'S' and resid 432 through 438 removed outlier: 4.226A pdb=" N GLY S 438 " --> pdb=" O ARG S 434 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 449 Processing helix chain 'S' and resid 459 through 482 removed outlier: 3.629A pdb=" N LEU S 480 " --> pdb=" O LYS S 476 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS S 481 " --> pdb=" O ARG S 477 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR S 482 " --> pdb=" O GLU S 478 " (cutoff:3.500A) Processing helix chain 'S' and resid 577 through 584 Processing helix chain 'V' and resid 15 through 29 removed outlier: 3.503A pdb=" N CYS V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG V 26 " --> pdb=" O MET V 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG V 27 " --> pdb=" O ALA V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.805A pdb=" N LYS V 47 " --> pdb=" O ALA V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 74 Processing helix chain 'V' and resid 92 through 102 removed outlier: 3.540A pdb=" N ALA V 98 " --> pdb=" O GLU V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 110 through 118 Processing helix chain 'V' and resid 122 through 130 removed outlier: 3.929A pdb=" N ALA V 130 " --> pdb=" O LEU V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 156 removed outlier: 3.854A pdb=" N ILE V 155 " --> pdb=" O PHE V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA V 194 " --> pdb=" O GLU V 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS V 197 " --> pdb=" O LYS V 193 " (cutoff:3.500A) Processing helix chain 'V' and resid 252 through 270 removed outlier: 4.056A pdb=" N ALA V 258 " --> pdb=" O THR V 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL V 270 " --> pdb=" O MET V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 300 through 308 removed outlier: 4.256A pdb=" N THR V 304 " --> pdb=" O GLU V 300 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 320 Processing helix chain 'V' and resid 399 through 413 removed outlier: 3.631A pdb=" N ASP V 412 " --> pdb=" O GLU V 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU V 413 " --> pdb=" O LYS V 409 " (cutoff:3.500A) Processing helix chain 'V' and resid 422 through 432 Processing helix chain 'V' and resid 432 through 438 removed outlier: 4.227A pdb=" N GLY V 438 " --> pdb=" O ARG V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 443 through 449 Processing helix chain 'V' and resid 459 through 482 removed outlier: 3.629A pdb=" N LEU V 480 " --> pdb=" O LYS V 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS V 481 " --> pdb=" O ARG V 477 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR V 482 " --> pdb=" O GLU V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 577 through 584 Processing helix chain 'X' and resid 15 through 29 removed outlier: 3.503A pdb=" N CYS X 19 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG X 26 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 49 removed outlier: 3.806A pdb=" N LYS X 47 " --> pdb=" O ALA X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 92 through 102 removed outlier: 3.540A pdb=" N ALA X 98 " --> pdb=" O GLU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 118 Processing helix chain 'X' and resid 122 through 130 removed outlier: 3.929A pdb=" N ALA X 130 " --> pdb=" O LEU X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 156 removed outlier: 3.855A pdb=" N ILE X 155 " --> pdb=" O PHE X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA X 194 " --> pdb=" O GLU X 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS X 197 " --> pdb=" O LYS X 193 " (cutoff:3.500A) Processing helix chain 'X' and resid 252 through 270 removed outlier: 4.055A pdb=" N ALA X 258 " --> pdb=" O THR X 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL X 270 " --> pdb=" O MET X 266 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 308 removed outlier: 4.256A pdb=" N THR X 304 " --> pdb=" O GLU X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 320 Processing helix chain 'X' and resid 399 through 413 removed outlier: 3.630A pdb=" N ASP X 412 " --> pdb=" O GLU X 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU X 413 " --> pdb=" O LYS X 409 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 432 Processing helix chain 'X' and resid 432 through 438 removed outlier: 4.226A pdb=" N GLY X 438 " --> pdb=" O ARG X 434 " (cutoff:3.500A) Processing helix chain 'X' and resid 443 through 449 Processing helix chain 'X' and resid 459 through 482 removed outlier: 3.629A pdb=" N LEU X 480 " --> pdb=" O LYS X 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS X 481 " --> pdb=" O ARG X 477 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR X 482 " --> pdb=" O GLU X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 577 through 584 Processing helix chain 'Z' and resid 15 through 29 removed outlier: 3.503A pdb=" N CYS Z 19 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 49 removed outlier: 3.805A pdb=" N LYS Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 66 through 74 Processing helix chain 'Z' and resid 92 through 102 removed outlier: 3.538A pdb=" N ALA Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 110 through 118 Processing helix chain 'Z' and resid 122 through 130 removed outlier: 3.928A pdb=" N ALA Z 130 " --> pdb=" O LEU Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 156 removed outlier: 3.855A pdb=" N ILE Z 155 " --> pdb=" O PHE Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA Z 194 " --> pdb=" O GLU Z 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS Z 197 " --> pdb=" O LYS Z 193 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 270 removed outlier: 4.056A pdb=" N ALA Z 258 " --> pdb=" O THR Z 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL Z 270 " --> pdb=" O MET Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 300 through 308 removed outlier: 4.257A pdb=" N THR Z 304 " --> pdb=" O GLU Z 300 " (cutoff:3.500A) Processing helix chain 'Z' and resid 311 through 320 Processing helix chain 'Z' and resid 399 through 413 removed outlier: 3.630A pdb=" N ASP Z 412 " --> pdb=" O GLU Z 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Z 413 " --> pdb=" O LYS Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 432 Processing helix chain 'Z' and resid 432 through 438 removed outlier: 4.226A pdb=" N GLY Z 438 " --> pdb=" O ARG Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 443 through 449 Processing helix chain 'Z' and resid 459 through 482 removed outlier: 3.629A pdb=" N LEU Z 480 " --> pdb=" O LYS Z 476 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS Z 481 " --> pdb=" O ARG Z 477 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR Z 482 " --> pdb=" O GLU Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 577 through 584 Processing helix chain 'Y' and resid 15 through 29 removed outlier: 3.502A pdb=" N CYS Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG Y 26 " --> pdb=" O MET Y 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 49 removed outlier: 3.806A pdb=" N LYS Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 74 Processing helix chain 'Y' and resid 92 through 102 removed outlier: 3.540A pdb=" N ALA Y 98 " --> pdb=" O GLU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 110 through 118 Processing helix chain 'Y' and resid 122 through 130 removed outlier: 3.929A pdb=" N ALA Y 130 " --> pdb=" O LEU Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 156 removed outlier: 3.854A pdb=" N ILE Y 155 " --> pdb=" O PHE Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 197 removed outlier: 3.560A pdb=" N ALA Y 194 " --> pdb=" O GLU Y 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS Y 197 " --> pdb=" O LYS Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 270 removed outlier: 4.057A pdb=" N ALA Y 258 " --> pdb=" O THR Y 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL Y 270 " --> pdb=" O MET Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 300 through 308 removed outlier: 4.256A pdb=" N THR Y 304 " --> pdb=" O GLU Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 311 through 320 Processing helix chain 'Y' and resid 399 through 413 removed outlier: 3.630A pdb=" N ASP Y 412 " --> pdb=" O GLU Y 408 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU Y 413 " --> pdb=" O LYS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 432 Processing helix chain 'Y' and resid 432 through 438 removed outlier: 4.228A pdb=" N GLY Y 438 " --> pdb=" O ARG Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 443 through 449 Processing helix chain 'Y' and resid 459 through 482 removed outlier: 3.629A pdb=" N LEU Y 480 " --> pdb=" O LYS Y 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS Y 481 " --> pdb=" O ARG Y 477 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR Y 482 " --> pdb=" O GLU Y 478 " (cutoff:3.500A) Processing helix chain 'Y' and resid 577 through 584 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.595A pdb=" N VAL B 53 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 137 through 138 removed outlier: 4.469A pdb=" N VAL B 203 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.631A pdb=" N THR B 339 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 394 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS B 341 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 392 " --> pdb=" O CYS B 341 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 343 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AA8, first strand: chain 'B' and resid 502 through 509 removed outlier: 5.632A pdb=" N GLY B 503 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL B 497 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 509 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 491 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 576 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 574 " --> pdb=" O SER B 496 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN B 565 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE B 554 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 610 removed outlier: 6.895A pdb=" N THR B 626 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 