Starting phenix.real_space_refine on Sun Dec 29 16:24:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.map" model { file = "/net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vra_21365/12_2024/6vra_21365.cif" } resolution = 3.3 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 72 5.16 5 C 36416 2.51 5 N 9808 2.21 5 O 11432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57744 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4274 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 518} Chain breaks: 2 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4283 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 518} Chain breaks: 2 Chain: "I" Number of atoms: 5875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5875 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: K, J, L, C, E, G, D, F, H Time building chain proxies: 21.31, per 1000 atoms: 0.37 Number of scatterers: 57744 At special positions: 0 Unit cell: (189.39, 189.39, 195.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 72 16.00 O 11432 8.00 N 9808 7.00 C 36416 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: 9.95 Conformation dependent library (CDL) restraints added in 5.5 seconds 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13680 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 92 sheets defined 32.6% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.772A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.854A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.752A pdb=" N VAL A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Proline residue: A 482 - end of helix removed outlier: 3.526A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 555 through 569 removed outlier: 3.534A pdb=" N GLN A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.755A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 616 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 637 Processing helix chain 'A' and resid 679 through 682 removed outlier: 3.653A pdb=" N ASN A 682 " --> pdb=" O LYS A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 682' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.533A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 476 through 479 removed outlier: 3.562A pdb=" N GLU B 479 " --> pdb=" O ASN B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 479' Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.540A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.509A pdb=" N THR B 516 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 517' Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 569 removed outlier: 3.565A pdb=" N GLN B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.501A pdb=" N VAL B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 Processing helix chain 'B' and resid 679 through 682 removed outlier: 3.668A pdb=" N ASN B 682 " --> pdb=" O LYS B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.772A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.854A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.752A pdb=" N VAL C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Proline residue: C 482 - end of helix removed outlier: 3.526A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 530 Processing helix chain 'C' and resid 555 through 569 removed outlier: 3.534A pdb=" N GLN C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 616 removed outlier: 3.755A pdb=" N VAL C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 616 " --> pdb=" O VAL C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 679 through 682 removed outlier: 3.653A pdb=" N ASN C 682 " --> pdb=" O LYS C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.533A pdb=" N ARG D 252 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 476 through 479 removed outlier: 3.562A pdb=" N GLU D 479 " --> pdb=" O ASN D 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 476 through 479' Processing helix chain 'D' and resid 480 through 487 removed outlier: 3.540A pdb=" N THR D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.509A pdb=" N THR D 516 " --> pdb=" O PRO D 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 517' Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 569 removed outlier: 3.565A pdb=" N GLN D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 616 removed outlier: 3.501A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 Processing helix chain 'D' and resid 679 through 682 removed outlier: 3.668A pdb=" N ASN D 682 " --> pdb=" O LYS D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 679 through 682' Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.772A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.854A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 351 Processing helix chain 'E' and resid 436 through 446 Processing helix chain 'E' and resid 476 through 487 removed outlier: 3.752A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Proline residue: E 482 - end of helix removed outlier: 3.526A pdb=" N THR E 487 " --> pdb=" O GLN E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 530 Processing helix chain 'E' and resid 555 through 569 removed outlier: 3.534A pdb=" N GLN E 565 " --> pdb=" O ASN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 616 removed outlier: 3.755A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS E 616 " --> pdb=" O VAL E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 637 Processing helix chain 'E' and resid 679 through 682 removed outlier: 3.653A pdb=" N ASN E 682 " --> pdb=" O LYS E 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 679 through 682' Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.533A pdb=" N ARG F 252 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 476 through 479 removed outlier: 3.562A pdb=" N GLU F 479 " --> pdb=" O ASN F 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 476 through 479' Processing helix chain 'F' and resid 480 through 487 removed outlier: 3.540A pdb=" N THR F 487 " --> pdb=" O GLN F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.509A pdb=" N THR F 516 " --> pdb=" O PRO F 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 513 through 517' Processing helix chain 'F' and resid 522 through 531 Processing helix chain 'F' and resid 555 through 569 removed outlier: 3.565A pdb=" N GLN F 565 " --> pdb=" O ASN F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 616 removed outlier: 3.501A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'F' and resid 679 through 682 removed outlier: 3.668A pdb=" N ASN F 682 " --> pdb=" O LYS F 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 679 through 682' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.772A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.854A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 351 Processing helix chain 'G' and resid 436 through 446 Processing helix chain 'G' and resid 476 through 487 removed outlier: 3.752A pdb=" N VAL G 480 " --> pdb=" O ASN G 476 " (cutoff:3.500A) Proline residue: G 482 - end of helix removed outlier: 3.526A pdb=" N THR G 487 " --> pdb=" O GLN G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 530 Processing helix chain 'G' and resid 555 through 569 removed outlier: 3.534A pdb=" N GLN G 565 " --> pdb=" O ASN G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 616 removed outlier: 3.755A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS G 616 " --> pdb=" O VAL G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 637 Processing helix chain 'G' and resid 679 through 682 removed outlier: 3.653A pdb=" N ASN G 682 " --> pdb=" O LYS G 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 679 through 682' Processing helix chain 'H' and resid 184 through 191 Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 234 through 241 Processing helix chain 'H' and resid 248 through 253 removed outlier: 3.533A pdb=" N ARG H 252 " --> pdb=" O PRO H 249 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS H 253 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 351 Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'H' and resid 476 through 479 removed outlier: 3.562A pdb=" N GLU H 479 " --> pdb=" O ASN H 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 476 through 479' Processing helix chain 'H' and resid 480 through 487 removed outlier: 3.540A pdb=" N THR H 487 " --> pdb=" O GLN H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 517 removed outlier: 3.509A pdb=" N THR H 516 " --> pdb=" O PRO H 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 513 through 517' Processing helix chain 'H' and resid 522 through 531 Processing helix chain 'H' and resid 555 through 569 removed outlier: 3.565A pdb=" N GLN H 565 " --> pdb=" O ASN H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 616 removed outlier: 3.501A pdb=" N VAL H 612 " --> pdb=" O ASP H 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 637 Processing helix chain 'H' and resid 679 through 682 removed outlier: 3.668A pdb=" N ASN H 682 " --> pdb=" O LYS H 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 679 through 682' Processing helix chain 'I' and resid 21 through 28 Processing helix chain 'I' and resid 41 through 54 removed outlier: 3.833A pdb=" N LYS I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE I 46 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN I 47 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 68 removed outlier: 3.847A pdb=" N LEU I 61 " --> pdb=" O PRO I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.830A pdb=" N ARG I 107 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.901A pdb=" N GLU I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 removed outlier: 4.720A pdb=" N ASP I 168 " --> pdb=" O LYS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 189 Processing helix chain 'I' and resid 193 through 200 removed outlier: 3.596A pdb=" N LYS I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 217 removed outlier: 3.615A pdb=" N PHE I 204 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 228 through 240 removed outlier: 3.503A pdb=" N PHE I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU I 233 " --> pdb=" O PRO I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 