Starting phenix.real_space_refine on Tue Sep 24 23:31:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_40474.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_40474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_40474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_40474.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/09_2024/8sgz_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 15.79, per 1000 atoms: 0.30 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: 10.10 Conformation dependent library (CDL) restraints added in 5.5 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: 6.10 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: 27.99 Time building geometry restraints manager: 12.16 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: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 3.440 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: 0.040 Extract box with map and model: 1.560 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 96.670 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.990 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 69 poor density : 904 time to evaluate : 4.539 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: 0.5721 time to fit residues: 898.3187 Evaluate side-chains 423 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 413 time to evaluate : 4.535 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 fitting. rotamer outliers: 89 poor density : 491 time to evaluate : 4.606 Fit side-chains REVERT: B 129 ARG cc_start: 0.5926 (tmt170) cc_final: 0.5545 (ptt180) REVERT: B 259 MET cc_start: 0.3381 (mmp) cc_final: 0.2759 (mmt) REVERT: E 46 ARG cc_start: 0.6559 (mtt180) cc_final: 0.6270 (mmt-90) REVERT: E 78 MET cc_start: 0.7745 (mmm) cc_final: 0.7235 (mmm) REVERT: E 197 MET cc_start: 0.8800 (mtp) cc_final: 0.8545 (mtp) REVERT: E 271 PRO cc_start: 0.7378 (Cg_endo) cc_final: 0.7173 (Cg_exo) REVERT: H 78 MET cc_start: 0.7774 (mmm) cc_final: 0.7278 (mmm) REVERT: H 204 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (ptt) REVERT: H 271 PRO cc_start: 0.7348 (Cg_endo) cc_final: 0.7142 (Cg_exo) REVERT: S 129 ARG cc_start: 0.5731 (tmt170) cc_final: 0.5174 (ptt180) REVERT: S 218 ILE cc_start: 0.4988 (OUTLIER) cc_final: 0.4626 (mm) REVERT: S 259 MET cc_start: 0.3726 (mmp) cc_final: 0.3077 (mmt) REVERT: S 455 LYS cc_start: 0.4241 (tptt) cc_final: 0.3778 (tptp) REVERT: V 129 ARG cc_start: 0.5841 (tmt170) cc_final: 0.5435 (ptt180) REVERT: V 259 MET cc_start: 0.3323 (mmp) cc_final: 0.2742 (mmt) REVERT: V 628 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: X 80 GLN cc_start: 0.4800 (pm20) cc_final: 0.4412 (mp10) REVERT: Z 129 ARG cc_start: 0.5749 (tmt170) cc_final: 0.5190 (ptt180) REVERT: Z 160 MET cc_start: 0.1988 (tpp) cc_final: 0.1777 (tpp) REVERT: Z 218 ILE cc_start: 0.4996 (OUTLIER) cc_final: 0.4660 (mm) REVERT: Z 259 MET cc_start: 0.3697 (mmp) cc_final: 0.3041 (mmt) REVERT: Z 455 LYS cc_start: 0.4207 (tptt) cc_final: 0.3778 (tptp) REVERT: Y 272 TYR cc_start: 0.3756 (t80) cc_final: 0.3543 (t80) REVERT: Y 295 THR cc_start: 0.3704 (t) cc_final: 0.3046 (m) REVERT: Y 466 MET cc_start: 0.7101 (ttp) cc_final: 0.6790 (ttp) outliers start: 89 outliers final: 35 residues processed: 545 average time/residue: 0.5461 time to fit residues: 493.9900 Evaluate side-chains 388 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 349 time to evaluate : 4.583 ------------------------------------------------------------------------------- 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 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 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 636 ILE Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL 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 636 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 342 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 512 optimal weight: 0.9990 chunk 419 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 616 optimal weight: 0.5980 chunk 666 optimal weight: 8.9990 chunk 549 optimal weight: 10.0000 chunk 611 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 494 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** S 280 ASN ** 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 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 212 HIS X 236 GLN X 280 ASN X 285 GLN ** X 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 280 ASN ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 443 ASN Y 13 ASN Y 212 HIS Y 236 GLN Y 280 ASN Y 285 GLN ** Y 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54480 Z= 0.154 Angle : 0.532 10.158 73716 Z= 0.278 Chirality : 0.045 0.149 8244 Planarity : 0.004 0.058 9630 Dihedral : 4.093 28.783 7658 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 1.87 % Allowed : 11.73 % Favored : 86.39 % 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: -0.85 (0.10), residues: 6852 helix: 1.01 (0.12), residues: 2178 sheet: -0.22 (0.17), residues: 1062 loop : -1.73 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 396 HIS 0.021 0.001 HIS Y 212 PHE 0.011 0.001 PHE V 353 TYR 0.023 0.001 TYR X 272 ARG 0.005 0.000 ARG X 436 *********************** 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 519 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 412 time to evaluate : 4.674 Fit side-chains REVERT: B 129 ARG cc_start: 0.5844 (tmt170) cc_final: 0.5459 (ptt180) REVERT: B 212 