622 through 623 removed outlier: 3.937A pdb=" N GLU B 622 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU C 102 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE C 103 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 194 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR C 195 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE C 242 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 197 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AB4, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB5, first strand: chain 'C' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS C 323 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE C 370 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS C 334 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE C 372 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 336 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP C 374 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN C 338 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N VAL C 375 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS C 414 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 442 " --> pdb=" O ALA C 415 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS C 323 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE C 370 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS C 334 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE C 372 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 336 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP C 374 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN C 338 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N VAL C 375 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS C 414 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 432 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA C 487 " --> pdb=" O ASN C 433 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 435 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU D 102 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE D 103 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 194 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR D 195 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE D 242 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET D 197 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AB9, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AC1, first strand: chain 'D' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS D 323 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE D 370 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS D 334 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE D 372 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 336 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP D 374 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN D 338 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL D 375 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS D 414 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 442 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS D 323 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE D 370 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS D 334 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE D 372 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 336 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP D 374 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN D 338 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL D 375 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS D 414 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D 432 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 487 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 435 " --> pdb=" O ALA D 487 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU E 102 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE E 103 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 194 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR E 195 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE E 242 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 197 " --> pdb=" O PHE E 242 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AC5, first strand: chain 'E' and resid 180 through 181 Processing sheet with id=AC6, first strand: chain 'E' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS E 323 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE E 370 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS E 334 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE E 372 " --> pdb=" O CYS E 334 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE E 336 " --> pdb=" O PHE E 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP E 374 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN E 338 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL E 375 " --> pdb=" O THR E 412 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS E 414 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 442 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS E 323 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE E 370 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS E 334 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE E 372 " --> pdb=" O CYS E 334 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE E 336 " --> pdb=" O PHE E 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP E 374 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN E 338 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL E 375 " --> pdb=" O THR E 412 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS E 414 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E 432 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA E 487 " --> pdb=" O ASN E 433 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 435 " --> pdb=" O ALA E 487 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 88 through 91 removed outlier: 3.786A pdb=" N LEU F 102 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE F 103 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE F 194 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR F 195 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE F 242 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET F 197 " --> pdb=" O PHE F 242 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AD1, first strand: chain 'F' and resid 180 through 181 Processing sheet with id=AD2, first strand: chain 'F' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS F 323 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE F 370 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS F 334 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE F 372 " --> pdb=" O CYS F 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 336 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP F 374 " --> pdb=" O ILE F 336 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN F 338 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N VAL F 375 " --> pdb=" O THR F 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS F 414 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 442 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS F 323 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE F 370 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS F 334 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE F 372 " --> pdb=" O CYS F 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 336 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP F 374 " --> pdb=" O ILE F 336 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN F 338 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N VAL F 375 " --> pdb=" O THR F 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS F 414 " --> pdb=" O VAL F 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 432 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 487 " --> pdb=" O ASN F 433 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 435 " --> pdb=" O ALA F 487 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU G 102 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE G 103 " --> pdb=" O PHE G 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 194 " --> pdb=" O GLN G 173 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR G 195 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE G 242 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET G 197 " --> pdb=" O PHE G 242 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AD6, first strand: chain 'G' and resid 180 through 181 Processing sheet with id=AD7, first strand: chain 'G' and resid 310 through 313 removed outlier: 4.633A pdb=" N CYS G 323 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE G 370 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS G 334 " --> pdb=" O ILE G 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE G 372 " --> pdb=" O CYS G 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 336 " --> pdb=" O PHE G 372 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP G 374 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN G 338 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL G 375 " --> pdb=" O THR G 412 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS G 414 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 442 " --> pdb=" O ALA G 415 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 310 through 313 removed outlier: 4.633A pdb=" N CYS G 323 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE G 370 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS G 334 " --> pdb=" O ILE G 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE G 372 " --> pdb=" O CYS G 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 336 " --> pdb=" O PHE G 372 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP G 374 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN G 338 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL G 375 " --> pdb=" O THR G 412 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS G 414 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 432 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA G 487 " --> pdb=" O ASN G 