255 Processing helix chain 'I' and resid 265 through 273 removed outlier: 3.709A pdb=" N LEU I 269 " --> pdb=" O GLY I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 290 Processing helix chain 'I' and resid 299 through 309 removed outlier: 3.649A pdb=" N THR I 303 " --> pdb=" O ASN I 299 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN I 304 " --> pdb=" O LYS I 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 338 removed outlier: 3.575A pdb=" N LEU I 337 " --> pdb=" O ASP I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 361 removed outlier: 3.697A pdb=" N HIS I 361 " --> pdb=" O SER I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 380 removed outlier: 3.549A pdb=" N GLU I 378 " --> pdb=" O HIS I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 384 Processing helix chain 'I' and resid 393 through 397 removed outlier: 4.268A pdb=" N GLY I 396 " --> pdb=" O ILE I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 475 Processing helix chain 'I' and resid 477 through 485 removed outlier: 3.704A pdb=" N VAL I 483 " --> pdb=" O GLU I 479 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL I 484 " --> pdb=" O TRP I 480 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN I 485 " --> pdb=" O ASP I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 505 removed outlier: 3.649A pdb=" N LYS I 492 " --> pdb=" O ASN I 488 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE I 505 " --> pdb=" O ILE I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 529 Processing helix chain 'I' and resid 530 through 532 No H-bonds generated for 'chain 'I' and resid 530 through 532' Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 626 through 639 Processing helix chain 'I' and resid 651 through 671 Processing helix chain 'I' and resid 680 through 703 removed outlier: 4.031A pdb=" N LYS I 684 " --> pdb=" O SER I 680 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 735 removed outlier: 3.606A pdb=" N HIS I 733 " --> pdb=" O LEU I 729 " (cutoff:3.500A) Processing helix chain 'I' and resid 739 through 747 removed outlier: 3.720A pdb=" N LEU I 743 " --> pdb=" O GLU I 739 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 765 removed outlier: 3.746A pdb=" N VAL I 759 " --> pdb=" O ASP I 755 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 28 Processing helix chain 'J' and resid 41 through 54 removed outlier: 3.833A pdb=" N LYS J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE J 46 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN J 47 " --> pdb=" O LEU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 68 removed outlier: 3.847A pdb=" N LEU J 61 " --> pdb=" O PRO J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.830A pdb=" N ARG J 107 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 144 removed outlier: 3.901A pdb=" N GLU J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR J 137 " --> pdb=" O SER J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 168 removed outlier: 4.720A pdb=" N ASP J 168 " --> pdb=" O LYS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 193 through 200 removed outlier: 3.596A pdb=" N LYS J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU J 199 " --> pdb=" O ASN J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 217 removed outlier: 3.615A pdb=" N PHE J 204 " --> pdb=" O ASN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 228 through 240 removed outlier: 3.503A pdb=" N PHE J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU J 233 " --> pdb=" O PRO J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 255 Processing helix chain 'J' and resid 265 through 273 removed outlier: 3.709A pdb=" N LEU J 269 " --> pdb=" O GLY J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 290 Processing helix chain 'J' and resid 299 through 309 removed outlier: 3.649A pdb=" N THR J 303 " --> pdb=" O ASN J 299 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN J 304 " --> pdb=" O LYS J 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU J 305 " --> pdb=" O LEU J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 338 removed outlier: 3.575A pdb=" N LEU J 337 " --> pdb=" O ASP J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 361 removed outlier: 3.697A pdb=" N HIS J 361 " --> pdb=" O SER J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 380 removed outlier: 3.549A pdb=" N GLU J 378 " --> pdb=" O HIS J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 384 Processing helix chain 'J' and resid 393 through 397 removed outlier: 4.268A pdb=" N GLY J 396 " --> pdb=" O ILE J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 475 Processing helix chain 'J' and resid 477 through 485 removed outlier: 3.704A pdb=" N VAL J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL J 484 " --> pdb=" O TRP J 480 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN J 485 " --> pdb=" O ASP J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 488 through 505 removed outlier: 3.649A pdb=" N LYS J 492 " --> pdb=" O ASN J 488 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE J 505 " --> pdb=" O ILE J 501 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 529 Processing helix chain 'J' and resid 530 through 532 No H-bonds generated for 'chain 'J' and resid 530 through 532' Processing helix chain 'J' and resid 574 through 586 Processing helix chain 'J' and resid 626 through 639 Processing helix chain 'J' and resid 651 through 671 Processing helix chain 'J' and resid 680 through 703 removed outlier: 4.031A pdb=" N LYS J 684 " --> pdb=" O SER J 680 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 735 removed outlier: 3.606A pdb=" N HIS J 733 " --> pdb=" O LEU J 729 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 747 removed outlier: 3.720A pdb=" N LEU J 743 " --> pdb=" O GLU J 739 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 765 removed outlier: 3.746A pdb=" N VAL J 759 " --> pdb=" O ASP J 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 28 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.833A pdb=" N LYS K 45 " --> pdb=" O GLU K 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE K 46 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN K 47 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 68 removed outlier: 3.847A pdb=" N LEU K 61 " --> pdb=" O PRO K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.830A pdb=" N ARG K 107 " --> pdb=" O PHE K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 144 removed outlier: 3.901A pdb=" N GLU K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 168 removed outlier: 4.720A pdb=" N ASP K 168 " --> pdb=" O LYS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 193 through 200 removed outlier: 3.596A pdb=" N LYS K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU K 199 " --> pdb=" O ASN K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 217 removed outlier: 3.615A pdb=" N PHE K 204 " --> pdb=" O ASN K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 228 through 240 removed outlier: 3.503A pdb=" N PHE K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU K 233 " --> pdb=" O PRO K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 255 Processing helix chain 'K' and resid 265 through 273 removed outlier: 3.709A pdb=" N LEU K 269 " --> pdb=" O GLY K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 290 Processing helix chain 'K' and resid 299 through 309 removed outlier: 3.649A pdb=" N THR K 303 " --> pdb=" O ASN K 299 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN K 304 " --> pdb=" O LYS K 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU K 305 " --> pdb=" O LEU K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 338 removed outlier: 3.575A pdb=" N LEU K 337 " --> pdb=" O ASP K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 361 removed outlier: 3.697A pdb=" N HIS K 361 " --> pdb=" O SER K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 380 removed outlier: 3.549A pdb=" N GLU K 378 " --> pdb=" O HIS K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 384 Processing helix chain 'K' and resid 393 through 397 removed outlier: 4.268A pdb=" N GLY K 396 " --> pdb=" O ILE K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 475 Processing helix chain 'K' and resid 477 through 485 removed outlier: 3.704A pdb=" N VAL K 483 " --> pdb=" O GLU K 479 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL K 484 " --> pdb=" O TRP K 480 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN K 485 " --> pdb=" O ASP K 481 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 505 removed outlier: 3.649A pdb=" N LYS K 492 " --> pdb=" O ASN K 488 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE K 505 " --> pdb=" O ILE K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 529 Processing helix chain 'K' and resid 530 through 532 No H-bonds generated for 'chain 'K' and resid 530 through 532' Processing helix chain 'K' and resid 574 through 586 Processing helix chain 'K' and resid 626 through 639 Processing helix chain 'K' and resid 651 through 671 Processing helix chain 'K' and resid 680 through 703 removed outlier: 4.031A pdb=" N LYS K 684 " --> pdb=" O SER K 680 " (cutoff:3.500A) Processing helix chain 'K' and resid 709 through 735 removed outlier: 3.606A pdb=" N HIS K 733 " --> pdb=" O LEU K 729 " (cutoff:3.500A) Processing helix chain 'K' and resid 739 through 747 removed outlier: 3.720A pdb=" N LEU K 743 " --> pdb=" O GLU K 739 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 765 removed outlier: 3.746A pdb=" N VAL K 759 " --> pdb=" O ASP K 755 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 28 Processing helix chain 'L' and resid 41 through 54 removed outlier: 3.833A pdb=" N LYS L 45 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE L 46 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 68 removed outlier: 3.847A pdb=" N LEU L 61 " --> pdb=" O PRO L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.830A pdb=" N ARG L 107 " --> pdb=" O PHE L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 144 removed outlier: 3.901A pdb=" N GLU L 135 " --> pdb=" O GLU L 131 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL L 136 " --> pdb=" O