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.5939 (t-170) REVERT: B 259 MET cc_start: 0.3474 (mmp) cc_final: 0.2875 (mmt) REVERT: B 295 THR cc_start: 0.4023 (t) cc_final: 0.3551 (m) REVERT: D 271 PRO cc_start: 0.7270 (Cg_endo) cc_final: 0.7033 (Cg_exo) REVERT: E 78 MET cc_start: 0.7848 (mmm) cc_final: 0.7314 (mmm) REVERT: E 197 MET cc_start: 0.8827 (mtp) cc_final: 0.8599 (mtp) REVERT: E 291 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8201 (t) REVERT: F 46 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6640 (mmt-90) REVERT: H 78 MET cc_start: 0.7855 (mmm) cc_final: 0.7323 (mmm) REVERT: H 197 MET cc_start: 0.8836 (mtp) cc_final: 0.8570 (mtp) REVERT: H 291 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8158 (t) REVERT: S 129 ARG cc_start: 0.5772 (tmt170) cc_final: 0.5292 (ptt180) REVERT: S 259 MET cc_start: 0.3565 (mmp) cc_final: 0.2841 (mmt) REVERT: S 463 MET cc_start: 0.7463 (mmm) cc_final: 0.7225 (mmm) REVERT: S 540 ILE cc_start: 0.7948 (mm) cc_final: 0.7589 (mm) REVERT: V 129 ARG cc_start: 0.5820 (tmt170) cc_final: 0.5385 (ptt180) REVERT: V 259 MET cc_start: 0.3478 (mmp) cc_final: 0.2897 (mmt) REVERT: V 628 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: X 91 GLU cc_start: 0.4217 (pm20) cc_final: 0.3946 (mt-10) REVERT: X 129 ARG cc_start: 0.5534 (tmt170) cc_final: 0.5289 (ptt180) REVERT: X 218 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4722 (mm) REVERT: X 293 MET cc_start: 0.6043 (tmm) cc_final: 0.5571 (tmm) REVERT: Z 129 ARG cc_start: 0.5690 (tmt170) cc_final: 0.5265 (ptt180) REVERT: Z 259 MET cc_start: 0.3627 (mmp) cc_final: 0.2923 (mmt) REVERT: Z 463 MET cc_start: 0.7472 (mmm) cc_final: 0.7227 (mmm) REVERT: Z 540 ILE cc_start: 0.7861 (mm) cc_final: 0.7482 (mm) REVERT: Y 91 GLU cc_start: 0.4271 (pm20) cc_final: 0.4009 (mt-10) REVERT: Y 129 ARG cc_start: 0.5542 (tmt170) cc_final: 0.5270 (ptt180) REVERT: Y 218 ILE cc_start: 0.5359 (OUTLIER) cc_final: 0.4797 (mm) REVERT: Y 293 MET cc_start: 0.6068 (tmm) cc_final: 0.5511 (tmm) REVERT: Y 295 THR cc_start: 0.3940 (t) cc_final: 0.3154 (m) REVERT: Y 466 MET cc_start: 0.6962 (ttp) cc_final: 0.6386 (ttp) outliers start: 107 outliers final: 63 residues processed: 488 average time/residue: 0.5383 time to fit residues: 442.5756 Evaluate side-chains 408 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 339 time to evaluate : 4.608 ------------------------------------------------------------------------------- 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 212 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 ILE 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 D residue 267 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain F residue 267 VAL 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 H residue 291 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 201 MET Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain S residue 465 LEU Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 612 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 277 THR 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 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 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 509 VAL Chi-restraints excluded: chain X residue 617 MET Chi-restraints excluded: chain X residue 636 ILE 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 201 MET Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 465 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 612 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 366 THR Chi-restraints excluded: chain Y residue 509 VAL Chi-restraints excluded: chain Y residue 617 MET Chi-restraints excluded: chain Y residue 636 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 609 optimal weight: 20.0000 chunk 463 optimal weight: 3.9990 chunk 320 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 294 optimal weight: 0.9990 chunk 414 optimal weight: 9.9990 chunk 619 optimal weight: 6.9990 chunk 655 optimal weight: 0.0570 chunk 323 optimal weight: 3.9990 chunk 586 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- 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 280 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN ** 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS X 280 ASN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 280 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 516 HIS Y 212 HIS Y 280 ASN ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54480 Z= 0.209 Angle : 0.559 10.055 73716 Z= 0.295 Chirality : 0.046 0.179 8244 Planarity : 0.005 0.064 9630 Dihedral : 4.339 31.621 7658 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 2.20 % Allowed : 12.35 % Favored : 85.45 % 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: -0.90 (0.10), residues: 6852 helix: 1.00 (0.12), residues: 2172 sheet: -0.39 (0.16), residues: 1146 loop : -1.76 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 396 HIS 0.040 0.001 HIS B 212 PHE 0.012 0.001 PHE B 353 TYR 0.014 0.001 TYR S 157 ARG 0.005 0.000 ARG S 268 *********************** 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 503 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 377 time to evaluate : 4.632 Fit side-chains REVERT: B 129 ARG cc_start: 0.5516 (tmt170) cc_final: 0.5152 (ptt180) REVERT: B 259 MET cc_start: 0.3660 (mmp) cc_final: 0.3014 (mmt) REVERT: B 617 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.5221 (tpt) REVERT: C 70 