433 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 435 " --> pdb=" O ALA G 487 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU H 102 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE H 103 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE H 194 " --> pdb=" O GLN H 173 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR H 195 " --> pdb=" O GLY H 240 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N PHE H 242 " --> pdb=" O THR H 195 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET H 197 " --> pdb=" O PHE H 242 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=AE2, first strand: chain 'H' and resid 180 through 181 Processing sheet with id=AE3, first strand: chain 'H' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS H 323 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE H 370 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS H 334 " --> pdb=" O ILE H 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE H 372 " --> pdb=" O CYS H 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE H 336 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP H 374 " --> pdb=" O ILE H 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN H 338 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL H 375 " --> pdb=" O THR H 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS H 414 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA H 442 " --> pdb=" O ALA H 415 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS H 323 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE H 370 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS H 334 " --> pdb=" O ILE H 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE H 372 " --> pdb=" O CYS H 334 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE H 336 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP H 374 " --> pdb=" O ILE H 336 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN H 338 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N VAL H 375 " --> pdb=" O THR H 412 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS H 414 " --> pdb=" O VAL H 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER H 432 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 487 " --> pdb=" O ASN H 433 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA H 435 " --> pdb=" O ALA H 487 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 33 through 36 removed outlier: 3.596A pdb=" N VAL S 53 " --> pdb=" O ALA S 34 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 137 through 138 removed outlier: 4.469A pdb=" N VAL S 203 " --> pdb=" O PHE S 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 226 through 227 Processing sheet with id=AE8, first strand: chain 'S' and resid 226 through 227 Processing sheet with id=AE9, first strand: chain 'S' and resid 236 through 237 Processing sheet with id=AF1, first strand: chain 'S' and resid 243 through 245 removed outlier: 6.631A pdb=" N THR S 339 " --> pdb=" O SER S 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER S 394 " --> pdb=" O THR S 339 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS S 341 " --> pdb=" O LYS S 392 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS S 392 " --> pdb=" O CYS S 341 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL S 343 " --> pdb=" O ILE S 390 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 346 through 347 Processing sheet with id=AF3, first strand: chain 'S' and resid 502 through 509 removed outlier: 5.632A pdb=" N GLY S 503 " --> pdb=" O VAL S 497 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL S 497 " --> pdb=" O GLY S 503 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 509 " --> pdb=" O ARG S 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG S 491 " --> pdb=" O VAL S 509 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET S 576 " --> pdb=" O TYR S 494 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN S 574 " --> pdb=" O SER S 496 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN S 565 " --> pdb=" O PHE S 554 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE S 554 " --> pdb=" O GLN S 565 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR S 626 " --> pdb=" O VAL S 608 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 622 through 623 removed outlier: 3.936A pdb=" N GLU S 622 " --> pdb=" O ALA S 638 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 33 through 36 removed outlier: 3.595A pdb=" N VAL V 53 " --> pdb=" O ALA V 34 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 137 through 138 removed outlier: 4.469A pdb=" N VAL V 203 " --> pdb=" O PHE V 138 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 226 through 227 Processing sheet with id=AF9, first strand: chain 'V' and resid 226 through 227 Processing sheet with id=AG1, first strand: chain 'V' and resid 236 through 237 Processing sheet with id=AG2, first strand: chain 'V' and resid 243 through 245 removed outlier: 6.631A pdb=" N THR V 339 " --> pdb=" O SER V 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER V 394 " --> pdb=" O THR V 339 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS V 341 " --> pdb=" O LYS V 392 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS V 392 " --> pdb=" O CYS V 341 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL V 343 " --> pdb=" O ILE V 390 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 346 through 347 Processing sheet with id=AG4, first strand: chain 'V' and resid 502 through 509 removed outlier: 5.633A pdb=" N GLY V 503 " --> pdb=" O VAL V 497 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL V 497 " --> pdb=" O GLY V 503 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL V 509 " --> pdb=" O ARG V 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG V 491 " --> pdb=" O VAL V 509 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET V 576 " --> pdb=" O TYR V 494 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN V 574 " --> pdb=" O SER V 496 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN V 565 " --> pdb=" O PHE V 554 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE V 554 " --> pdb=" O GLN V 565 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 606 through 610 removed outlier: 6.895A pdb=" N THR V 626 " --> pdb=" O VAL V 608 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 622 through 623 removed outlier: 3.936A pdb=" N GLU V 622 " --> pdb=" O ALA V 638 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 33 through 36 removed outlier: 3.595A pdb=" N VAL X 53 " --> pdb=" O ALA X 34 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'X' and resid 137 through 138 removed outlier: 4.470A pdb=" N VAL X 203 " --> pdb=" O PHE X 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 226 through 227 Processing sheet with id=AH1, first strand: chain 'X' and resid 226 through 227 Processing sheet with id=AH2, first strand: chain 'X' and resid 236 through 237 Processing sheet with id=AH3, first strand: chain 'X' and resid 243 through 245 removed outlier: 6.630A pdb=" N THR X 339 " --> pdb=" O SER X 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER X 394 " --> pdb=" O THR X 339 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS X 341 " --> pdb=" O LYS X 392 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS X 392 " --> pdb=" O CYS X 341 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL X 343 " --> pdb=" O ILE X 390 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'X' and resid 346 through 347 Processing sheet with id=AH5, first strand: chain 'X' and resid 502 through 509 removed outlier: 5.632A pdb=" N GLY X 503 " --> pdb=" O VAL X 497 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL X 497 " --> pdb=" O GLY X 503 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL X 509 " --> pdb=" O ARG X 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG X 491 " --> pdb=" O VAL X 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET X 576 " --> pdb=" O TYR X 494 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN X 574 " --> pdb=" O SER X 496 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN X 565 " --> pdb=" O PHE X 554 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE X 554 " --> pdb=" O GLN X 565 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR X 626 " --> pdb=" O VAL X 608 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 622 through 623 removed outlier: 3.936A pdb=" N GLU X 622 " --> pdb=" O ALA X 638 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 33 through 36 removed outlier: 3.596A pdb=" N VAL Z 53 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 137 through 138 removed outlier: 4.469A pdb=" N VAL Z 203 " --> pdb=" O PHE Z 138 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Z' and resid 226 through 227 Processing sheet with id=AI2, first strand: chain 'Z' and resid 226 through 227 Processing sheet with id=AI3, first strand: chain 'Z' and resid 236 through 237 Processing sheet with id=AI4, first strand: chain 'Z' and resid 243 through 245 removed outlier: 6.630A pdb=" N THR Z 339 " --> pdb=" O SER Z 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER Z 394 " --> pdb=" O THR Z 339 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS Z 341 " --> pdb=" O LYS Z 392 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS Z 392 " --> pdb=" O CYS Z 341 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL Z 343 " --> pdb=" O ILE Z 390 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 346 through 347 Processing sheet with id=AI6, first strand: chain 'Z' and resid 502 through 509 removed outlier: 5.633A pdb=" N GLY Z 503 " --> pdb=" O VAL Z 497 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL Z 497 " --> pdb=" O GLY Z 503 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Z 509 " --> pdb=" O ARG Z 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG Z 491 " --> pdb=" O VAL Z 509 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET Z 576 " --> pdb=" O TYR Z 494 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN Z 574 " --> pdb=" O SER Z 496 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN Z 565 " --> pdb=" O PHE Z 554 