GLN L 132 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR L 137 " --> pdb=" O SER L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 168 removed outlier: 4.720A pdb=" N ASP L 168 " --> pdb=" O LYS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 189 Processing helix chain 'L' and resid 193 through 200 removed outlier: 3.596A pdb=" N LYS L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU L 199 " --> pdb=" O ASN L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 217 removed outlier: 3.615A pdb=" N PHE L 204 " --> pdb=" O ASN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 228 through 240 removed outlier: 3.503A pdb=" N PHE L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU L 233 " --> pdb=" O PRO L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 255 Processing helix chain 'L' and resid 265 through 273 removed outlier: 3.709A pdb=" N LEU L 269 " --> pdb=" O GLY L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 290 Processing helix chain 'L' and resid 299 through 309 removed outlier: 3.649A pdb=" N THR L 303 " --> pdb=" O ASN L 299 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN L 304 " --> pdb=" O LYS L 300 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 338 removed outlier: 3.575A pdb=" N LEU L 337 " --> pdb=" O ASP L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 361 removed outlier: 3.697A pdb=" N HIS L 361 " --> pdb=" O SER L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 380 removed outlier: 3.549A pdb=" N GLU L 378 " --> pdb=" O HIS L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 384 Processing helix chain 'L' and resid 393 through 397 removed outlier: 4.268A pdb=" N GLY L 396 " --> pdb=" O ILE L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 475 Processing helix chain 'L' and resid 477 through 485 removed outlier: 3.704A pdb=" N VAL L 483 " --> pdb=" O GLU L 479 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL L 484 " --> pdb=" O TRP L 480 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN L 485 " --> pdb=" O ASP L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 505 removed outlier: 3.649A pdb=" N LYS L 492 " --> pdb=" O ASN L 488 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE L 505 " --> pdb=" O ILE L 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 529 Processing helix chain 'L' and resid 530 through 532 No H-bonds generated for 'chain 'L' and resid 530 through 532' Processing helix chain 'L' and resid 574 through 586 Processing helix chain 'L' and resid 626 through 639 Processing helix chain 'L' and resid 651 through 671 Processing helix chain 'L' and resid 680 through 703 removed outlier: 4.031A pdb=" N LYS L 684 " --> pdb=" O SER L 680 " (cutoff:3.500A) Processing helix chain 'L' and resid 709 through 735 removed outlier: 3.606A pdb=" N HIS L 733 " --> pdb=" O LEU L 729 " (cutoff:3.500A) Processing helix chain 'L' and resid 739 through 747 removed outlier: 3.720A pdb=" N LEU L 743 " --> pdb=" O GLU L 739 " (cutoff:3.500A) Processing helix chain 'L' and resid 755 through 765 removed outlier: 3.746A pdb=" N VAL L 759 " --> pdb=" O ASP L 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.820A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS A 273 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR A 357 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.853A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 295 through 297 removed outlier: 3.791A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 332 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 448 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 462 removed outlier: 4.173A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.944A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.516A pdb=" N LYS A 545 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.626A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 619 through 622 removed outlier: 6.659A pdb=" N LEU A 628 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER A 622 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 629 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.523A pdb=" N VAL A 696 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 728 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 698 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 292 removed outlier: 6.758A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.715A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 296 through 297 removed outlier: 3.751A pdb=" N SER B 296 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 459 through 463 removed outlier: 4.135A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 468 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 501 through 505 removed outlier: 6.405A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.531A pdb=" N LYS B 545 " --> pdb=" O TYR B 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 596 through 598 removed outlier: 6.539A pdb=" N HIS B 597 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 619 through 622 removed outlier: 6.455A pdb=" N LEU B 628 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER B 622 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 629 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 673 " --> pdb=" O ARG B 669 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 639 through 647 removed outlier: 3.514A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 698 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.820A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 269 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN C 361 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 271 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG C 359 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS C 273 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 357 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 409 through 410 removed outlier: 3.853A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.791A pdb=" N ASN C 328 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 332 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 392 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 385 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR C 390 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 459 through 462 removed outlier: 4.173A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.944A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.516A pdb=" N LYS C 545 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 596 through 598 removed outlier: 3.626A pdb=" N GLY C 606 " --> pdb=" O HIS C 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 619 through 622 removed outlier: 6.659A pdb=" N LEU C 628 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER C 622 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY C 626 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 629 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.523A pdb=" N VAL C 696 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 728 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 698 " --> pdb=" O ILE C 726 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AD5, first strand: chain 'D' and resid 289 through 292 removed outlier: 6.758A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.715A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 296 through 297 removed outlier: 3.751A pdb=" N SER D 296 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN D 328 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 459 through 463 removed outlier: 4.135A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 468 " --> pdb=" O ASN D 463 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 501 through 505 removed outlier: 6.405A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 541 through 542 removed outlier: 3.531A pdb=" N LYS D 545 " --> pdb=" O TYR D 542 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 596 through 598 removed outlier: 6.539A pdb=" N HIS D 597 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 619 through 622 removed outlier: 6.455A pdb=" N LEU D 628 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER D 622 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY D 626 " --> pdb=" O SER D 622 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 629 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS D 673 " --> pdb=" O ARG D 669 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 639 through 647 removed outlier: 3.514A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL D 698 " --> pdb=" O ILE D 726 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AE6, first strand: chain 'E' and resid 288 through 292 removed outlier: 6.820A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS E 273 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR E 357 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 409 through 410 removed outlier: 3.853A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 295 through 297 removed outlier: 3.791A pdb=" N ASN E 328 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 332 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 448 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 459 through 462 removed outlier: 4.173A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.944A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 541 through 542 removed outlier: 3.516A pdb=" N LYS E 545 " --> pdb=" O TYR E 542 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 596 through 598 removed outlier: 3.626A pdb=" N GLY E 606 " --> pdb=" O HIS E 597 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 619 through 622 removed outlier: 6.659A pdb=" N LEU E 628 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER E 622 " --> pdb=" O GLY E 626 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY E 626 " --> pdb=" O SER E 622 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU E 629 " --> pdb=" O THR E 674 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.523A pdb=" N VAL E 696 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER E 728 " --> pdb=" O VAL E 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 698 " --> pdb=" O