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: F 46 ARG cc_start: 0.7063 (mmt-90) cc_final: 0.6784 (mmt-90) REVERT: G 70 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: H 197 MET cc_start: 0.8971 (mtp) cc_final: 0.8747 (mtp) REVERT: S 129 ARG cc_start: 0.5641 (tmt170) cc_final: 0.5244 (ptt180) REVERT: S 259 MET cc_start: 0.3636 (mmp) cc_final: 0.3014 (mmt) REVERT: S 463 MET cc_start: 0.7606 (mmm) cc_final: 0.7281 (mmm) REVERT: V 129 ARG cc_start: 0.5547 (tmt170) cc_final: 0.5180 (ptt180) REVERT: V 212 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.6112 (t-170) REVERT: V 259 MET cc_start: 0.3590 (mmp) cc_final: 0.2943 (mmt) REVERT: X 91 GLU cc_start: 0.3899 (pm20) cc_final: 0.3668 (mt-10) REVERT: X 463 MET cc_start: 0.7674 (mmm) cc_final: 0.7423 (mmt) REVERT: Z 129 ARG cc_start: 0.5651 (tmt170) cc_final: 0.5255 (ptt180) REVERT: Z 259 MET cc_start: 0.3542 (mmp) cc_final: 0.3078 (mmt) REVERT: Z 463 MET cc_start: 0.7616 (mmm) cc_final: 0.7287 (mmm) REVERT: Y 91 GLU cc_start: 0.3902 (pm20) cc_final: 0.3695 (mt-10) REVERT: Y 407 MET cc_start: 0.7570 (tpp) cc_final: 0.6977 (tpp) outliers start: 126 outliers final: 75 residues processed: 472 average time/residue: 0.5039 time to fit residues: 406.9056 Evaluate side-chains 401 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 4.539 ------------------------------------------------------------------------------- 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 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 509 VAL 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 78 MET 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 277 THR Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 465 LEU Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 619 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 212 HIS Chi-restraints excluded: chain V residue 277 THR 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 509 VAL Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL 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 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 325 LEU Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 509 VAL Chi-restraints excluded: chain X residue 636 ILE 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 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR 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 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 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 366 THR Chi-restraints excluded: chain Y residue 505 THR Chi-restraints excluded: chain Y residue 509 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 545 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 487 optimal weight: 20.0000 chunk 270 optimal weight: 0.0870 chunk 559 optimal weight: 5.9990 chunk 453 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 588 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- 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 280 ASN ** 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** ** 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 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** ** 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 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 464 GLN Y 516 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54480 Z= 0.250 Angle : 0.581 10.721 73716 Z= 0.307 Chirality : 0.046 0.179 8244 Planarity : 0.005 0.061 9630 Dihedral : 4.562 45.739 7658 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.64 % Allowed : 12.89 % Favored : 84.47 % 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: -0.95 (0.10), residues: 6852 helix: 0.94 (0.12), residues: 2148 sheet: -0.47 (0.16), residues: 1212 loop : -1.75 (0.10), residues: 3492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 396 HIS 0.026 0.002 HIS V 212 PHE 0.028 0.002 PHE B 290 TYR 0.022 0.002 TYR S 444 ARG 0.004 0.001 ARG V 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 498 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 347 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5577 (tmt170) cc_final: 0.4601 (ttm170) REVERT: B 259 MET cc_start: 0.3759 (mmp) cc_final: 0.3020 (mmt) REVERT: B 363 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: B 617 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4873 (tpt) REVERT: C 70 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: G 70 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: S 129 ARG cc_start: 0.5819 (tmt170) cc_final: 0.5252 (ptt180) REVERT: S 135 ILE cc_start: 0.4266 (OUTLIER) cc_final: 0.3956 (tp) REVERT: S 218 ILE cc_start: 0.4638 (OUTLIER) cc_final: 0.4245 (mm) REVERT: S 259 MET cc_start: 0.3477 (mmp) cc_final: 0.2839 (mmt) REVERT: S 455 LYS cc_start: 0.4884 (tptt) cc_final: 0.4316 (tptp) REVERT: S 463 MET cc_start: 0.7687 (mmm) cc_final: 0.7330 (mmm) REVERT: V 129 ARG cc_start: 0.5663 (tmt170) cc_final: 0.5039 (ptt180) REVERT: V 259 MET cc_start: 0.3703 (mmp) cc_final: 0.2964 (mmt) REVERT: V 363 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: X 91 GLU cc_start: 0.3627 (pm20) cc_final: 0.3336 (mt-10) REVERT: X 135 ILE cc_start: 0.4691 (OUTLIER) cc_final: 0.4291 (tt) REVERT: X 463 MET cc_start: 0.7743 (mmm) cc_final: 0.7457 (mmt) REVERT: X 468 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: Z 129 ARG cc_start: 0.5795 (tmt170) cc_final: 0.5254 (ptt180) REVERT: Z 135 ILE cc_start: 0.4280 (OUTLIER) cc_final: 0.3949 (tp) REVERT: Z 218 