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE Z 554 " --> pdb=" O GLN Z 565 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 606 through 610 removed outlier: 6.896A pdb=" N THR Z 626 " --> pdb=" O VAL Z 608 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Z' and resid 622 through 623 removed outlier: 3.937A pdb=" N GLU Z 622 " --> pdb=" O ALA Z 638 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Y' and resid 33 through 36 removed outlier: 3.596A pdb=" N VAL Y 53 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Y' and resid 137 through 138 removed outlier: 4.470A pdb=" N VAL Y 203 " --> pdb=" O PHE Y 138 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Y' and resid 226 through 227 Processing sheet with id=AJ3, first strand: chain 'Y' and resid 226 through 227 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 236 through 237 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 243 through 245 removed outlier: 6.632A pdb=" N THR Y 339 " --> pdb=" O SER Y 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER Y 394 " --> pdb=" O THR Y 339 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS Y 341 " --> pdb=" O LYS Y 392 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS Y 392 " --> pdb=" O CYS Y 341 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL Y 343 " --> pdb=" O ILE Y 390 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 346 through 347 Processing sheet with id=AJ7, first strand: chain 'Y' and resid 502 through 509 removed outlier: 5.633A pdb=" N GLY Y 503 " --> pdb=" O VAL Y 497 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL Y 497 " --> pdb=" O GLY Y 503 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Y 509 " --> pdb=" O ARG Y 491 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG Y 491 " --> pdb=" O VAL Y 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET Y 576 " --> pdb=" O TYR Y 494 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN Y 574 " --> pdb=" O SER Y 496 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Y 565 " --> pdb=" O PHE Y 554 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE Y 554 " --> pdb=" O GLN Y 565 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Y' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR Y 626 " --> pdb=" O VAL Y 608 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Y' and resid 622 through 623 removed outlier: 3.936A pdb=" N GLU Y 622 " --> pdb=" O ALA Y 638 " (cutoff:3.500A) 1992 hydrogen bonds defined for protein. 5616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.08 Time building geometry restraints manager: 11.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11878 1.33 - 1.45: 11227 1.45 - 1.57: 30805 1.57 - 1.69: 0 1.69 - 1.81: 570 Bond restraints: 54480 Sorted by residual: bond pdb=" C2 BTI H 801 " pdb=" S1 BTI H 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 BTI D 801 " pdb=" S1 BTI D 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 BTI C 801 " pdb=" S1 BTI C 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C2 BTI E 801 " pdb=" S1 BTI E 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C2 BTI G 801 " pdb=" S1 BTI G 801 " ideal model delta sigma weight residual 1.822 1.759 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 54475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 70425 1.70 - 3.40: 2733 3.40 - 5.10: 402 5.10 - 6.80: 126 6.80 - 8.50: 30 Bond angle restraints: 73716 Sorted by residual: angle pdb=" N GLY Z 309 " pdb=" CA GLY Z 309 " pdb=" C GLY Z 309 " ideal model delta sigma weight residual 115.64 107.31 8.33 1.46e+00 4.69e-01 3.26e+01 angle pdb=" N GLY V 309 " pdb=" CA GLY V 309 " pdb=" C GLY V 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.22e+01 angle pdb=" N GLY B 309 " pdb=" CA GLY B 309 " pdb=" C GLY B 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.22e+01 angle pdb=" N GLY S 309 " pdb=" CA GLY S 309 " pdb=" C GLY S 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.21e+01 angle pdb=" N GLY X 309 " pdb=" CA GLY X 309 " pdb=" C GLY X 309 " ideal model delta sigma weight residual 115.64 107.39 8.25 1.46e+00 4.69e-01 3.20e+01 ... (remaining 73711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 30006 17.64 - 35.29: 2592 35.29 - 52.93: 398 52.93 - 70.58: 90 70.58 - 88.22: 22 Dihedral angle restraints: 33108 sinusoidal: 13332 harmonic: 19776 Sorted by residual: dihedral pdb=" CA THR C 200 " pdb=" C THR C 200 " pdb=" N SER C 201 " pdb=" CA SER C 201 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR D 200 " pdb=" C THR D 200 " pdb=" N SER D 201 " pdb=" CA SER D 201 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR F 200 " pdb=" C THR F 200 " pdb=" N SER F 201 " pdb=" CA SER F 201 " ideal model delta harmonic sigma weight residual 180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 33105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5211 0.035 - 0.071: 1967 0.071 - 0.106: 657 0.106 - 0.142: 370 0.142 - 0.177: 39 Chirality restraints: 8244 Sorted by residual: chirality pdb=" C4 BTI C 801 " pdb=" C2 BTI C 801 " pdb=" C5 BTI C 801 " pdb=" N2 BTI C 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" C4 BTI F 801 " pdb=" C2 BTI F 801 " pdb=" C5 BTI F 801 " pdb=" N2 BTI F 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C4 BTI G 801 " pdb=" C2 BTI G 801 " pdb=" C5 BTI G 801 " pdb=" N2 BTI G 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 8241 not shown) Planarity restraints: 9630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI C 801 " -0.009 2.00e-02 2.50e+03 2.02e-02 6.13e+00 pdb=" C4 BTI C 801 " 0.002 2.00e-02 2.50e+03 pdb=" C5 BTI C 801 " 0.027 2.00e-02 2.50e+03 pdb=" N2 BTI C 801 " -0.013 2.00e-02 2.50e+03 pdb=" N3 BTI C 801 " -0.030 2.00e-02 2.50e+03 pdb=" O3 BTI C 801 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 801 " 0.009 2.00e-02 2.50e+03 2.01e-02 6.08e+00 pdb=" C4 BTI G 801 " -0.002 2.00e-02 2.50e+03 pdb=" C5 BTI G 801 " -0.026 2.00e-02 2.50e+03 pdb=" N2 BTI G 801 " 0.014 2.00e-02 2.50e+03 pdb=" N3 BTI G 801 " 0.030 2.00e-02 2.50e+03 pdb=" O3 BTI G 801 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " -0.009 2.00e-02 2.50e+03 2.01e-02 6.07e+00 pdb=" C4 BTI D 801 " 0.002 2.00e-02 2.50e+03 pdb=" C5 BTI D 801 " 0.026 2.00e-02 2.50e+03 pdb=" N2 BTI D 801 " -0.014 2.00e-02 2.50e+03 pdb=" N3 BTI D 801 " -0.030 2.00e-02 2.50e+03 pdb=" O3 BTI D 801 " 0.024 2.00e-02 2.50e+03 ... (remaining 9627 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1978 2.70 - 3.25: 54525 3.25 - 3.80: 81932 3.80 - 4.35: 104947 4.35 - 4.90: 177643 Nonbonded interactions: 421025 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 646 " pdb=" NZ LYS Y 648 " model vdw 2.154 3.120 nonbonded pdb=" OE2 GLU Z 646 " pdb=" NZ LYS Z 648 " model vdw 2.154 3.120 nonbonded pdb=" OE2 GLU X 646 " pdb=" NZ LYS X 648 " model vdw 2.155 3.120 nonbonded pdb=" OE2 GLU V 646 " pdb=" NZ LYS V 648 " model vdw 2.155 3.120 nonbonded pdb=" OE2 GLU S 646 " pdb=" NZ LYS S 648 " model vdw 2.155 3.120 ... (remaining 421020 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: 0.32 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.470 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 85.370 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.004 0.064 54480 Z= 0.293 Angle : 0.786 8.501 73716 Z= 0.470 Chirality : 0.046 0.177 8244 Planarity : 0.005 0.051 9630 Dihedral : 13.298 88.222 20448 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 1.21 % Allowed : 2.75 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 6852 helix: 0.32 (0.12), residues: 2130 sheet: -0.12 (0.19), residues: 840 loop : -2.18 (0.09), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 514 HIS 0.004 0.001 HIS Z 209 PHE 0.008 0.001 PHE E 62 TYR 0.011 0.001 TYR S 289 ARG 0.005 0.000 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 904 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.4588 (mtm) cc_final: 0.4211 (mmm) REVERT: B 129 ARG cc_start: 0.6194 (tmt170) cc_final: 0.5246 (ttp-170) REVERT: B 259 MET cc_start: 0.3725 (mmp) cc_final: 0.3219 (mmt) REVERT: B 363 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: B 545 ASP cc_start: 0.6547 (t0) cc_final: 0.6110 (p0) REVERT: D 197 MET cc_start: 0.8776 (mtp) cc_final: 0.8559 (mtp) REVERT: S 117 MET cc_start: 0.4603 (mtm) cc_final: 0.4336 (mmm) REVERT: S 129 ARG cc_start: 0.6014 (tmt170) cc_final: 0.5199 (ttp-170) REVERT: S 259 MET cc_start: 0.3652 (mmp) cc_final: 0.3087 (mmt) REVERT: S 444 TYR cc_start: 0.6346 (t80) cc_final: 0.6045 (t80) REVERT: S 545 ASP cc_start: 0.6711 (t0) cc_final: 0.6122 (p0) REVERT: V 117 MET cc_start: 0.4593 (mtm) cc_final: 0.4214 (mmm) REVERT: V 129 ARG cc_start: 0.6215 (tmt170) cc_final: 0.5269 (ttp-170) REVERT: V 259 MET cc_start: 0.3867 (mmp) cc_final: 0.3199 (mmt) REVERT: V 363 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6759 (pt0) REVERT: V 545 ASP cc_start: 0.6573 (t0) cc_final: 0.6124 (p0) REVERT: X 129 ARG cc_start: 0.5941 (tmt170) cc_final: 0.5255 (ttp-170) REVERT: X 331 ASP cc_start: 0.5511 (t0) cc_final: 0.5183 (p0) REVERT: X 566 MET cc_start: 0.6540 (tpt) cc_final: 0.6307 (tpt) REVERT: Z 117 MET cc_start: 0.4613 (mtm) cc_final: 0.4364 (mmm) REVERT: Z 129 ARG cc_start: 0.5966 (tmt170) cc_final: 0.5170 (ttp-170) REVERT: Z 259 MET cc_start: 0.3661 (mmp) cc_final: 0.3091 (mmt) REVERT: Z 444 TYR cc_start: 0.6322 (t80) cc_final: 0.5833 (t80) REVERT: Z 545 ASP cc_start: 0.6678 (t0) cc_final: 0.6090 (p0) REVERT: Z 628 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: Y 129 ARG cc_start: 0.5895 (tmt170) cc_final: 0.5204 (ttp-170) REVERT: Y 331 ASP cc_start: 0.5512 (t0) cc_final: 0.5181 (p0) REVERT: Y 566 MET cc_start: 0.6532 (tpt) cc_final: 0.6294 (tpt) outliers start: 69 outliers final: 7 residues processed: 969 average time/residue: 0.5788 time to fit residues: 905.8675 Evaluate side-chains 423 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 413 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 628 GLU Chi-restraints excluded: chain Y residue 363 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 572 optimal weight: 0.9990 chunk 513 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 346 optimal weight: 6.9990 chunk 274 optimal weight: 0.2980 chunk 531 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 323 optimal weight: 0.9980 chunk 395 optimal weight: 0.0170 chunk 615 optimal weight: 1.