ILE E 726 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AF7, first strand: chain 'F' and resid 289 through 292 removed outlier: 6.758A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 409 through 410 removed outlier: 3.715A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 296 through 297 removed outlier: 3.751A pdb=" N SER F 296 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 328 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 459 through 463 removed outlier: 4.135A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG F 468 " --> pdb=" O ASN F 463 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 501 through 505 removed outlier: 6.405A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 541 through 542 removed outlier: 3.531A pdb=" N LYS F 545 " --> pdb=" O TYR F 542 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.539A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 619 through 622 removed outlier: 6.455A pdb=" N LEU F 628 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER F 622 " --> pdb=" O GLY F 626 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY F 626 " --> pdb=" O SER F 622 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 629 " --> pdb=" O THR F 674 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 673 " --> pdb=" O ARG F 669 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 639 through 647 removed outlier: 3.514A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL F 698 " --> pdb=" O ILE F 726 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AG8, first strand: chain 'G' and resid 288 through 292 removed outlier: 6.820A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS G 273 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR G 357 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 409 through 410 removed outlier: 3.853A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 295 through 297 removed outlier: 3.791A pdb=" N ASN G 328 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 332 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 448 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 459 through 462 removed outlier: 4.173A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.944A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 541 through 542 removed outlier: 3.516A pdb=" N LYS G 545 " --> pdb=" O TYR G 542 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 596 through 598 removed outlier: 3.626A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 619 through 622 removed outlier: 6.659A pdb=" N LEU G 628 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER G 622 " --> pdb=" O GLY G 626 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY G 626 " --> pdb=" O SER G 622 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU G 629 " --> pdb=" O THR G 674 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.523A pdb=" N VAL G 696 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER G 728 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL G 698 " --> pdb=" O ILE G 726 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 192 through 196 Processing sheet with id=AH9, first strand: chain 'H' and resid 289 through 292 removed outlier: 6.758A pdb=" N ASN H 363 " --> pdb=" O GLU H 267 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE H 269 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN H 361 " --> pdb=" O ILE H 269 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU H 271 " --> pdb=" O ARG H 359 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG H 359 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 409 through 410 removed outlier: 3.715A pdb=" N ASN H 409 " --> pdb=" O ASN H 368 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE H 432 " --> pdb=" O LEU H 360 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 296 through 297 removed outlier: 3.751A pdb=" N SER H 296 " --> pdb=" O THR H 331 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN H 328 " --> pdb=" O THR H 452 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA H 392 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU H 385 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR H 390 " --> pdb=" O LEU H 385 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 459 through 463 removed outlier: 4.135A pdb=" N ILE H 459 " --> pdb=" O ASP H 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG H 468 " --> pdb=" O ASN H 463 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 501 through 505 removed outlier: 6.405A pdb=" N ARG H 490 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE H 591 " --> pdb=" O ARG H 490 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE H 492 " --> pdb=" O ILE H 591 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP H 593 " --> pdb=" O ILE H 492 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 541 through 542 removed outlier: 3.531A pdb=" N LYS H 545 " --> pdb=" O TYR H 542 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 596 through 598 removed outlier: 6.539A pdb=" N HIS H 597 " --> pdb=" O VAL H 605 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 619 through 622 removed outlier: 6.455A pdb=" N LEU H 628 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER H 622 " --> pdb=" O GLY H 626 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY H 626 " --> pdb=" O SER H 622 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 629 " --> pdb=" O THR H 674 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 673 " --> pdb=" O ARG H 669 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 639 through 647 removed outlier: 3.514A pdb=" N GLY H 641 " --> pdb=" O VAL H 701 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL H 698 " --> pdb=" O ILE H 726 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 71 through 74 removed outlier: 5.853A pdb=" N TYR I 72 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 460 through 461 removed outlier: 4.087A pdb=" N ASP I 460 " --> pdb=" O ARG I 296 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 463 through 464 Processing sheet with id=AJ3, first strand: chain 'J' and resid 71 through 74 removed outlier: 5.853A pdb=" N TYR J 72 " --> pdb=" O ILE J 121 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 460 through 461 removed outlier: 4.087A pdb=" N ASP J 460 " --> pdb=" O ARG J 296 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 463 through 464 Processing sheet with id=AJ6, first strand: chain 'K' and resid 71 through 74 removed outlier: 5.853A pdb=" N TYR K 72 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 460 through 461 removed outlier: 4.087A pdb=" N ASP K 460 " --> pdb=" O ARG K 296 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 463 through 464 Processing sheet with id=AJ9, first strand: chain 'L' and resid 71 through 74 removed outlier: 5.853A pdb=" N TYR L 72 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 460 through 461 removed outlier: 4.087A pdb=" N ASP L 460 " --> pdb=" O ARG L 296 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 463 through 464 1816 hydrogen bonds defined for protein. 5112 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: 25.42 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 17400 1.33 - 1.45: 8284 1.45 - 1.57: 32892 1.57 - 1.69: 4 1.69 - 1.81: 144 Bond restraints: 58724 Sorted by residual: bond pdb=" N ASP A 425 " pdb=" CA ASP A 425 " ideal model delta sigma weight residual 1.461 1.523 -0.062 1.49e-02 4.50e+03 1.74e+01 bond pdb=" N ASP G 425 " pdb=" CA ASP G 425 " ideal model delta sigma weight residual 1.461 1.523 -0.062 1.49e-02 4.50e+03 1.74e+01 bond pdb=" N ASP E 425 " pdb=" CA ASP E 425 " ideal model delta sigma weight residual 1.461 1.523 -0.062 1.49e-02 4.50e+03 1.74e+01 bond pdb=" N ASP C 425 " pdb=" CA ASP C 425 " ideal model delta sigma weight residual 1.461 1.523 -0.062 1.49e-02 4.50e+03 1.74e+01 bond pdb=" C ASP A 425 " pdb=" N ASP A 426 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.33e-02 5.65e+03 1.15e+01 ... (remaining 58719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 77756 3.02 - 6.03: 1360 6.03 - 9.05: 148 9.05 - 12.06: 48 12.06 - 15.08: 4 Bond angle restraints: 79316 Sorted by residual: angle pdb=" O GLN C 424 " pdb=" C GLN C 424 " pdb=" N ASP C 425 " ideal model delta sigma weight residual 122.39 111.47 10.92 1.30e+00 5.92e-01 7.05e+01 angle pdb=" O GLN A 424 " pdb=" C GLN A 424 " pdb=" N ASP A 425 " ideal model delta sigma weight residual 122.39 111.47 10.92 1.30e+00 5.92e-01 7.05e+01 angle pdb=" O GLN E 424 " pdb=" C GLN E 424 " pdb=" N ASP E 425 " ideal model delta sigma weight residual 122.39 111.47 10.92 1.30e+00 5.92e-01 7.05e+01 angle pdb=" O GLN G 424 " pdb=" C GLN G 424 " pdb=" N ASP G 425 " ideal model delta sigma weight residual 122.39 111.47 10.92 1.30e+00 5.92e-01 7.05e+01 angle pdb=" CA GLN C 424 " pdb=" C GLN C 424 " pdb=" N ASP C 425 " ideal model delta sigma weight residual 118.08 128.76 -10.68 1.30e+00 5.92e-01 6.75e+01 ... (remaining 79311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31516 17.97 - 35.94: 3748 35.94 - 53.92: 552 53.92 - 71.89: 140 71.89 - 89.86: 64 Dihedral angle restraints: 36020 sinusoidal: 14876 harmonic: 21144 Sorted by residual: dihedral pdb=" C ASP E 425 " pdb=" N ASP E 425 " pdb=" CA ASP E 425 " pdb=" CB ASP E 425 " ideal model delta harmonic sigma weight residual -122.60 -150.61 28.01 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C ASP A 425 " pdb=" N ASP A 425 " pdb=" CA ASP A 425 " pdb=" CB ASP A 425 " ideal model delta harmonic sigma weight residual -122.60 -150.61 28.01 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C ASP G 425 " pdb=" N ASP G 425 " pdb=" CA ASP G 425 " pdb=" CB ASP G 425 " ideal model delta harmonic sigma weight residual -122.60 -150.61 28.01 0 2.50e+00 1.60e-01 1.26e+02 ... (remaining 36017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 8872 0.207 - 0.415: 12 0.415 - 0.622: 0 0.622 - 0.829: 0 0.829 - 1.037: 4 Chirality restraints: 8888 Sorted by residual: chirality pdb=" CA ASP E 425 " pdb=" N ASP E 425 " pdb=" C ASP E 425 " pdb=" CB ASP E 425 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 chirality pdb=" CA ASP A 425 " pdb=" N ASP A 425 " pdb=" C ASP A 425 " pdb=" CB ASP A 425 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 chirality pdb=" CA ASP G 425 " pdb=" N ASP G 425 " pdb=" C ASP G 425 " pdb=" CB ASP G 425 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 8885 not shown) Planarity restraints: 10312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 424 " -0.025 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLN G 424 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN G 424 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP G 425 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 424 " -0.025 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLN E 424 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN E 424 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 425 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 424 " -0.025 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLN A 424 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN A 424 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP A 425 " -0.027 2.00e-02 2.50e+03 ... (remaining 10309 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 7988 2.75 - 3.29: 52852 3.29 - 3.83: 92356 3.83 - 4.36: 109352 4.36 - 4.90: 190604 Nonbonded interactions: 453152 Sorted by model distance: nonbonded pdb=" O ALA G 423 " pdb=" OD1 ASP G 425 " model vdw 2.214 3.040 nonbonded pdb=" O ALA A 423 " pdb=" OD1 ASP A 425 " model vdw 2.214 3.040 nonbonded pdb=" O ALA E 423 " pdb=" OD1 ASP E 425 " model vdw 2.214 3.040 nonbonded pdb=" O ALA C 423 " pdb=" OD1 ASP C 425 " model vdw 2.214 3.040 nonbonded pdb=" O ARG D 344 " pdb=" OG1 THR D 349 " model vdw 2.232 3.040 ... (remaining 453147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'B' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'C' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'D' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'E' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'F' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'G' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) selection = (chain 'H' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 511 or resid 513 through 735 or resid 801 through 802)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.090 Extract box with map and model: 1.700 Check model and map are aligned: 0.340 Set scattering table: 0.410 Process input model: 97.390 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.200 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.008 0.099 58724 Z= 0.536 Angle : 1.028 15.079 79316 Z= 0.599 Chirality : 0.061 1.037 8888 Planarity : 0.007 0.061 10312 Dihedral : 15.672 89.861 22340 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.80 % Allowed : 8.47 % Favored : 90.72 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.12 % 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: -3.93 (0.08), residues: 7136 helix: -2.77 (0.08), residues: 2008 sheet: -1.29 (0.15), residues: 1052 loop : -2.99 (0.08), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 226 HIS 0.009 0.002 HIS D 299 PHE 0.018 0.002 PHE B 493 TYR 0.019 0.002 TYR C 375 ARG 0.005 0.000 ARG E 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 551 ASP cc_start: 0.7636 (t0) cc_final: 0.7378 (p0) REVERT: A 662 MET cc_start: 0.8016 (mtt) cc_final: 0.7472 (mtt) REVERT: B 350 MET cc_start: 0.8472 (mtp) cc_final: 0.8157 (mtp) REVERT: B 436 TYR cc_start: 0.8810 (t80) cc_final: 0.8575 (t80) REVERT: B 662 MET cc_start: 0.7684 (ttm) cc_final: 0.6989 (tpp) REVERT: B 664 ASN cc_start: 0.8305 (t0) cc_final: 0.7956 (p0) REVERT: C 224 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 551 ASP cc_start: 0.7636 (t0) cc_final: 0.7378 (p0) REVERT: C 662 MET cc_start: 0.8017 (mtt) cc_final: 0.7472 (mtt) REVERT: D 350 MET cc_start: 0.8472 (mtp) cc_final: 0.8156 (mtp) REVERT: D 436 TYR cc_start: 0.8810 (t80) cc_final: 0.8575 (t80) REVERT: D 662 MET cc_start: 0.7687 (ttm) cc_final: 0.6991 (tpp) REVERT: D 664 ASN cc_start: 0.8306 (t0) cc_final: 0.7956 (p0) REVERT: E 224 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7834 (mt-10) REVERT: E 551 ASP cc_start: 0.7636 (t0) cc_final: 0.7379 (p0) REVERT: E 662 MET cc_start: 0.8017 (mtt) cc_final: 0.7474 (mtt) REVERT: F 350 MET cc_start: 0.8473 (mtp) cc_final: 0.8157 (mtp) REVERT: F 436 TYR cc_start: 0.8809 (t80) cc_final: 0.8573 (t80) REVERT: F 662 MET cc_start: 0.7687 (ttm) cc_final: 0.6989 (tpp) REVERT: F 664 ASN cc_start: 0.8305 (t0) cc_final: 0.7956 (p0) REVERT: G 224 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7834 (mt-10) REVERT: G 551 ASP cc_start: 0.7634 (t0) cc_final: 0.7378 (p0) REVERT: G 662 MET cc_start: 0.8018 (mtt) cc_final: 0.7473 (mtt) REVERT: H 350 MET cc_start: 0.8470 (mtp) cc_final: 0.8155 (mtp) REVERT: H 436 TYR cc_start: 0.8809 (t80) cc_final: 0.8573 (t80) REVERT: H 662 MET cc_start: 0.7684 (ttm) cc_final: 0.6988 (tpp) REVERT: H 664 ASN cc_start: 0.8304 (t0) cc_final: 0.7955 (p0) REVERT: I 85 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8364 (tm-30) REVERT: I 231 MET cc_start: 0.8911 (tpp) cc_final: 0.8687 (tpp) REVERT: I 761 GLN cc_start: 0.8733 (tt0) cc_final: 0.8519 (tt0) REVERT: J 85 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8364 (tm-30) REVERT: J 231 MET cc_start: 0.8914 (tpp) cc_final: 0.8686 (tpp) REVERT: J 761 GLN cc_start: 0.8732 (tt0) cc_final: 0.8520 (tt0) REVERT: K 85 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8365 (tm-30) REVERT: K 231 MET cc_start: 0.8913 (tpp) cc_final: 0.8687 (tpp) REVERT: K 761 GLN cc_start: 0.8732 (tt0) cc_final: 0.8519 (tt0) REVERT: L 85 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8364 (tm-30) REVERT: L 231 MET cc_start: 0.8913 (tpp) cc_final: 0.8685 (tpp) REVERT: L 761 GLN cc_start: 0.8734 (tt0) cc_final: 0.8521 (tt0) outliers start: 52 outliers final: 4 residues processed: 484 average time/residue: 0.6428 time to fit residues: 492.9083 Evaluate side-chains 280 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 276 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain H residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.0050 chunk 545 optimal weight: 50.0000 chunk 302 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 368 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 564 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 420 optimal weight: 30.0000 chunk 653 optimal weight: 0.0970 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 458 ASN A 483 GLN A 537 ASN A 543 GLN A 584 ASN A 588 ASN A 601 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN B 376 ASN B 409 ASN B 458 ASN B 543 GLN B 573 ASN B 584 ASN B 588 ASN B 693 ASN C 211 HIS C 458 ASN C 483 GLN C 537 ASN C 543 GLN C 584 ASN C 588 ASN C 601 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN D 376 ASN D 409 ASN D 458 ASN D 543 GLN D 573 ASN D 584 ASN D 588 ASN D 693 ASN E 211 HIS E 458 ASN E 483 GLN E 537 ASN E 543 GLN E 584 ASN E 588 ASN E 601 ASN ** F 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN F 376 ASN F 409 ASN F 458 ASN F 543 GLN F 573 ASN F 584 ASN F 588 ASN F 693 ASN G 211 HIS G 458 ASN G 483 GLN G 537 ASN G 543 GLN G 584 ASN G 588 ASN G 601 ASN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 GLN H 376 ASN H 409 ASN H 458 ASN H 543 GLN H 573 ASN H 584 ASN H 588 ASN H 693 ASN I 48 GLN I 290 ASN I 351 ASN I 383 ASN I 585 ASN I 676 ASN I 728 GLN I 737 ASN J 48 GLN J 290 ASN J 351 ASN J 383 ASN J 585 ASN J 676 ASN J 728 GLN J 737 ASN K 48 GLN K 290 ASN K 351 ASN K 383 ASN K 585 ASN K 676 ASN K 728 GLN K 737 ASN L 48 GLN L 290 ASN L 351 ASN L 383 ASN L 585 ASN L 676 ASN L 728 GLN L 737 ASN Total number of N/Q/H flips: 100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 58724 Z= 0.174 Angle : 0.561 8.874 79316 Z= 0.300 Chirality : 0.044 0.183 8888 Planarity : 0.005 0.064 10312 Dihedral : 5.136 29.258 7720 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.87 % Allowed : 11.32 % Favored : 87.82 % 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: -2.61 (0.09), residues: 7136 helix: -0.90 (0.11), residues: 2040 sheet: -0.97 (0.15), residues: 1124 loop : -2.51 (0.08), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 226 HIS 0.007 0.001 HIS L 220 PHE 0.014 0.001 PHE G 439 TYR 0.014 0.001 TYR A 375 ARG 0.007 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 240 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9287 (t) REVERT: B 350 MET cc_start: 0.8295 (mtp) cc_final: 0.7994 (mtp) REVERT: B 436 TYR cc_start: 0.8788 (t80) cc_final: 0.8557 (t80) REVERT: B 664 ASN cc_start: 0.8302 (t0) cc_final: 0.8080 (p0) REVERT: B 673 LYS cc_start: 0.9300 (mttp) cc_final: 0.9055 (mmtp) REVERT: D 240 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9286 (t) REVERT: D 350 MET cc_start: 0.8296 (mtp) cc_final: 0.7995 (mtp) REVERT: D 436 TYR cc_start: 0.8789 (t80) cc_final: 0.8558 (t80) REVERT: D 664 ASN cc_start: 0.8301 (t0) cc_final: 0.8080 (p0) REVERT: D 673 LYS cc_start: 0.9301 (mttp) cc_final: 0.9055 (mmtp) REVERT: F 240 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9286 (t) REVERT: F 350 MET cc_start: 0.8296 (mtp) cc_final: 0.7996 (mtp) REVERT: F 436 TYR cc_start: 0.8788 (t80) cc_final: 0.8555 (t80) REVERT: F 664 ASN cc_start: 0.8302 (t0) cc_final: 0.8081 (p0) REVERT: F 673 LYS cc_start: 0.9301 (mttp) cc_final: 0.9056 (mmtp) REVERT: H 240 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9285 (t) REVERT: H 350 MET cc_start: 0.8295 (mtp) cc_final: 0.7995 (mtp) REVERT: H 436 TYR cc_start: 0.8787 (t80) cc_final: 0.8555 (t80) REVERT: H 664 ASN cc_start: 0.8302 (t0) cc_final: 0.8080 (p0) REVERT: H 673 LYS cc_start: 0.9300 (mttp) cc_final: 0.9055 (mmtp) REVERT: I 85 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 381 LYS cc_start: 0.4283 (mmtt) cc_final: 0.4069 (mmmt) REVERT: I 594 TYR cc_start: 0.6591 (m-10) cc_final: 0.6368 (m-10) REVERT: I 761 GLN cc_start: 0.8792 (tt0) cc_final: 0.8169 (tm-30) REVERT: J 85 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8215 (tm-30) REVERT: J 381 LYS cc_start: 0.4283 (mmtt) cc_final: 0.4070 (mmmt) REVERT: J 594 TYR cc_start: 0.6592 (m-10) cc_final: 0.6369 (m-10) REVERT: J 761 GLN cc_start: 0.8791 (tt0) cc_final: 0.8169 (tm-30) REVERT: K 85 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8216 (tm-30) REVERT: K 381 