ILE cc_start: 0.4787 (OUTLIER) cc_final: 0.4413 (mm) REVERT: Z 259 MET cc_start: 0.3679 (mmp) cc_final: 0.3051 (mmt) REVERT: Z 455 LYS cc_start: 0.4887 (tptt) cc_final: 0.4335 (tptp) REVERT: Z 463 MET cc_start: 0.7692 (mmm) cc_final: 0.7329 (mmm) REVERT: Y 91 GLU cc_start: 0.3598 (pm20) cc_final: 0.3374 (mt-10) REVERT: Y 135 ILE cc_start: 0.4710 (OUTLIER) cc_final: 0.4316 (tt) REVERT: Y 463 MET cc_start: 0.7725 (mmm) cc_final: 0.7450 (mmt) REVERT: Y 468 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7312 (mp0) outliers start: 151 outliers final: 102 residues processed: 468 average time/residue: 0.4995 time to fit residues: 403.0434 Evaluate side-chains 423 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 308 time to evaluate : 4.561 ------------------------------------------------------------------------------- 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 155 ILE 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 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 617 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 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 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain G residue 40 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 200 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 135 ILE Chi-restraints excluded: chain S residue 155 ILE 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 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 619 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 155 ILE Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL 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 135 ILE 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 325 LEU Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 468 GLU 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 135 ILE 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 325 LEU Chi-restraints excluded: chain Z residue 366 THR 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 Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 135 ILE 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 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 505 THR 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 220 optimal weight: 6.9990 chunk 590 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 161 optimal weight: 0.1980 chunk 655 optimal weight: 0.9980 chunk 544 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 443 ASN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54480 Z= 0.194 Angle : 0.547 11.253 73716 Z= 0.288 Chirality : 0.045 0.246 8244 Planarity : 0.004 0.065 9630 Dihedral : 4.414 57.616 7658 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.89 % Allowed : 13.10 % Favored : 84.02 % 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: -0.89 (0.10), residues: 6852 helix: 0.98 (0.11), residues: 2178 sheet: -0.59 (0.16), residues: 1254 loop : -1.67 (0.10), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 396 HIS 0.004 0.001 HIS C 392 PHE 0.018 0.001 PHE B 290 TYR 0.012 0.001 TYR V 444 ARG 0.007 0.000 ARG V 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 514 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 349 time to evaluate : 4.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5636 (tmt170) cc_final: 0.4981 (ptt180) REVERT: B 259 MET cc_start: 0.3725 (mmp) cc_final: 0.3085 (mmt) REVERT: B 617 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.5397 (tpt) REVERT: D 50 MET cc_start: 0.8496 (tpt) cc_final: 0.8108 (tpt) REVERT: F 50 MET cc_start: 0.8500 (tpt) cc_final: 0.8115 (tpt) REVERT: S 129 ARG cc_start: 0.5700 (tmt170) cc_final: 0.5198 (ptt180) REVERT: S 218 ILE cc_start: 0.4688 (OUTLIER) cc_final: 0.4245 (mm) REVERT: S 259 MET cc_start: 0.3740 (mmp) cc_final: 0.3064 (mmt) REVERT: S 378 GLU cc_start: 0.6806 (tp30) cc_final: 0.6454 (tp30) REVERT: S 455 LYS cc_start: 0.4600 (tptt) cc_final: 0.4297 (tptp) REVERT: S 463 MET cc_start: 0.7749 (mmm) cc_final: 0.7382 (mmm) REVERT: V 129 ARG cc_start: 0.5670 (tmt170) cc_final: 0.5091 (ptt180) REVERT: V 363 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: X 407 MET cc_start: 0.7552 (tpp) cc_final: 0.7026 (tpp) REVERT: X 463 MET cc_start: 0.7637 (mmm) cc_final: 0.7384 (mmt) REVERT: Z 129 ARG cc_start: 0.5779 (tmt170) cc_final: 0.5233 (ptt180) REVERT: Z 135 ILE cc_start: 0.4507 (OUTLIER) cc_final: 0.4282 (tp) REVERT: Z 218 ILE cc_start: 0.4690 (OUTLIER) cc_final: 0.4289 (mm) REVERT: Z 259 MET cc_start: 0.3719 (mmp) cc_final: 0.3082 (mmt) REVERT: Z 378 GLU cc_start: 0.6803 (tp30) cc_final: 0.6457 (tp30) REVERT: Z 455 LYS cc_start: 0.4576 (tptt) cc_final: 0.4285 (tptp) REVERT: Z 463 MET cc_start: 0.7749 (mmm) cc_final: 0.7375 (mmm) REVERT: Y 463 MET cc_start: 0.7614 (mmm) cc_final: 0.7355 (mmt) outliers start: 165 outliers final: 107 residues processed: 480 average time/residue: 0.5081 time to fit residues: 419.6165 Evaluate side-chains 422 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 310 time to evaluate : 4.599 ------------------------------------------------------------------------------- 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 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 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 78 MET 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 281 SER 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 267 VAL Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 522 LEU 