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 236 GLN B 271 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS B 634 ASN S 271 GLN ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 301 HIS ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 634 ASN ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS V 236 GLN V 271 GLN ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 516 HIS V 634 ASN ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS X 271 GLN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 634 ASN Z 271 GLN ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 HIS ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 634 ASN Y 13 ASN Y 212 HIS Y 271 GLN ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 634 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.150327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.117198 restraints weight = 101615.899| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.00 r_work: 0.3283 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54480 Z= 0.164 Angle : 0.577 9.566 73716 Z= 0.303 Chirality : 0.046 0.140 8244 Planarity : 0.005 0.065 9630 Dihedral : 4.579 38.857 7682 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 1.56 % Allowed : 9.22 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 6852 helix: 0.78 (0.12), residues: 2160 sheet: -0.05 (0.17), residues: 966 loop : -1.88 (0.10), residues: 3726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 396 HIS 0.004 0.001 HIS C 229 PHE 0.013 0.001 PHE G 76 TYR 0.016 0.001 TYR X 86 ARG 0.004 0.000 ARG S 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 491 time to evaluate : 4.491 Fit side-chains REVERT: B 129 ARG cc_start: 0.6534 (tmt170) cc_final: 0.5629 (ptt180) REVERT: B 259 MET cc_start: 0.3642 (mmp) cc_final: 0.2858 (mmt) REVERT: B 409 LYS cc_start: 0.7719 (tttt) cc_final: 0.7115 (ttpt) REVERT: C 78 MET cc_start: 0.7856 (tpp) cc_final: 0.7636 (mmm) REVERT: E 46 ARG cc_start: 0.6922 (mtt180) cc_final: 0.6293 (mmt-90) REVERT: E 78 MET cc_start: 0.8353 (mmm) cc_final: 0.7909 (mmm) REVERT: E 197 MET cc_start: 0.8904 (mtp) cc_final: 0.8650 (mtp) REVERT: H 78 MET cc_start: 0.8359 (mmm) cc_final: 0.7926 (mmm) REVERT: H 204 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8342 (ptt) REVERT: S 129 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5252 (ptt180) REVERT: S 172 MET cc_start: 0.3499 (OUTLIER) cc_final: 0.3105 (tmm) REVERT: S 218 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4665 (mm) REVERT: S 238 ARG cc_start: 0.5953 (mmt90) cc_final: 0.5436 (ttm110) REVERT: S 259 MET cc_start: 0.3823 (mmp) cc_final: 0.3072 (mmt) REVERT: S 455 LYS cc_start: 0.4382 (tptt) cc_final: 0.3823 (tptp) REVERT: S 628 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: S 632 MET cc_start: 0.8454 (tpt) cc_final: 0.8081 (tpp) REVERT: V 129 ARG cc_start: 0.6471 (tmt170) cc_final: 0.5543 (ptt180) REVERT: V 259 MET cc_start: 0.3593 (mmp) cc_final: 0.2841 (mmt) REVERT: V 409 LYS cc_start: 0.7689 (tttt) cc_final: 0.7073 (ttpt) REVERT: V 628 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: X 80 GLN cc_start: 0.4403 (pm20) cc_final: 0.4085 (mp10) REVERT: X 272 TYR cc_start: 0.3662 (t80) cc_final: 0.3378 (t80) REVERT: X 331 ASP cc_start: 0.5667 (t0) cc_final: 0.5324 (p0) REVERT: X 389 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (tp) REVERT: X 436 ARG cc_start: 0.5474 (mtm-85) cc_final: 0.5261 (mtp85) REVERT: X 463 MET cc_start: 0.7399 (tpt) cc_final: 0.7157 (mmm) REVERT: Z 129 ARG cc_start: 0.6333 (tmt170) cc_final: 0.5269 (ptt180) REVERT: Z 172 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.3094 (tmm) REVERT: Z 218 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4693 (mm) REVERT: Z 238 ARG cc_start: 0.5886 (mmt90) cc_final: 0.5495 (ttm110) REVERT: Z 259 MET cc_start: 0.3830 (mmp) cc_final: 0.3068 (mmt) REVERT: Z 455 LYS cc_start: 0.4317 (tptt) cc_final: 0.3809 (tptp) REVERT: Z 632 MET cc_start: 0.8369 (tpt) cc_final: 0.8124 (tpp) REVERT: Y 272 TYR cc_start: 0.3643 (t80) cc_final: 0.3343 (t80) REVERT: Y 295 THR cc_start: 0.4021 (t) cc_final: 0.3377 (m) REVERT: Y 331 ASP cc_start: 0.5664 (t0) cc_final: 0.5317 (p0) REVERT: Y 389 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7751 (tp) REVERT: Y 463 MET cc_start: 0.7400 (tpt) cc_final: 0.7150 (mmm) REVERT: Y 466 MET cc_start: 0.7432 (ttp) cc_final: 0.7064 (ttp) outliers start: 89 outliers final: 35 residues processed: 545 average time/residue: 0.5736 time to fit residues: 521.7842 Evaluate side-chains 397 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 628 GLU Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 389 LEU Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 13 ASN Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 389 LEU Chi-restraints excluded: chain Y residue 636 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 555 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 610 optimal weight: 7.9990 chunk 383 optimal weight: 6.9990 chunk 463 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 522 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 652 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 516 HIS ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 236 GLN X 285 GLN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 443 ASN ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 443 ASN Z 516 HIS Y 13 ASN Y 236 GLN Y 285 GLN ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 443 ASN Y 464 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114311 restraints weight = 100202.327| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.01 r_work: 0.3178 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 54480 Z= 0.318 Angle : 0.649 10.156 73716 Z= 0.346 Chirality : 0.049 0.182 8244 Planarity : 0.006 0.059 9630 Dihedral : 4.950 44.371 7658 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.36 % Allowed : 12.00 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.10), residues: 6852 helix: 0.65 (0.11), residues: 2148 sheet: -0.69 (0.16), residues: 1194 loop : -1.93 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 396 HIS 0.017 0.002 HIS Y 212 PHE 0.014 0.002 PHE D 194 TYR 0.017 0.002 TYR Z 414 ARG 0.006 0.001 ARG Y 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 391 time to evaluate : 4.568 Fit side-chains REVERT: B 129 ARG cc_start: 0.6239 (tmt170) cc_final: 0.4566 (tpp80) REVERT: B 259 MET cc_start: 0.4008 (mmp) cc_final: 0.3109 (mmt) REVERT: B 295 THR cc_start: 0.4515 (t) cc_final: 0.4179 (m) REVERT: B 409 LYS cc_start: 0.7963 (tttt) cc_final: 0.7443 (ttpt) REVERT: B 617 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4750 (tpt) REVERT: C 70 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 200 THR cc_start: 0.7983 (t) cc_final: 0.7622 (m) REVERT: D 46 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.6815 (mmt-90) REVERT: E 46 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6802 (mmt-90) REVERT: G 70 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: G 200 THR cc_start: 0.7977 (t) cc_final: 0.7613 (m) REVERT: H 197 MET cc_start: 0.9050 (mtp) cc_final: 0.8830 (mtp) REVERT: S 74 CYS cc_start: 0.6984 (m) cc_final: 0.6652 (t) REVERT: S 129 ARG cc_start: 0.6252 (tmt170) cc_final: 0.5114 (ttp-170) REVERT: S 172 MET cc_start: 0.3467 (OUTLIER) cc_final: 0.3083 (tmm) REVERT: S 238 ARG cc_start: 0.5969 (mmt90) cc_final: 0.5408 (mtm180) REVERT: S 259 MET cc_start: 0.3870 (mmp) cc_final: 0.3085 (mmt) REVERT: S 455 LYS cc_start: 0.4800 (tptt) cc_final: 0.4188 (tptp) REVERT: S 632 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8283 (tpp) REVERT: V 77 THR cc_start: 0.3808 (OUTLIER) cc_final: 0.3487 (t) REVERT: V 129 ARG cc_start: 0.6230 (tmt170) cc_final: 0.4574 (tpp80) REVERT: V 259 MET cc_start: 0.3988 (mmp) cc_final: 0.3108 (mmt) REVERT: V 409 LYS cc_start: 0.7999 (tttt) cc_final: 0.7497 (ttpt) REVERT: V 617 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4773 (tpt) REVERT: X 363 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7270 (pt0) REVERT: X 407 MET cc_start: 0.7770 (tpt) cc_final: 0.7346 (tpp) REVERT: Z 74 CYS cc_start: 0.7014 (m) cc_final: 0.6623 (t) REVERT: Z 129 ARG cc_start: 0.6260 (tmt170) cc_final: 0.5131 (ttp-170) REVERT: Z 172 MET cc_start: 0.3470 (OUTLIER) cc_final: 0.3084 (tmm) REVERT: Z 238 ARG cc_start: 0.5926 (mmt90) cc_final: 0.5342 (mtm180) REVERT: Z 259 MET cc_start: 0.3856 (mmp) cc_final: 0.3017 (mmt) REVERT: Z 363 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: Z 443 ASN cc_start: 0.6804 (m-40) cc_final: 0.6571 (m110) REVERT: Z 455 LYS cc_start: 0.4794 (tptt) cc_final: 0.4193 (tptp) REVERT: Y 91 GLU cc_start: 0.5267 (pm20) cc_final: 0.4517 (mt-10) REVERT: Y 295 THR cc_start: 0.4126 (t) cc_final: 0.3636 (t) REVERT: Y 363 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7269 (pt0) outliers start: 135 outliers final: 74 residues processed: 493 average time/residue: 0.5097 time to fit residues: 427.6015 Evaluate side-chains 413 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 328 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 632 MET Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 617 MET Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 389 LEU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 201 MET Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 341 CYS Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 389 LEU Chi-restraints excluded: chain Y residue 505 THR Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 471 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 635 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 470 optimal weight: 4.9990 chunk 609 optimal weight: 2.9990 chunk 617 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.149065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115766 restraints weight = 99349.554| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.08 r_work: 0.3178 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 54480 Z= 0.244 Angle : 0.582 9.923 73716 Z= 0.307 