LYS cc_start: 0.4282 (mmtt) cc_final: 0.4069 (mmmt) REVERT: K 594 TYR cc_start: 0.6592 (m-10) cc_final: 0.6368 (m-10) REVERT: K 761 GLN cc_start: 0.8791 (tt0) cc_final: 0.8169 (tm-30) REVERT: L 85 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8216 (tm-30) REVERT: L 381 LYS cc_start: 0.4282 (mmtt) cc_final: 0.4071 (mmmt) REVERT: L 594 TYR cc_start: 0.6591 (m-10) cc_final: 0.6368 (m-10) REVERT: L 761 GLN cc_start: 0.8791 (tt0) cc_final: 0.8169 (tm-30) outliers start: 56 outliers final: 24 residues processed: 344 average time/residue: 0.5973 time to fit residues: 337.3050 Evaluate side-chains 292 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 668 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 668 LEU Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 544 optimal weight: 50.0000 chunk 445 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 655 optimal weight: 1.9990 chunk 707 optimal weight: 5.9990 chunk 583 optimal weight: 7.9990 chunk 649 optimal weight: 8.9990 chunk 223 optimal weight: 0.8980 chunk 525 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 HIS G 403 GLN ** G 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS J 81 HIS J 440 ASN K 81 HIS L 81 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 58724 Z= 0.395 Angle : 0.633 8.953 79316 Z= 0.333 Chirality : 0.047 0.180 8888 Planarity : 0.005 0.053 10312 Dihedral : 5.312 31.062 7720 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.62 % Allowed : 14.35 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.08 (0.09), residues: 7136 helix: -0.11 (0.12), residues: 2048 sheet: -0.88 (0.15), residues: 1140 loop : -2.33 (0.09), residues: 3948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 226 HIS 0.007 0.001 HIS I 220 PHE 0.018 0.002 PHE G 727 TYR 0.014 0.002 TYR D 375 ARG 0.004 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 280 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ARG cc_start: 0.7958 (mmp-170) cc_final: 0.7755 (mmm160) REVERT: B 350 MET cc_start: 0.8507 (mtp) cc_final: 0.8285 (mtp) REVERT: B 436 TYR cc_start: 0.8853 (t80) cc_final: 0.8616 (t80) REVERT: B 662 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6900 (ttp) REVERT: B 664 ASN cc_start: 0.8463 (t0) cc_final: 0.8044 (p0) REVERT: B 673 LYS cc_start: 0.9293 (mttp) cc_final: 0.9053 (mmtp) REVERT: B 699 TYR cc_start: 0.8330 (m-80) cc_final: 0.8035 (m-80) REVERT: C 600 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7754 (mmm160) REVERT: D 350 MET cc_start: 0.8507 (mtp) cc_final: 0.8285 (mtp) REVERT: D 436 TYR cc_start: 0.8852 (t80) cc_final: 0.8615 (t80) REVERT: D 662 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6896 (ttp) REVERT: D 664 ASN cc_start: 0.8463 (t0) cc_final: 0.8044 (p0) REVERT: D 673 LYS cc_start: 0.9292 (mttp) cc_final: 0.9052 (mmtp) REVERT: D 699 TYR cc_start: 0.8333 (m-80) cc_final: 0.8038 (m-80) REVERT: E 600 ARG cc_start: 0.7958 (mmp-170) cc_final: 0.7751 (mmm160) REVERT: F 350 MET cc_start: 0.8507 (mtp) cc_final: 0.8282 (mtp) REVERT: F 436 TYR cc_start: 0.8852 (t80) cc_final: 0.8616 (t80) REVERT: F 662 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6900 (ttp) REVERT: F 664 ASN cc_start: 0.8462 (t0) cc_final: 0.8043 (p0) REVERT: F 673 LYS cc_start: 0.9293 (mttp) cc_final: 0.9053 (mmtp) REVERT: F 699 TYR cc_start: 0.8333 (m-80) cc_final: 0.8038 (m-80) REVERT: G 600 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7756 (mmm160) REVERT: H 350 MET cc_start: 0.8508 (mtp) cc_final: 0.8284 (mtp) REVERT: H 436 TYR cc_start: 0.8851 (t80) cc_final: 0.8616 (t80) REVERT: H 662 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6899 (ttp) REVERT: H 664 ASN cc_start: 0.8462 (t0) cc_final: 0.8043 (p0) REVERT: H 673 LYS cc_start: 0.9293 (mttp) cc_final: 0.9053 (mmtp) REVERT: H 699 TYR cc_start: 0.8331 (m-80) cc_final: 0.8038 (m-80) REVERT: I 85 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8246 (tm-30) REVERT: I 156 ASP cc_start: 0.7692 (t0) cc_final: 0.7353 (t70) REVERT: J 85 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8245 (tm-30) REVERT: J 156 ASP cc_start: 0.7691 (t0) cc_final: 0.7352 (t70) REVERT: K 85 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8246 (tm-30) REVERT: K 156 ASP cc_start: 0.7692 (t0) cc_final: 0.7353 (t70) REVERT: L 85 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8245 (tm-30) REVERT: L 156 ASP cc_start: 0.7690 (t0) cc_final: 0.7351 (t70) outliers start: 105 outliers final: 64 residues processed: 361 average time/residue: 0.5759 time to fit residues: 343.7087 Evaluate side-chains 324 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 256 time to evaluate : 4.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 662 MET Chi-restraints excluded: chain F residue 668 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 668 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 594 TYR Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 594 TYR Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 594 TYR Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 0.9990 chunk 492 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 312 optimal weight: 40.0000 chunk 439 optimal weight: 7.9990 chunk 657 optimal weight: 3.9990 chunk 695 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 623 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN C 709 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN F 601 ASN G 709 ASN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 601 ASN L 440 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 58724 Z= 0.233 Angle : 0.547 9.862 79316 Z= 0.290 Chirality : 0.044 0.188 8888 Planarity : 0.004 0.073 10312 Dihedral : 4.879 28.085 7720 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.12 % Allowed : 15.29 % Favored : 82.59 % 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: -1.71 (0.10), residues: 7136 helix: 0.22 (0.12), residues: 2068 sheet: -0.68 (0.15), residues: 1172 loop : -2.12 (0.09), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 226 HIS 0.008 0.001 HIS L 220 PHE 0.015 0.001 PHE C 727 TYR 0.014 0.001 TYR G 375 ARG 0.004 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 284 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LEU cc_start: 0.7434 (mt) cc_final: 0.7226 (pp) REVERT: A 662 MET cc_start: 0.7569 (mtt) cc_final: 0.7255 (mtm) REVERT: B 240 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9328 (t) REVERT: B 350 MET cc_start: 0.8429 (mtp) cc_final: 0.8156 (mtp) REVERT: B 436 TYR cc_start: 0.8825 (t80) cc_final: 0.8587 (t80) REVERT: B 515 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 662 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6812 (ttp) REVERT: B 664 ASN cc_start: 0.8373 (t0) cc_final: 0.8108 (p0) REVERT: B 673 LYS cc_start: 0.9248 (mttp) cc_final: 0.9040 (mmtp) REVERT: C 338 LEU cc_start: 0.7440 (mt) cc_final: 0.7228 (pp) REVERT: C 662 MET cc_start: 0.7570 (mtt) cc_final: 0.7255 (mtm) REVERT: D 240 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9329 (t) REVERT: D 350 MET cc_start: 0.8428 (mtp) cc_final: 0.8157 (mtp) REVERT: D 436 TYR cc_start: 0.8824 (t80) cc_final: 0.8585 (t80) REVERT: D 515 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: D 662 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6811 (ttp) REVERT: D 664 ASN cc_start: 0.8374 (t0) cc_final: 0.8106 (p0) REVERT: D 673 LYS cc_start: 0.9249 (mttp) cc_final: 0.9042 (mmtp) REVERT: E 338 LEU cc_start: 0.7440 (mt) cc_final: 0.7226 (pp) REVERT: E 662 MET cc_start: 0.7572 (mtt) cc_final: 0.7258 (mtm) REVERT: F 240 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9328 (t) REVERT: F 350 MET cc_start: 0.8430 (mtp) cc_final: 0.8157 (mtp) REVERT: F 436 TYR cc_start: 0.8825 (t80) cc_final: 0.8587 (t80) REVERT: F 515 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: F 662 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6810 (ttp) REVERT: F 664 ASN cc_start: 0.8373 (t0) cc_final: 0.8105 (p0) REVERT: F 673 LYS cc_start: 0.9249 (mttp) cc_final: 0.9042 (mmtp) REVERT: G 338 LEU cc_start: 0.7435 (mt) cc_final: 0.7225 (pp) REVERT: G 662 MET cc_start: 0.7576 (mtt) cc_final: 0.7258 (mtm) REVERT: H 240 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9326 (t) REVERT: H 350 MET cc_start: 0.8430 (mtp) cc_final: 0.8159 (mtp) REVERT: H 436 TYR cc_start: 0.8824 (t80) cc_final: 0.8586 (t80) REVERT: H 515 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: H 662 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6810 (ttp) REVERT: H 664 ASN cc_start: 0.8373 (t0) cc_final: 0.8105 (p0) REVERT: H 673 LYS cc_start: 0.9248 (mttp) cc_final: 0.9040 (mmtp) REVERT: I 85 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8178 (tm-30) REVERT: I 156 ASP cc_start: 0.7645 (t0) cc_final: 0.7325 (t0) REVERT: J 85 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8177 (tm-30) REVERT: J 156 ASP cc_start: 0.7646 (t0) cc_final: 0.7327 (t0) REVERT: K 85 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8176 (tm-30) REVERT: K 156 ASP cc_start: 0.7647 (t0) cc_final: 0.7327 (t0) REVERT: L 85 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8179 (tm-30) REVERT: L 156 ASP cc_start: 0.7646 (t0) cc_final: 0.7326 (t0) outliers start: 137 outliers final: 80 residues processed: 389 average time/residue: 0.5945 time to fit residues: 381.9949 Evaluate side-chains 348 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 256 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 725 LEU Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 662 MET Chi-restraints excluded: chain F residue 668 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 250 GLU Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 668 LEU Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 594 TYR Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 594 TYR Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 594 TYR Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 518 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 593 optimal weight: 9.9990 chunk 481 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 624 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 HIS I 81 HIS I 205 GLN ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS J 205 GLN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS K 205 GLN ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 HIS L 205 GLN ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 58724 Z= 0.206 Angle : 0.537 10.681 79316 Z= 0.281 Chirality : 0.044 0.187 8888 Planarity : 0.004 0.042 10312 Dihedral : 4.674 27.528 7720 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.86 % Allowed : 16.02 % Favored : 82.13 % 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: -1.40 (0.10), residues: 7136 helix: 0.56 (0.12), residues: 2032 sheet: -0.47 (0.15), residues: 1176 loop : -1.97 (0.09), residues: 3928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 226 HIS 0.007 0.001 HIS K 220 PHE 0.018 0.001 PHE E 439 TYR 0.014 0.001 TYR E 375 ARG 0.006 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 276 time to evaluate : 5.