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 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 218 ILE 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 366 THR 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 135 ILE Chi-restraints excluded: chain V residue 155 ILE 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 612 VAL 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 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 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 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 135 ILE 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 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 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 505 THR Chi-restraints excluded: chain Y residue 509 VAL 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 632 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 373 optimal weight: 0.6980 chunk 479 optimal weight: 20.0000 chunk 371 optimal weight: 4.9990 chunk 552 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 653 optimal weight: 8.9990 chunk 408 optimal weight: 9.9990 chunk 398 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 294 ASN ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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** Z 294 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54480 Z= 0.242 Angle : 0.577 10.819 73716 Z= 0.305 Chirality : 0.046 0.251 8244 Planarity : 0.005 0.059 9630 Dihedral : 4.639 42.684 7658 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.71 % Allowed : 13.62 % Favored : 83.67 % 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: -0.97 (0.10), residues: 6852 helix: 0.95 (0.12), residues: 2148 sheet: -0.70 (0.15), residues: 1254 loop : -1.70 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 396 HIS 0.005 0.001 HIS G 392 PHE 0.016 0.002 PHE B 290 TYR 0.019 0.001 TYR V 444 ARG 0.008 0.000 ARG S 268 *********************** 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 476 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 321 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5659 (tmt170) cc_final: 0.4589 (ttm170) REVERT: B 363 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: B 617 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5240 (tpt) REVERT: C 70 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: E 50 MET cc_start: 0.8319 (tpp) cc_final: 0.8006 (tpt) REVERT: G 70 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: H 50 MET cc_start: 0.8317 (tpp) cc_final: 0.8017 (tpt) REVERT: S 129 ARG cc_start: 0.5855 (tmt170) cc_final: 0.5254 (ptt180) REVERT: S 259 MET cc_start: 0.3733 (mmp) cc_final: 0.3051 (mmt) REVERT: S 455 LYS cc_start: 0.4692 (tptt) cc_final: 0.4405 (tptp) REVERT: S 463 MET cc_start: 0.7808 (mmm) cc_final: 0.7430 (mmm) REVERT: V 129 ARG cc_start: 0.5734 (tmt170) cc_final: 0.4677 (ttm170) REVERT: V 259 MET cc_start: 0.3639 (mmp) cc_final: 0.2983 (mmt) REVERT: V 363 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: X 135 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4740 (tt) REVERT: X 463 MET cc_start: 0.7723 (mmm) cc_final: 0.7416 (mmt) REVERT: X 468 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: Z 129 ARG cc_start: 0.5851 (tmt170) cc_final: 0.5276 (ptt180) REVERT: Z 135 ILE cc_start: 0.5037 (OUTLIER) cc_final: 0.4556 (tp) REVERT: Z 259 MET cc_start: 0.3839 (mmp) cc_final: 0.3097 (mmt) REVERT: Z 455 LYS cc_start: 0.4680 (tptt) cc_final: 0.4396 (tptp) REVERT: Z 463 MET cc_start: 0.7801 (mmm) cc_final: 0.7417 (mmm) REVERT: Y 135 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4778 (tt) REVERT: Y 463 MET cc_start: 0.7704 (mmm) cc_final: 0.7392 (mmt) REVERT: Y 468 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 155 outliers final: 120 residues processed: 436 average time/residue: 0.4998 time to fit residues: 373.4630 Evaluate side-chains 440 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 310 time to evaluate : 4.595 ------------------------------------------------------------------------------- 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 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 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 617 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 70 GLU Chi-restraints excluded: chain C residue 78 MET 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 522 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 F residue 78 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 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 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 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 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 366 THR Chi-restraints excluded: chain S residue 382 ILE 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR 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 135 ILE 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 366 THR Chi-restraints excluded: chain X residue 468 GLU 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 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 135 ILE 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 366 THR Chi-restraints excluded: chain Z residue 382 ILE 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 Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 135 ILE 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 366 THR Chi-restraints excluded: chain Y residue 468 GLU Chi-restraints excluded: chain Y residue 505 THR Chi-restraints excluded: chain Y residue 509 VAL 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 404 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 390 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 415 optimal weight: 5.9990 chunk 445 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 513 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** X 329 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54480 Z= 0.239 Angle : 0.573 11.843 73716 Z= 0.303 Chirality : 0.046 0.259 8244 Planarity : 0.005 0.065 9630 Dihedral : 4.727 57.879 7658 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.85 % Allowed : 13.69 % Favored : 83.46 % 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: -0.99 (0.10), residues: 6852 helix: 0.92 (0.12), residues: 2148 sheet: -0.72 (0.15), residues: 1254 loop : -1.69 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP V 396 HIS 0.005 0.001 HIS C 392 PHE 0.014 0.001 PHE B 290 TYR 0.016 0.001 TYR Z 444 ARG 0.009 0.000 ARG V 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 483 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 320 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5776 (tmt170) cc_final: 0.4653 (ttm170) REVERT: B 135 ILE cc_start: 0.4571 (OUTLIER) cc_final: 0.4108 (mm) REVERT: B 259 MET cc_start: 0.3811 (mmp) cc_final: 0.3150 (mmt) REVERT: B 363 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7010 (pt0) REVERT: B 378 GLU cc_start: 0.6655 (tp30) cc_final: 0.6379 (tp30) REVERT: C 70 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: D 46 ARG cc_start: 0.6975 (mmt-90) cc_final: 0.6744 (mmt-90) REVERT: E 252 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8512 (mp) REVERT: F 46 ARG cc_start: 0.6977 (mmt-90) cc_final: 0.6746 (mmt-90) REVERT: G 70 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: S 259 MET cc_start: 0.3801 (mmp) cc_final: 0.3105 (mmt) REVERT: S 378 GLU cc_start: 0.6829 (tp30) cc_final: 0.6503 (tp30) REVERT: S 455 LYS cc_start: 0.5009 (tptt) cc_final: 0.4353 (tptp) REVERT: S 463 MET cc_start: 0.7718 (mmm) cc_final: 0.7323 (mmm) REVERT: V 129 ARG cc_start: 0.5806 (tmt170) cc_final: 0.4715 (ttm170) REVERT: V 135 ILE cc_start: 0.4665 (OUTLIER) cc_final: 0.4092 (mm) REVERT: V 259 MET cc_start: 0.3678 (mmp) cc_final: 0.3001 (mmt) REVERT: V 363 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: V 378 GLU cc_start: 0.6604 (tp30) cc_final: 0.6341 (tp30) REVERT: X 135 ILE cc_start: 0.5116 (OUTLIER) cc_final: 0.4697 (mt) REVERT: X 172 MET cc_start: 0.3314 (tpt) cc_final: 0.2124 (tmm) REVERT: X 463 MET cc_start: 0.7729 (mmm) cc_final: 0.7420 (mmt) REVERT: X 468 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: Z 135 ILE cc_start: 0.5260 (OUTLIER) cc_final: 0.4630 (mt) REVERT: Z 378 GLU cc_start: 0.6760 (tp30) cc_final: 0.6430 (tp30) REVERT: Z 455 LYS cc_start: 0.4988 (tptt) cc_final: 0.4351 (tptp) REVERT: Z 463 MET cc_start: 0.7714 (mmm) cc_final: 0.7321 (mmm) REVERT: Y 135 ILE cc_start: 0.5324 (OUTLIER) cc_final: 0.4869 (mt) REVERT: Y 172 MET cc_start: 0.3313 (tpt) cc_final: 0.2302 (tmm) REVERT: Y 363 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: Y 463 MET cc_start: 0.7703 (mmm) cc_final: 0.7393 (mmt) REVERT: Y 468 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7009 (mp0) outliers start: 163 outliers final: 122 residues processed: 447 average time/residue: 0.4996 time to fit residues: 386.9662 Evaluate side-chains 443 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 308 time to evaluate : 4.608 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR 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 70 GLU Chi-restraints excluded: chain C residue 78 MET 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 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 F residue 78 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 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 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 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 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 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 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR 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 135 ILE 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 366 THR 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 135 ILE 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 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 550 THR 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 135 ILE 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 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 594 optimal weight: 0.9990 chunk 626 optimal weight: 20.0000 chunk 571 optimal weight: 7.9990 chunk 608 optimal weight: 20.0000 chunk 625 optimal weight: 8.9990 chunk 366 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 478 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 550 optimal weight: 0.0010 chunk 575 optimal weight: 6.