Chirality : 0.047 0.192 8244 Planarity : 0.005 0.059 9630 Dihedral : 4.774 55.630 7658 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.73 % Allowed : 12.89 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 6852 helix: 0.76 (0.11), residues: 2148 sheet: -0.68 (0.16), residues: 1248 loop : -1.89 (0.10), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 396 HIS 0.030 0.001 HIS B 212 PHE 0.015 0.002 PHE B 353 TYR 0.016 0.002 TYR Z 157 ARG 0.007 0.000 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 359 time to evaluate : 4.613 Fit side-chains revert: symmetry clash REVERT: B 129 ARG cc_start: 0.6061 (tmt170) cc_final: 0.4322 (tpp80) REVERT: B 259 MET cc_start: 0.3841 (mmp) cc_final: 0.2943 (mmt) REVERT: B 409 LYS cc_start: 0.7999 (tttt) cc_final: 0.7448 (ttpt) REVERT: B 419 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6571 (mt) REVERT: D 46 ARG cc_start: 0.7159 (mmt-90) cc_final: 0.6924 (mmt-90) REVERT: F 46 ARG cc_start: 0.7170 (mmt-90) cc_final: 0.6923 (mmt-90) REVERT: S 129 ARG cc_start: 0.6370 (tmt170) cc_final: 0.5281 (ttp-170) REVERT: S 172 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3229 (tmm) REVERT: S 218 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.4299 (mm) REVERT: S 238 ARG cc_start: 0.6087 (mmt90) cc_final: 0.5440 (mtm180) REVERT: S 259 MET cc_start: 0.3863 (mmp) cc_final: 0.2900 (mmt) REVERT: S 419 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6549 (mp) REVERT: S 455 LYS cc_start: 0.4885 (tptt) cc_final: 0.4246 (tptp) REVERT: V 129 ARG cc_start: 0.6088 (tmt170) cc_final: 0.4342 (tpp80) REVERT: V 259 MET cc_start: 0.3810 (mmp) cc_final: 0.2934 (mmt) REVERT: V 409 LYS cc_start: 0.8025 (tttt) cc_final: 0.7449 (ttpt) REVERT: V 419 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6587 (mt) REVERT: V 440 ILE cc_start: 0.5695 (pt) cc_final: 0.5183 (tp) REVERT: V 443 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5760 (t0) REVERT: X 91 GLU cc_start: 0.4757 (pm20) cc_final: 0.4288 (mt-10) REVERT: X 396 TRP cc_start: 0.6793 (t60) cc_final: 0.6493 (t60) REVERT: X 419 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6562 (mt) REVERT: Z 129 ARG cc_start: 0.6288 (tmt170) cc_final: 0.5250 (ttp-170) REVERT: Z 172 MET cc_start: 0.3694 (OUTLIER) cc_final: 0.3244 (tmm) REVERT: Z 218 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4351 (mm) REVERT: Z 259 MET cc_start: 0.3817 (mmp) cc_final: 0.3040 (mmt) REVERT: Z 419 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6547 (mp) REVERT: Z 455 LYS cc_start: 0.4900 (tptt) cc_final: 0.4270 (tptp) REVERT: Z 603 MET cc_start: 0.5534 (ttp) cc_final: 0.5200 (ttp) REVERT: Y 91 GLU cc_start: 0.4997 (pm20) cc_final: 0.4264 (mt-10) REVERT: Y 419 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6557 (mt) outliers start: 156 outliers final: 101 residues processed: 489 average time/residue: 0.5007 time to fit residues: 417.0371 Evaluate side-chains 428 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 316 time to evaluate : 4.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 303 ILE Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 419 LEU Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 465 LEU Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 443 ASN Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 201 MET Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 303 ILE Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 419 LEU Chi-restraints excluded: chain Z residue 465 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 662 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 22 optimal weight: 0.0040 chunk 254 optimal weight: 8.9990 chunk 240 optimal weight: 0.5980 chunk 440 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 294 optimal weight: 0.5980 chunk 550 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 298 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 294 ASN ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 212 HIS Y 280 ASN ** Y 301 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 = 0.4125 r_free = 0.4125 target = 0.148978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.116197 restraints weight = 98436.229| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.09 r_work: 0.3216 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54480 Z= 0.136 Angle : 0.512 10.608 73716 Z= 0.267 Chirality : 0.044 0.234 8244 Planarity : 0.004 0.061 9630 Dihedral : 4.194 46.150 7658 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.59 % Allowed : 13.50 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.10), residues: 6852 helix: 1.00 (0.12), residues: 2178 sheet: -0.10 (0.17), residues: 1032 loop : -1.73 (0.10), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 396 HIS 0.002 0.001 HIS C 229 PHE 0.033 0.001 PHE Y 288 TYR 0.014 0.001 TYR B 157 ARG 0.006 0.000 ARG X 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 382 time to evaluate : 4.527 Fit side-chains REVERT: B 129 ARG cc_start: 0.6133 (tmt170) cc_final: 0.5207 (ptt180) REVERT: B 259 MET cc_start: 0.3682 (mmp) cc_final: 0.2847 (mmt) REVERT: B 295 THR cc_start: 0.4399 (t) cc_final: 0.3994 (m) REVERT: B 409 LYS cc_start: 0.8018 (tttt) cc_final: 0.7429 (ttpt) REVERT: B 564 MET cc_start: 0.7730 (mtp) cc_final: 0.7424 (mtp) REVERT: B 617 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5341 (tpt) REVERT: C 70 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: D 46 ARG cc_start: 0.7155 (mmt-90) cc_final: 0.6770 (mmt-90) REVERT: F 46 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6916 (mmt-90) REVERT: G 70 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: S 91 GLU cc_start: 0.4421 (pm20) cc_final: 0.3822 (mt-10) REVERT: S 129 ARG cc_start: 0.6207 (tmt170) cc_final: 0.5181 (ptt180) REVERT: S 238 ARG cc_start: 0.5998 (mmt90) cc_final: 0.5669 (ttm110) REVERT: S 259 MET cc_start: 0.3798 (mmp) cc_final: 0.2881 (mmt) REVERT: S 455 LYS cc_start: 0.4805 (tptt) cc_final: 0.4276 (tptp) REVERT: S 603 MET cc_start: 0.5731 (ttp) cc_final: 0.5529 (ttp) REVERT: S 617 MET cc_start: 0.6092 (tpp) cc_final: 0.5815 (tpp) REVERT: V 129 ARG cc_start: 0.6090 (tmt170) cc_final: 0.5181 (ptt180) REVERT: V 259 MET cc_start: 0.3679 (mmp) cc_final: 0.2808 (mmt) REVERT: V 409 LYS cc_start: 0.8033 (tttt) cc_final: 0.7416 (ttpt) REVERT: V 440 ILE cc_start: 0.5591 (pt) cc_final: 0.5167 (tp) REVERT: V 564 MET cc_start: 0.7698 (mtp) cc_final: 0.7390 (mtp) REVERT: X 91 GLU cc_start: 0.4603 (pm20) cc_final: 0.4223 (mt-10) REVERT: X 293 MET cc_start: 0.4917 (tmm) cc_final: 0.4213 (tmm) REVERT: Z 91 GLU cc_start: 0.4485 (pm20) cc_final: 0.3897 (mt-10) REVERT: Z 129 ARG cc_start: 0.6157 (tmt170) cc_final: 0.5246 (ptt180) REVERT: Z 218 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4430 (mm) REVERT: Z 259 MET cc_start: 0.4037 (mmp) cc_final: 0.2989 (mmt) REVERT: Z 455 LYS cc_start: 0.4830 (tptt) cc_final: 0.4275 (tptp) REVERT: Z 603 MET cc_start: 0.5446 (ttp) cc_final: 0.5196 (ttp) REVERT: Y 91 GLU cc_start: 0.5074 (pm20) cc_final: 0.4468 (mt-10) REVERT: Y 293 MET cc_start: 0.4971 (tmm) cc_final: 0.4166 (tmm) REVERT: Y 295 THR cc_start: 0.4207 (t) cc_final: 0.3822 (m) REVERT: Y 396 TRP cc_start: 0.6415 (t60) cc_final: 0.6203 (t60) REVERT: Y 468 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7974 (mp0) outliers start: 148 outliers final: 89 residues processed: 496 average time/residue: 0.5524 time to fit residues: 469.4192 Evaluate side-chains 422 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 328 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 619 VAL Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 212 HIS Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 494 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 466 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 584 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS F 164 ASN H 42 HIS ** S 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 212 HIS Y 280 ASN ** Y 301 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 = 0.4076 r_free = 0.4076 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113884 restraints weight = 98957.757| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.99 r_work: 0.3156 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 54480 Z= 0.298 Angle : 0.613 10.403 73716 Z= 0.325 Chirality : 0.047 0.329 8244 Planarity : 0.005 0.059 9630 Dihedral : 4.914 52.224 7658 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.25 % Allowed : 13.47 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.10), residues: 6852 helix: 0.82 (0.12), residues: 2154 sheet: -0.50 (0.16), residues: 1182 loop : -1.79 (0.10), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 396 HIS 0.013 0.001 HIS V 212 PHE 0.018 0.002 PHE Y 288 TYR 0.021 0.002 TYR Z 414 ARG 0.006 0.001 ARG Z 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 330 time to evaluate : 4.537 Fit side-chains REVERT: B 129 ARG cc_start: 0.6116 (tmt170) cc_final: 0.4646 (ttm170) REVERT: B 259 MET cc_start: 0.3939 (mmp) cc_final: 0.3118 (mmt) REVERT: B 295 THR cc_start: 0.4638 (t) cc_final: 0.4254 (m) REVERT: B 409 LYS cc_start: 0.8014 (tttt) cc_final: 0.7460 (ttpt) REVERT: B 419 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6482 (mt) REVERT: C 70 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: D 50 MET cc_start: 0.8849 (tpt) cc_final: 0.8522 (tpt) REVERT: D 126 MET cc_start: 0.8970 (mtp) cc_final: 0.8711 (mtm) REVERT: E 50 MET cc_start: 0.8593 (tpp) cc_final: 0.8333 (tpt) REVERT: F 46 ARG cc_start: 0.7137 (mmt-90) cc_final: 0.6897 (mmt-90) REVERT: F 50 MET cc_start: 0.8846 (tpt) cc_final: 0.8517 (tpt) REVERT: G 70 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: H 50 MET cc_start: 0.8594 (tpp) cc_final: 0.8339 (tpt) REVERT: S 91 GLU cc_start: 0.4902 (pm20) cc_final: 0.4221 (mt-10) REVERT: S 129 ARG cc_start: 0.6314 (tmt170) cc_final: 0.5204 (ptt180) REVERT: S 172 MET cc_start: 0.3457 (OUTLIER) cc_final: 0.3000 (tmm) REVERT: S 259 MET cc_start: 0.3868 (mmp) cc_final: 0.3185 (mmt) REVERT: S 419 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6938 (mt) REVERT: S 455 LYS cc_start: 0.4893 (tptt) cc_final: 0.4317 (tptp) REVERT: S 530 MET cc_start: 0.7925 (ptp) cc_final: 0.7713 (ptp) REVERT: V 129 ARG cc_start: 0.6148 (tmt170) cc_final: 0.4684 (ttm170) REVERT: V 259 MET cc_start: 0.3944 (mmp) cc_final: 0.3276 (mmt) REVERT: V 419 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6588 (mt) REVERT: V 440 ILE cc_start: 0.6224 (pt) cc_final: 0.5743 (tp) REVERT: X 91 GLU cc_start: 0.4912 (pm20) cc_final: 0.4365 (mt-10) REVERT: X 172 MET cc_start: 0.3573 (tpt) cc_final: 0.2505 (tmm) REVERT: X 363 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7028 (pt0) REVERT: X 443 ASN cc_start: 0.5924 (OUTLIER) cc_final: 0.5510 (t0) REVERT: X 468 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: Z 91 GLU cc_start: 0.4929 (pm20) cc_final: 0.4249 (mt-10) REVERT: Z 129 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5219 (ptt180) REVERT: Z 172 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.2984 (tmm) REVERT: Z 419 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6928 (mt) REVERT: Z 455 LYS cc_start: 0.4900 (tptt) cc_final: 0.4329 (tptp) REVERT: Y 91 GLU cc_start: 0.5016 (pm20) cc_final: 0.4462 (mt-10) REVERT: Y 295 THR cc_start: 0.4383 (t) cc_final: 0.3944 (m) REVERT: Y 363 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7035 (pt0) REVERT: Y 443 ASN cc_start: 0.5931 (OUTLIER) cc_final: 0.5494 (t0) REVERT: Y 468 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7785 (mp0) outliers start: 186 outliers final: 129 residues processed: 479 average time/residue: 0.4899 time to fit residues: 402.3218 Evaluate side-chains 454 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 311 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 385 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 419 LEU Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 465 LEU Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 468 GLU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 419 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 526 optimal weight: 7.9990 chunk 471 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 561 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 666 optimal weight: 7.9990 chunk 636 optimal weight: 7.9990 chunk 512 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 516 HIS ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 516 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.144589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111190 restraints weight = 97953.791| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.04 r_work: 0.3146 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 54480 Z= 0.341 Angle : 0.645 11.568 73716 Z= 0.343 Chirality : 0.049 0.306 8244 Planarity : 0.005 0.062 9630 Dihedral : 5.206 54.807 7658 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.38 % Allowed : 14.13 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.10), residues: 6852 helix: 0.57 (0.11), residues: 2154 sheet: -0.79 (0.16), residues: 1164 loop : -1.86 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 396 HIS 0.025 0.002 HIS Y 212 PHE 0.015 0.002 PHE Y 288 TYR 0.023 0.002 TYR S 414 ARG 0.006 0.001 ARG X 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 328 time to evaluate : 4.668 Fit side-chains REVERT: B 259 MET cc_start: 0.3811 (mmp) cc_final: 0.3044 (mmt) REVERT: B 378 GLU cc_start: 0.7109 (tp30) cc_final: 0.6829 (tp30) REVERT: B 419 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6512 (mt) REVERT: C 70 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: D 50 MET cc_start: 0.8825 (tpt) cc_final: 0.8528 (tpt) REVERT: D 126 MET cc_start: 0.8970 (mtp) cc_final: 0.8735 (mtm) REVERT: E 50 MET cc_start: 0.8647 (tpp) cc_final: 0.8408 (tpt) REVERT: F 46 ARG cc_start: 0.7249 (mmt-90) cc_final: 0.6993 (mmt-90) REVERT: F 50 MET cc_start: 0.8809 (tpt) cc_final: 0.8501 (tpt) REVERT: G 70 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: H 50 MET cc_start: 0.8641 (tpp) cc_final: 0.8440 (tpt) REVERT: S 172 MET cc_start: 0.3259 (OUTLIER) cc_final: 0.2994 (tmm) REVERT: S 259 MET cc_start: 0.3814 (mmp) cc_final: 0.3099 (mmt) REVERT: S 419 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7138 (mt) REVERT: S 455 LYS cc_start: 0.4946 (tptt) cc_final: 0.4260 (tptp) REVERT: V 259 MET cc_start: 0.3861 (mmp) cc_final: 0.3231 (mmt) REVERT: V 419 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6976 (mt) REVERT: X 91 GLU cc_start: 0.4951 (pm20) cc_final: 0.4152 (mt-10) REVERT: X 117 MET cc_start: 0.6416 (mtm) cc_final: 0.6106 (mtt) REVERT: X 363 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: X 407 MET cc_start: 0.6964 (tpp) cc_final: 0.6431 (tpp) REVERT: X 419 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6890 (mt) REVERT: X 443 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5705 (t0) REVERT: X 468 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: Z 129 ARG cc_start: 0.6459 (tmt170) cc_final: 0.5279 (ttp-170) REVERT: Z 172 MET cc_start: 0.3493 (OUTLIER) cc_final: 0.3026 (tmm) REVERT: Z 259 MET cc_start: 0.3983 (mmp) cc_final: 0.3286 (mmt) REVERT: Z 419 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7143 (mt) REVERT: Z 455 LYS cc_start: 0.5004 (tptt) cc_final: 0.4340 (tptp) REVERT: Y 91 GLU cc_start: 0.5123 (pm20) cc_final: 0.4312 (mt-10) REVERT: Y 117 MET cc_start: 0.6375 (mtm) cc_final: 0.6081 (mtt) REVERT: Y 363 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: Y 407 MET cc_start: 0.7213 (tpp) cc_final: 0.6510 (tpp) REVERT: Y 419 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6827 (mt) REVERT: Y 443 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5665 (t0) REVERT: Y 468 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7875 (mp0) outliers start: 193 outliers final: 132 residues processed: 484 average time/residue: 0.5024 time to fit residues: 415.1532 Evaluate side-chains 445 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 297 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 419 LEU Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 465 LEU Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 468 GLU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 419 LEU Chi-restraints excluded: chain Z residue 465 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 555 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 345 optimal weight: 0.3980 chunk 215 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 671 optimal weight: 7.9990 chunk 449 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 639 GLN ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 280 ASN ** Y 301 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 = 0.4093 r_free = 0.4093 target = 0.147647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.114497 restraints weight = 99225.728| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.02 r_work: 0.3204 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54480 Z= 0.166 Angle : 0.541 11.615 73716 Z= 0.284 Chirality : 0.045 0.327 8244 Planarity : 0.004 0.063 9630 Dihedral : 4.614 58.426 7658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.67 % Favored : 95.32 % Rotamer: Outliers : 2.55 % Allowed : 14.53 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 6852 helix: 0.85 (0.12), residues: 2178 sheet: -0.68 (0.15), residues: 1194 loop : -1.73 (0.10), residues: 3480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 396 HIS 0.003 0.001 HIS Y 421 PHE 0.021 0.001 PHE S 353 TYR 0.017 0.001 TYR Z 444 ARG 0.006 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 327 time to evaluate : 4.577 Fit side-chains REVERT: B 135 ILE cc_start: 0.4979 (OUTLIER) cc_final: 0.4427 (mt) REVERT: B 259 MET cc_start: 0.3653 (mmp) cc_final: 0.2834 (mmt) REVERT: B 378 GLU cc_start: 0.6811 (tp30) cc_final: 0.6581 (tp30) REVERT: B 564 MET cc_start: 0.7775 (mtp) cc_final: 0.7546 (mtp) REVERT: B 566 MET cc_start: 0.7362 (tpt) cc_final: 0.6983 (ttt) REVERT: B 628 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: C 70 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 46 ARG cc_start: 0.7003 (mmt-90) cc_final: 0.6735 (mmt-90) REVERT: F 46 ARG cc_start: 0.7222 (mmt-90) cc_final: 0.6993 (mmt-90) REVERT: G 70 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: S 91 GLU cc_start: 0.4709 (pm20) cc_final: 0.4010 (mt-10) REVERT: S 259 MET cc_start: 0.3638 (mmp) cc_final: 0.2971 (mmt) REVERT: S 378 GLU cc_start: 0.7136 (tp30) cc_final: 0.6818 (tp30) REVERT: S 455 LYS cc_start: 0.5002 (tptt) cc_final: 0.4354 (tptp) REVERT: V 135 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4410 (mt) REVERT: V 259 MET cc_start: 0.3659 (mmp) cc_final: 0.2815 (mmt) REVERT: V 378 GLU cc_start: 0.6781 (tp30) cc_final: 0.6550 (tp30) REVERT: V 419 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6897 (mt) REVERT: V 547 GLU cc_start: 0.5518 (pm20) cc_final: 0.5127 (pm20) REVERT: V 564 MET cc_start: 0.7767 (mtp) cc_final: 0.7534 (mtp) REVERT: V 566 MET cc_start: 0.7342 (tpt) cc_final: 0.6971 (ttt) REVERT: V 603 MET cc_start: 0.5639 (ttp) cc_final: 0.4814 (mpp) REVERT: X 91 GLU cc_start: 0.4970 (pm20) cc_final: 0.4433 (mt-10) REVERT: X 172 MET cc_start: 0.3542 (tpt) cc_final: 0.2490 (tmm) REVERT: X 293 MET cc_start: 0.4020 (tmm) cc_final: 0.3762 (tmm) REVERT: X 363 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: X 407 MET cc_start: 0.7736 (tpp) cc_final: 0.7232 (tpp) REVERT: X 419 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6715 (mt) REVERT: X 468 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: Z 91 GLU cc_start: 0.4678 (pm20) cc_final: 0.4004 (mt-10) REVERT: Z 129 ARG cc_start: 0.6342 (tmt170) cc_final: 0.5234 (ttp-170) REVERT: Z 259 MET cc_start: 0.3896 (mmp) cc_final: 0.3232 (mmt) REVERT: Z 293 MET cc_start: 0.4996 (tmm) cc_final: 0.4695 (tmm) REVERT: Z 378 GLU cc_start: 0.7077 (tp30) cc_final: 0.6740 (tp30) REVERT: Z 455 LYS cc_start: 0.5001 (tptt) cc_final: 0.4356 (tptp) REVERT: Y 91 GLU cc_start: 0.5077 (pm20) cc_final: 0.4504 (mt-10) REVERT: Y 172 MET cc_start: 0.3526 (tpt) cc_final: 0.2503 (tmm) REVERT: Y 293 MET cc_start: 0.4350 (tmm) cc_final: 0.4111 (tmm) REVERT: Y 294 ASN cc_start: 0.5153 (t0) cc_final: 0.4907 (m-40) REVERT: Y 363 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: Y 419 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6678 (mt) REVERT: Y 468 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7627 (mp0) outliers start: 146 outliers final: 114 residues processed: 441 average time/residue: 0.5140 time to fit residues: 387.7575 Evaluate side-chains 430 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 304 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 86 TYR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain S residue 639 GLN Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 86 TYR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 468 GLU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 634 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 314 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 375 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 494 optimal weight: 3.