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: B 350 MET cc_start: 0.8437 (mtp) cc_final: 0.8135 (mtp) REVERT: B 436 TYR cc_start: 0.8773 (t80) cc_final: 0.8507 (t80) REVERT: B 515 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: B 662 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6974 (ptm) REVERT: C 465 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: D 350 MET cc_start: 0.8438 (mtp) cc_final: 0.8137 (mtp) REVERT: D 436 TYR cc_start: 0.8772 (t80) cc_final: 0.8506 (t80) REVERT: D 515 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 662 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6974 (ptm) REVERT: D 664 ASN cc_start: 0.8360 (t0) cc_final: 0.8160 (p0) REVERT: E 465 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: F 350 MET cc_start: 0.8439 (mtp) cc_final: 0.8138 (mtp) REVERT: F 436 TYR cc_start: 0.8773 (t80) cc_final: 0.8508 (t80) REVERT: F 515 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: F 662 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6973 (ptm) REVERT: F 664 ASN cc_start: 0.8361 (t0) cc_final: 0.8160 (p0) REVERT: G 465 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: H 350 MET cc_start: 0.8440 (mtp) cc_final: 0.8139 (mtp) REVERT: H 436 TYR cc_start: 0.8773 (t80) cc_final: 0.8508 (t80) REVERT: H 515 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: H 662 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6974 (ptm) REVERT: H 664 ASN cc_start: 0.8359 (t0) cc_final: 0.8159 (p0) REVERT: I 85 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8242 (tm-30) REVERT: I 156 ASP cc_start: 0.7561 (t0) cc_final: 0.7206 (t0) REVERT: I 444 MET cc_start: -0.0833 (OUTLIER) cc_final: -0.1121 (mmt) REVERT: I 761 GLN cc_start: 0.8994 (tt0) cc_final: 0.8491 (tm-30) REVERT: J 85 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8240 (tm-30) REVERT: J 156 ASP cc_start: 0.7559 (t0) cc_final: 0.7203 (t0) REVERT: J 444 MET cc_start: -0.0839 (OUTLIER) cc_final: -0.1127 (mmt) REVERT: J 761 GLN cc_start: 0.8993 (tt0) cc_final: 0.8490 (tm-30) REVERT: K 85 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8241 (tm-30) REVERT: K 156 ASP cc_start: 0.7558 (t0) cc_final: 0.7201 (t0) REVERT: K 444 MET cc_start: -0.0830 (OUTLIER) cc_final: -0.1120 (mmt) REVERT: K 761 GLN cc_start: 0.8993 (tt0) cc_final: 0.8490 (tm-30) REVERT: L 85 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8241 (tm-30) REVERT: L 156 ASP cc_start: 0.7558 (t0) cc_final: 0.7203 (t0) REVERT: L 444 MET cc_start: -0.0841 (OUTLIER) cc_final: -0.1121 (mmt) REVERT: L 761 GLN cc_start: 0.8997 (tt0) cc_final: 0.8493 (tm-30) outliers start: 120 outliers final: 60 residues processed: 368 average time/residue: 0.5981 time to fit residues: 364.4452 Evaluate side-chains 319 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 662 MET Chi-restraints excluded: chain F residue 668 LEU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 668 LEU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 594 TYR Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 594 TYR Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 594 TYR Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 594 TYR Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 0.9990 chunk 626 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 408 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 696 optimal weight: 10.0000 chunk 578 optimal weight: 3.9990 chunk 322 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 365 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 58724 Z= 0.162 Angle : 0.518 9.693 79316 Z= 0.270 Chirality : 0.043 0.191 8888 Planarity : 0.004 0.053 10312 Dihedral : 4.420 27.504 7720 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.09 % Allowed : 16.13 % Favored : 81.79 % 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: -1.21 (0.10), residues: 7136 helix: 0.73 (0.12), residues: 2032 sheet: -0.35 (0.15), residues: 1164 loop : -1.86 (0.09), residues: 3940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.007 0.001 HIS K 220 PHE 0.014 0.001 PHE E 727 TYR 0.014 0.001 TYR C 375 ARG 0.009 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 259 time to evaluate : 5.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: B 304 HIS cc_start: 0.0428 (OUTLIER) cc_final: -0.0384 (t70) REVERT: B 350 MET cc_start: 0.8390 (mtp) cc_final: 0.8006 (mtp) REVERT: B 436 TYR cc_start: 0.8769 (t80) cc_final: 0.8458 (t80) REVERT: B 465 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 515 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: B 662 MET cc_start: 0.7386 (mtp) cc_final: 0.7079 (ptm) REVERT: C 465 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: D 304 HIS cc_start: 0.0429 (OUTLIER) cc_final: -0.0385 (t70) REVERT: D 350 MET cc_start: 0.8391 (mtp) cc_final: 0.8007 (mtp) REVERT: D 436 TYR cc_start: 0.8770 (t80) cc_final: 0.8460 (t80) REVERT: D 465 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: D 515 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: D 662 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6924 (ptm) REVERT: E 465 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: F 304 HIS cc_start: 0.0427 (OUTLIER) cc_final: -0.0385 (t70) REVERT: F 350 MET cc_start: 0.8394 (mtp) cc_final: 0.8009 (mtp) REVERT: F 436 TYR cc_start: 0.8770 (t80) cc_final: 0.8459 (t80) REVERT: F 465 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: F 515 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: F 662 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6925 (ptm) REVERT: G 465 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: H 304 HIS cc_start: 0.0427 (OUTLIER) cc_final: -0.0384 (t70) REVERT: H 350 MET cc_start: 0.8393 (mtp) cc_final: 0.8008 (mtp) REVERT: H 436 TYR cc_start: 0.8771 (t80) cc_final: 0.8459 (t80) REVERT: H 465 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: H 515 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: H 662 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6925 (ptm) REVERT: I 85 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8124 (tm-30) REVERT: I 156 ASP cc_start: 0.7297 (t0) cc_final: 0.6818 (t0) REVERT: J 85 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8124 (tm-30) REVERT: J 156 ASP cc_start: 0.7297 (t0) cc_final: 0.6818 (t0) REVERT: K 85 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8124 (tm-30) REVERT: K 156 ASP cc_start: 0.7296 (t0) cc_final: 0.6820 (t0) REVERT: L 85 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8125 (tm-30) REVERT: L 156 ASP cc_start: 0.7295 (t0) cc_final: 0.6818 (t0) outliers start: 135 outliers final: 64 residues processed: 375 average time/residue: 0.5523 time to fit residues: 351.3135 Evaluate side-chains 311 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 465 GLU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 304 HIS Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 662 MET Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 465 GLU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 304 HIS Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 465 GLU Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 396 optimal weight: 0.8980 chunk 508 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 586 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 chunk 693 optimal weight: 7.9990 chunk 434 optimal weight: 3.9990 chunk 423 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 HIS D 211 HIS H 211 HIS ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 ASN ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 58724 Z= 0.309 Angle : 0.583 9.223 79316 Z= 0.303 Chirality : 0.046 0.181 8888 Planarity : 0.004 0.042 10312 Dihedral : 4.694 28.877 7716 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.09 % Allowed : 16.57 % Favored : 81.34 % 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: -1.26 (0.10), residues: 7136 helix: 0.65 (0.12), residues: 2032 sheet: -0.30 (0.15), residues: 1144 loop : -1.89 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 480 HIS 0.007 0.001 HIS K 220 PHE 0.015 0.002 PHE G 727 TYR 0.013 0.001 TYR F 375 ARG 0.009 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 236 time to evaluate : 4.