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 329 GLN ** 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54480 Z= 0.260 Angle : 0.596 21.023 73716 Z= 0.313 Chirality : 0.047 0.319 8244 Planarity : 0.005 0.062 9630 Dihedral : 4.864 58.399 7658 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.75 % Allowed : 13.96 % Favored : 83.30 % 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: 0.86 (0.12), residues: 2148 sheet: -0.78 (0.15), residues: 1254 loop : -1.73 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 514 HIS 0.005 0.001 HIS C 392 PHE 0.015 0.002 PHE B 290 TYR 0.018 0.002 TYR X 444 ARG 0.006 0.000 ARG B 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 480 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 323 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 ILE cc_start: 0.4828 (OUTLIER) cc_final: 0.4206 (mt) REVERT: B 259 MET cc_start: 0.3885 (mmp) cc_final: 0.3175 (mmt) REVERT: B 363 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: B 378 GLU cc_start: 0.6659 (tp30) cc_final: 0.6362 (tp30) REVERT: B 547 GLU cc_start: 0.4634 (pm20) cc_final: 0.4311 (pm20) REVERT: C 70 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: D 46 ARG cc_start: 0.6994 (mmt-90) cc_final: 0.6760 (mmt-90) REVERT: E 50 MET cc_start: 0.8320 (tpp) cc_final: 0.8007 (tpt) REVERT: F 46 ARG cc_start: 0.7000 (mmt-90) cc_final: 0.6770 (mmt-90) REVERT: G 70 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: H 50 MET cc_start: 0.8322 (tpp) cc_final: 0.8018 (tpt) REVERT: S 160 MET cc_start: 0.1886 (ppp) cc_final: 0.1231 (ptm) REVERT: S 259 MET cc_start: 0.3773 (mmp) cc_final: 0.3077 (mmt) REVERT: S 378 GLU cc_start: 0.6806 (tp30) cc_final: 0.6430 (tp30) REVERT: S 455 LYS cc_start: 0.5193 (tptt) cc_final: 0.4557 (tptp) REVERT: S 463 MET cc_start: 0.7721 (mmm) cc_final: 0.7331 (mmm) REVERT: V 135 ILE cc_start: 0.4883 (OUTLIER) cc_final: 0.4272 (mt) REVERT: V 259 MET cc_start: 0.3632 (mmp) cc_final: 0.3002 (mmt) REVERT: V 363 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: V 378 GLU cc_start: 0.6662 (tp30) cc_final: 0.6400 (tp30) REVERT: X 26 ARG cc_start: 0.5936 (mmm160) cc_final: 0.5493 (mmp80) REVERT: X 135 ILE cc_start: 0.5377 (OUTLIER) cc_final: 0.4976 (mt) REVERT: X 172 MET cc_start: 0.3284 (tpt) cc_final: 0.2220 (tmm) REVERT: X 468 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: Z 135 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4430 (mt) REVERT: Z 455 LYS cc_start: 0.5170 (tptt) cc_final: 0.4538 (tptp) REVERT: Z 463 MET cc_start: 0.7720 (mmm) cc_final: 0.7323 (mmm) REVERT: Y 117 MET cc_start: 0.3909 (mpp) cc_final: 0.3311 (mmm) REVERT: Y 135 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4868 (mt) REVERT: Y 172 MET cc_start: 0.3307 (tpt) cc_final: 0.2296 (tmm) REVERT: Y 363 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7010 (pt0) REVERT: Y 468 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7142 (mp0) outliers start: 157 outliers final: 123 residues processed: 445 average time/residue: 0.4975 time to fit residues: 383.5113 Evaluate side-chains 440 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 305 time to evaluate : 4.635 ------------------------------------------------------------------------------- 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 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 550 THR 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 70 GLU Chi-restraints excluded: chain C residue 78 MET 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 522 LEU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 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 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 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 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 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR 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 135 ILE 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 366 THR Chi-restraints excluded: chain X residue 382 ILE 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 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 135 ILE 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 366 THR Chi-restraints excluded: chain Z residue 382 ILE 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 Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 135 ILE 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 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 606 optimal weight: 2.9990 chunk 399 optimal weight: 0.9990 chunk 643 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 447 optimal weight: 4.9990 chunk 675 optimal weight: 10.0000 chunk 621 optimal weight: 8.9990 chunk 537 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 415 optimal weight: 0.0060 overall best weight: 3.0004 ------------------------------------------------------------------------------- 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 285 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 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 285 GLN ** 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** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54480 Z= 0.273 Angle : 0.605 18.048 73716 Z= 0.318 Chirality : 0.048 0.308 8244 Planarity : 0.005 0.065 9630 Dihedral : 4.926 59.592 7658 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.57 % Allowed : 14.22 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.11 (0.10), residues: 6852 helix: 0.80 (0.12), residues: 2148 sheet: -0.70 (0.15), residues: 1176 loop : -1.78 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 514 HIS 0.005 0.001 HIS C 392 PHE 0.021 0.002 PHE S 353 TYR 0.017 0.002 TYR V 444 ARG 0.006 0.001 ARG B 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 461 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 