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 280 ASN ** Y 301 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 = 0.4066 r_free = 0.4066 target = 0.145597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.111688 restraints weight = 98509.137| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.00 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54480 Z= 0.298 Angle : 0.612 14.596 73716 Z= 0.323 Chirality : 0.048 0.313 8244 Planarity : 0.005 0.064 9630 Dihedral : 5.017 58.896 7658 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 2.76 % Allowed : 14.76 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.10), residues: 6852 helix: 0.71 (0.11), residues: 2154 sheet: -0.76 (0.15), residues: 1188 loop : -1.81 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Y 396 HIS 0.005 0.001 HIS G 392 PHE 0.016 0.002 PHE S 353 TYR 0.017 0.002 TYR S 414 ARG 0.007 0.001 ARG Z 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 307 time to evaluate : 4.994 Fit side-chains REVERT: B 135 ILE cc_start: 0.5281 (OUTLIER) cc_final: 0.4712 (mt) REVERT: B 259 MET cc_start: 0.3650 (mmp) cc_final: 0.2852 (mmt) REVERT: B 378 GLU cc_start: 0.6970 (tp30) cc_final: 0.6691 (tp30) REVERT: B 566 MET cc_start: 0.7339 (tpt) cc_final: 0.6960 (ttt) REVERT: C 70 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: D 46 ARG cc_start: 0.7063 (mmt-90) cc_final: 0.6815 (mmt-90) REVERT: E 50 MET cc_start: 0.8583 (tpp) cc_final: 0.8330 (tpt) REVERT: F 46 ARG cc_start: 0.7232 (mmt-90) cc_final: 0.7005 (mmt-90) REVERT: G 70 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: H 50 MET cc_start: 0.8571 (tpp) cc_final: 0.8355 (tpt) REVERT: S 259 MET cc_start: 0.3653 (mmp) cc_final: 0.2954 (mmt) REVERT: S 378 GLU cc_start: 0.7131 (tp30) cc_final: 0.6786 (tp30) REVERT: V 135 ILE cc_start: 0.5296 (OUTLIER) cc_final: 0.4715 (mt) REVERT: V 259 MET cc_start: 0.3808 (mmp) cc_final: 0.3135 (mmt) REVERT: V 378 GLU cc_start: 0.6908 (tp30) cc_final: 0.6632 (tp30) REVERT: V 419 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6932 (mt) REVERT: X 91 GLU cc_start: 0.4837 (pm20) cc_final: 0.4084 (mt-10) REVERT: X 172 MET cc_start: 0.3375 (tpt) cc_final: 0.2447 (tmm) REVERT: X 363 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: X 407 MET cc_start: 0.7746 (tpp) cc_final: 0.7243 (tpp) REVERT: X 419 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6748 (mt) REVERT: X 468 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: Z 160 MET cc_start: 0.3187 (ppp) cc_final: 0.1747 (ptm) REVERT: Z 172 MET cc_start: 0.3866 (OUTLIER) cc_final: 0.3385 (tmm) REVERT: Z 259 MET cc_start: 0.3932 (mmp) cc_final: 0.3186 (mmt) REVERT: Z 293 MET cc_start: 0.4588 (tmm) cc_final: 0.4375 (tmm) REVERT: Z 378 GLU cc_start: 0.7092 (tp30) cc_final: 0.6737 (tp30) REVERT: Z 419 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6962 (mt) REVERT: Y 91 GLU cc_start: 0.5039 (pm20) cc_final: 0.4260 (mt-10) REVERT: Y 172 MET cc_start: 0.3399 (tpt) cc_final: 0.2514 (tmm) REVERT: Y 363 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: Y 419 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6769 (mt) REVERT: Y 468 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7646 (mp0) outliers start: 158 outliers final: 128 residues processed: 431 average time/residue: 0.4962 time to fit residues: 368.4418 Evaluate side-chains 434 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 293 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 468 GLU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 419 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 411 optimal weight: 0.0570 chunk 358 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 605 optimal weight: 10.0000 chunk 656 optimal weight: 5.9990 chunk 488 optimal weight: 0.8980 chunk 545 optimal weight: 9.9990 chunk 673 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 0.0170 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 118 ASN G 118 ASN ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 639 GLN V 301 HIS ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 280 ASN Y 301 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.147498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115047 restraints weight = 97273.083| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.90 r_work: 0.3221 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54480 Z= 0.143 Angle : 0.525 12.914 73716 Z= 0.273 Chirality : 0.045 0.316 8244 Planarity : 0.004 0.065 9630 Dihedral : 4.391 58.775 7658 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 2.15 % Allowed : 15.34 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.10), residues: 6852 helix: 0.96 (0.12), residues: 2178 sheet: -0.45 (0.16), residues: 1134 loop : -1.68 (0.10), residues: 3540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP Y 396 HIS 0.002 0.001 HIS F 148 PHE 0.013 0.001 PHE S 353 TYR 0.018 0.001 TYR S 444 ARG 0.006 0.000 ARG V 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 334 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.6037 (tmt170) cc_final: 0.5012 (ptt180) REVERT: B 135 ILE cc_start: 0.5158 (OUTLIER) cc_final: 0.4669 (mt) REVERT: B 259 MET cc_start: 0.3708 (mmp) cc_final: 0.2885 (mmt) REVERT: B 363 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: B 547 GLU cc_start: 0.5411 (pm20) cc_final: 0.4992 (pm20) REVERT: B 566 MET cc_start: 0.7300 (tpt) cc_final: 0.6929 (ttt) REVERT: C 70 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: D 46 ARG cc_start: 0.7016 (mmt-90) cc_final: 0.6676 (mmt-90) REVERT: F 46 ARG cc_start: 0.7211 (mmt-90) cc_final: 0.7000 (mmt-90) REVERT: G 70 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: S 172 MET cc_start: 0.3459 (OUTLIER) cc_final: 0.3204 (tmm) REVERT: S 238 ARG cc_start: 0.5937 (mmt90) cc_final: 0.5698 (tpm170) REVERT: S 259 MET cc_start: 0.3948 (mmp) cc_final: 0.3271 (mmt) REVERT: S 378 GLU cc_start: 0.6992 (tp30) cc_final: 0.6666 (tp30) REVERT: S 455 LYS cc_start: 0.4776 (tptt) cc_final: 0.4230 (tptp) REVERT: S 603 MET cc_start: 0.5150 (ptm) cc_final: 0.4820 (ttp) REVERT: V 129 ARG cc_start: 0.6074 (tmt170) cc_final: 0.4999 (ptt180) REVERT: V 135 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4634 (mt) REVERT: V 363 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: V 547 GLU cc_start: 0.5400 (pm20) cc_final: 0.4982 (pm20) REVERT: V 566 MET cc_start: 0.7343 (tpt) cc_final: 0.7059 (ttt) REVERT: X 26 ARG cc_start: 0.6051 (mmm160) cc_final: 0.5640 (mmp80) REVERT: X 91 GLU cc_start: 0.4760 (pm20) cc_final: 0.4210 (mt-10) REVERT: X 172 MET cc_start: 0.3609 (tpt) cc_final: 0.2473 (tmm) REVERT: X 419 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6739 (mt) REVERT: Z 160 MET cc_start: 0.3022 (ppp) cc_final: 0.1878 (ptm) REVERT: Z 172 MET cc_start: 0.3474 (OUTLIER) cc_final: 0.2974 (tmm) REVERT: Z 259 MET cc_start: 0.3772 (mmp) cc_final: 0.3069 (mmt) REVERT: Z 378 GLU cc_start: 0.6982 (tp30) cc_final: 0.6645 (tp30) REVERT: Z 455 LYS cc_start: 0.4698 (tptt) cc_final: 0.4149 (tptp) REVERT: Z 603 MET cc_start: 0.5097 (ptm) cc_final: 0.4761 (ttp) REVERT: Y 91 GLU cc_start: 0.4930 (pm20) cc_final: 0.4359 (mt-10) REVERT: Y 172 MET cc_start: 0.3563 (tpt) cc_final: 0.2492 (tmm) REVERT: Y 396 TRP cc_start: 0.6619 (t60) cc_final: 0.6269 (t60) REVERT: Y 419 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6716 (mt) REVERT: Y 443 ASN cc_start: 0.6004 (m110) cc_final: 0.5448 (t0) outliers start: 123 outliers final: 106 residues processed: 428 average time/residue: 0.5086 time to fit residues: 369.7728 Evaluate side-chains 428 residues out of total 5718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 312 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 172 MET Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain S residue 639 GLN Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 135 ILE Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 86 TYR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 468 GLU Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 612 VAL Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 86 TYR Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 172 MET Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 660 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 447 optimal weight: 6.9990 chunk 595 optimal weight: 10.0000 chunk 274 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 631 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 602 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115635 restraints weight = 100251.647| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.02 r_work: 0.3217 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 54480 Z= 0.174 Angle : 0.601 59.132 73716 Z= 0.326 Chirality : 0.045 0.347 8244 Planarity : 0.004 0.065 9630 Dihedral : 4.381 58.812 7657 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 2.40 % Allowed : 15.30 % Favored : 82.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.10), residues: 6852 helix: 0.97 (0.12), residues: 2178 sheet: -0.44 (0.16), residues: 1134 loop : -1.67 (0.10), residues: 3540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Y 396 HIS 0.002 0.001 HIS F 517 PHE 0.011 0.001 PHE S 353 TYR 0.036 0.001 TYR B 272 ARG 0.005 0.000 ARG B 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26236.36 seconds wall clock time: 450 minutes 16.67 seconds (27016.67 seconds total)