314 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 ILE cc_start: 0.5096 (OUTLIER) cc_final: 0.4518 (mt) REVERT: B 259 MET cc_start: 0.3827 (mmp) cc_final: 0.3137 (mmt) REVERT: B 363 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: B 378 GLU cc_start: 0.6628 (tp30) cc_final: 0.6367 (tp30) REVERT: B 547 GLU cc_start: 0.4572 (pm20) cc_final: 0.4277 (pm20) REVERT: B 566 MET cc_start: 0.6978 (tpt) cc_final: 0.6772 (ttt) REVERT: C 70 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: D 46 ARG cc_start: 0.6953 (mmt-90) cc_final: 0.6695 (mmt-90) REVERT: E 50 MET cc_start: 0.8322 (tpp) cc_final: 0.8004 (tpt) REVERT: F 46 ARG cc_start: 0.6946 (mmt-90) cc_final: 0.6697 (mmt-90) REVERT: G 70 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: H 50 MET cc_start: 0.8324 (tpp) cc_final: 0.8010 (tpt) REVERT: S 160 MET cc_start: 0.1896 (ppp) cc_final: 0.0557 (ptm) REVERT: S 259 MET cc_start: 0.3768 (mmp) cc_final: 0.3074 (mmt) REVERT: S 378 GLU cc_start: 0.6761 (tp30) cc_final: 0.6427 (tp30) REVERT: S 463 MET cc_start: 0.7733 (mmm) cc_final: 0.7345 (mmm) REVERT: S 603 MET cc_start: 0.5030 (ttp) cc_final: 0.4799 (ttp) REVERT: V 135 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4495 (mt) REVERT: V 259 MET cc_start: 0.3582 (mmp) cc_final: 0.2990 (mmt) REVERT: V 363 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: V 378 GLU cc_start: 0.6674 (tp30) cc_final: 0.6428 (tp30) REVERT: V 547 GLU cc_start: 0.4489 (pm20) cc_final: 0.4174 (pm20) REVERT: X 26 ARG cc_start: 0.5948 (mmm160) cc_final: 0.5508 (mmp80) REVERT: X 135 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4798 (mt) REVERT: X 172 MET cc_start: 0.3280 (tpt) cc_final: 0.2230 (tmm) REVERT: X 468 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: Z 117 MET cc_start: 0.3333 (mmt) cc_final: 0.2981 (mmt) REVERT: Z 135 ILE cc_start: 0.5366 (OUTLIER) cc_final: 0.4766 (mt) REVERT: Z 259 MET cc_start: 0.3593 (mmp) cc_final: 0.3146 (mmt) REVERT: Z 378 GLU cc_start: 0.6789 (tp30) cc_final: 0.6424 (tp30) REVERT: Z 463 MET cc_start: 0.7685 (mmm) cc_final: 0.7284 (mmm) REVERT: Y 26 ARG cc_start: 0.5949 (mmm160) cc_final: 0.5507 (mmp80) REVERT: Y 117 MET cc_start: 0.3159 (mpp) cc_final: 0.2767 (mpp) REVERT: Y 135 ILE cc_start: 0.5283 (OUTLIER) cc_final: 0.4803 (mt) REVERT: Y 172 MET cc_start: 0.3326 (tpt) cc_final: 0.2346 (tmm) REVERT: Y 363 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7051 (pt0) REVERT: Y 468 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7115 (mp0) outliers start: 147 outliers final: 118 residues processed: 433 average time/residue: 0.5177 time to fit residues: 382.0179 Evaluate side-chains 436 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 306 time to evaluate : 4.580 ------------------------------------------------------------------------------- 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 468 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU 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 188 SER 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 40 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 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 188 SER Chi-restraints excluded: chain H residue 267 VAL 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 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 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 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 468 GLU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL 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 135 ILE 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 366 THR Chi-restraints excluded: chain X residue 382 ILE 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 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 135 ILE 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 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE 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 Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 135 ILE 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 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 329 optimal weight: 3.9990 chunk 427 optimal weight: 0.0770 chunk 572 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 495 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 538 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 553 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 639 GLN ** 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 639 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.148366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116185 restraints weight = 99525.170| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.04 r_work: 0.3246 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 54480 Z= 0.142 Angle : 0.525 18.579 73716 Z= 0.273 Chirality : 0.045 0.308 8244 Planarity : 0.004 0.064 9630 Dihedral : 4.345 59.072 7658 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.06 % Allowed : 14.66 % 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: -0.77 (0.10), residues: 6852 helix: 1.05 (0.12), residues: 2178 sheet: -0.20 (0.16), residues: 1104 loop : -1.66 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 396 HIS 0.002 0.001 HIS G 105 PHE 0.021 0.001 PHE V 353 TYR 0.021 0.001 TYR X 444 ARG 0.012 0.000 ARG S 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10285.83 seconds wall clock time: 180 minutes 47.81 seconds (10847.81 seconds total)