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 304 HIS cc_start: 0.0414 (OUTLIER) cc_final: -0.0540 (t70) REVERT: B 350 MET cc_start: 0.8568 (mtp) cc_final: 0.8033 (mtp) REVERT: B 436 TYR cc_start: 0.8855 (t80) cc_final: 0.8600 (t80) REVERT: B 465 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: B 515 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 617 ARG cc_start: 0.7173 (mtp-110) cc_final: 0.6965 (mtp-110) REVERT: B 662 MET cc_start: 0.7552 (mtp) cc_final: 0.7141 (ptp) REVERT: D 304 HIS cc_start: 0.0413 (OUTLIER) cc_final: -0.0541 (t70) REVERT: D 350 MET cc_start: 0.8571 (mtp) cc_final: 0.8033 (mtp) REVERT: D 436 TYR cc_start: 0.8856 (t80) cc_final: 0.8600 (t80) REVERT: D 465 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 515 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: D 617 ARG cc_start: 0.7170 (mtp-110) cc_final: 0.6963 (mtp-110) REVERT: D 662 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7184 (ptm) REVERT: F 304 HIS cc_start: 0.0412 (OUTLIER) cc_final: -0.0540 (t70) REVERT: F 350 MET cc_start: 0.8571 (mtp) cc_final: 0.8033 (mtp) REVERT: F 436 TYR cc_start: 0.8856 (t80) cc_final: 0.8600 (t80) REVERT: F 465 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: F 515 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: F 617 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6963 (mtp-110) REVERT: F 662 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7182 (ptm) REVERT: H 304 HIS cc_start: 0.0411 (OUTLIER) cc_final: -0.0542 (t70) REVERT: H 350 MET cc_start: 0.8570 (mtp) cc_final: 0.8031 (mtp) REVERT: H 436 TYR cc_start: 0.8857 (t80) cc_final: 0.8600 (t80) REVERT: H 465 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: H 515 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: H 617 ARG cc_start: 0.7172 (mtp-110) cc_final: 0.6964 (mtp-110) REVERT: H 662 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7184 (ptm) REVERT: I 85 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8168 (tm-30) REVERT: I 156 ASP cc_start: 0.7484 (t0) cc_final: 0.7051 (t0) REVERT: J 85 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8166 (tm-30) REVERT: J 156 ASP cc_start: 0.7486 (t0) cc_final: 0.7052 (t0) REVERT: K 85 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8167 (tm-30) REVERT: K 156 ASP cc_start: 0.7485 (t0) cc_final: 0.7051 (t0) REVERT: L 85 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8168 (tm-30) REVERT: L 156 ASP cc_start: 0.7485 (t0) cc_final: 0.7051 (t0) outliers start: 135 outliers final: 76 residues processed: 348 average time/residue: 0.5672 time to fit residues: 335.7943 Evaluate side-chains 331 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 240 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 662 MET Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 304 HIS Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 662 MET Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 304 HIS Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 465 GLU Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain H residue 662 MET Chi-restraints excluded: chain H residue 687 LEU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 414 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 441 optimal weight: 0.0170 chunk 472 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 545 optimal weight: 8.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN C 602 ASN E 602 ASN G 602 ASN ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 93 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 58724 Z= 0.147 Angle : 0.525 9.487 79316 Z= 0.271 Chirality : 0.043 0.248 8888 Planarity : 0.004 0.046 10312 Dihedral : 4.333 26.610 7716 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.56 % Allowed : 17.38 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.10), residues: 7136 helix: 0.91 (0.12), residues: 2004 sheet: -0.18 (0.16), residues: 1148 loop : -1.75 (0.09), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.007 0.001 HIS K 220 PHE 0.014 0.001 PHE A 439 TYR 0.037 0.001 TYR K 594 ARG 0.010 0.000 ARG G 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 281 time to evaluate : 6.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5794 (p0) REVERT: B 304 HIS cc_start: 0.0697 (OUTLIER) cc_final: -0.0157 (t70) REVERT: B 350 MET cc_start: 0.8431 (mtp) cc_final: 0.7852 (mtp) REVERT: B 436 TYR cc_start: 0.8704 (t80) cc_final: 0.8386 (t80) REVERT: B 465 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 617 ARG cc_start: 0.7122 (mtp-110) cc_final: 0.6921 (mtp-110) REVERT: B 662 MET cc_start: 0.7465 (mtp) cc_final: 0.7088 (ptp) REVERT: B 687 LEU cc_start: 0.8468 (tp) cc_final: 0.8235 (tt) REVERT: B 699 TYR cc_start: 0.8311 (m-80) cc_final: 0.7668 (m-80) REVERT: C 426 ASP cc_start: 0.6068 (OUTLIER) cc_final: 0.5795 (p0) REVERT: D 304 HIS cc_start: 0.0702 (OUTLIER) cc_final: -0.0155 (t70) REVERT: D 350 MET cc_start: 0.8430 (mtp) cc_final: 0.7851 (mtp) REVERT: D 436 TYR cc_start: 0.8705 (t80) cc_final: 0.8388 (t80) REVERT: D 465 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: D 617 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6921 (mtp-110) REVERT: D 662 MET cc_start: 0.7546 (mtp) cc_final: 0.7192 (ptp) REVERT: D 687 LEU cc_start: 0.8467 (tp) cc_final: 0.8235 (tt) REVERT: D 699 TYR cc_start: 0.8332 (m-80) cc_final: 0.7723 (m-80) REVERT: E 426 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5792 (p0) REVERT: F 304 HIS cc_start: 0.0701 (OUTLIER) cc_final: -0.0154 (t70) REVERT: F 350 MET cc_start: 0.8430 (mtp) cc_final: 0.7851 (mtp) REVERT: F 436 TYR cc_start: 0.8705 (t80) cc_final: 0.8387 (t80) REVERT: F 465 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: F 617 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6920 (mtp-110) REVERT: F 662 MET cc_start: 0.7547 (mtp) cc_final: 0.7190 (ptp) REVERT: F 687 LEU cc_start: 0.8467 (tp) cc_final: 0.8234 (tt) REVERT: F 699 TYR cc_start: 0.8331 (m-80) cc_final: 0.7721 (m-80) REVERT: G 426 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5793 (p0) REVERT: H 304 HIS cc_start: 0.0699 (OUTLIER) cc_final: -0.0157 (t70) REVERT: H 350 MET cc_start: 0.8430 (mtp) cc_final: 0.7850 (mtp) REVERT: H 436 TYR cc_start: 0.8704 (t80) cc_final: 0.8387 (t80) REVERT: H 465 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: H 617 ARG cc_start: 0.7120 (mtp-110) cc_final: 0.6918 (mtp-110) REVERT: H 662 MET cc_start: 0.7548 (mtp) cc_final: 0.7189 (ptp) REVERT: H 687 LEU cc_start: 0.8468 (tp) cc_final: 0.8235 (tt) REVERT: H 699 TYR cc_start: 0.8334 (m-80) cc_final: 0.7723 (m-80) REVERT: I 85 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8123 (tm-30) REVERT: I 156 ASP cc_start: 0.7381 (t0) cc_final: 0.7003 (t0) REVERT: I 594 TYR cc_start: 0.6137 (m-10) cc_final: 0.5829 (m-80) REVERT: J 85 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8122 (tm-30) REVERT: J 156 ASP cc_start: 0.7383 (t0) cc_final: 0.7006 (t0) REVERT: J 594 TYR cc_start: 0.6136 (m-10) cc_final: 0.5828 (m-80) REVERT: K 85 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8125 (tm-30) REVERT: K 156 ASP cc_start: 0.7381 (t0) cc_final: 0.7004 (t0) REVERT: K 594 TYR cc_start: 0.6135 (m-10) cc_final: 0.5826 (m-80) REVERT: L 85 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8123 (tm-30) REVERT: L 156 ASP cc_start: 0.7381 (t0) cc_final: 0.7005 (t0) REVERT: L 594 TYR cc_start: 0.6136 (m-10) cc_final: 0.5827 (m-80) outliers start: 101 outliers final: 68 residues processed: 370 average time/residue: 0.5648 time to fit residues: 354.3587 Evaluate side-chains 311 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 231 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 304 HIS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 304 HIS Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 304 HIS Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 304 HIS Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 465 GLU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 0.9980 chunk 664 optimal weight: 4.9990 chunk 606 optimal weight: 30.0000 chunk 646 optimal weight: 0.9990 chunk 389 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 507 optimal weight: 0.0670 chunk 198 optimal weight: 0.5980 chunk 584 optimal weight: 1.9990 chunk 611 optimal weight: 0.8980 chunk 644 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 299 HIS ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 488 ASN ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 488 ASN ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 58724 Z= 0.145 Angle : 0.518 8.317 79316 Z= 0.268 Chirality : 0.043 0.229 8888 Planarity : 0.004 0.040 10312 Dihedral : 4.168 26.661 7716 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.24 % Allowed : 17.84 % Favored : 80.92 % 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: 7136 helix: 0.99 (0.12), residues: 2008 sheet: -0.05 (0.16), residues: 1148 loop : -1.68 (0.09), residues: 3980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 519 HIS 0.007 0.001 HIS I 220 PHE 0.013 0.001 PHE G 727 TYR 0.024 0.001 TYR J 594 ARG 0.010 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 274 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5778 (p0) REVERT: A 712 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6345 (pp20) REVERT: B 304 HIS cc_start: 0.0648 (OUTLIER) cc_final: -0.0127 (t70) REVERT: B 350 MET cc_start: 0.8392 (mtp) cc_final: 0.8013 (mtp) REVERT: B 436 TYR cc_start: 0.8715 (t80) cc_final: 0.8360 (t80) REVERT: B 465 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: B 662 MET cc_start: 0.7523 (mtp) cc_final: 0.7197 (ptp) REVERT: B 687 LEU cc_start: 0.8429 (tp) cc_final: 0.8194 (tt) REVERT: B 699 TYR cc_start: 0.8351 (m-80) cc_final: 0.7719 (m-80) REVERT: C 426 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.5776 (p0) REVERT: C 712 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6344 (pp20) REVERT: D 304 HIS cc_start: 0.0609 (OUTLIER) cc_final: -0.0146 (t70) REVERT: D 350 MET cc_start: 0.8390 (mtp) cc_final: 0.8013 (mtp) REVERT: D 436 TYR cc_start: 0.8745 (t80) cc_final: 0.8396 (t80) REVERT: D 465 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: D 662 MET cc_start: 0.7563 (mtp) cc_final: 0.7087 (ptp) REVERT: D 687 LEU cc_start: 0.8429 (tp) cc_final: 0.8193 (tt) REVERT: D 699 TYR cc_start: 0.8352 (m-80) cc_final: 0.7724 (m-80) REVERT: E 426 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.5777 (p0) REVERT: E 712 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6345 (pp20) REVERT: F 304 HIS cc_start: 0.0648 (OUTLIER) cc_final: -0.0126 (t70) REVERT: F 350 MET cc_start: 0.8391 (mtp) cc_final: 0.8015 (mtp) REVERT: F 436 TYR cc_start: 0.8745 (t80) cc_final: 0.8397 (t80) REVERT: F 465 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: F 662 MET cc_start: 0.7561 (mtp) cc_final: 0.7084 (ptp) REVERT: F 687 LEU cc_start: 0.8427 (tp) cc_final: 0.8193 (tt) REVERT: F 699 TYR cc_start: 0.8353 (m-80) cc_final: 0.7727 (m-80) REVERT: G 426 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5778 (p0) REVERT: G 712 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6378 (pp20) REVERT: H 304 HIS cc_start: 0.0650 (OUTLIER) cc_final: -0.0127 (t70) REVERT: H 350 MET cc_start: 0.8392 (mtp) cc_final: 0.8014 (mtp) REVERT: H 436 TYR cc_start: 0.8745 (t80) cc_final: 0.8395 (t80) REVERT: H 465 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: H 662 MET cc_start: 0.7560 (mtp) cc_final: 0.7083 (ptp) REVERT: H 687 LEU cc_start: 0.8428 (tp) cc_final: 0.8193 (tt) REVERT: H 699 TYR cc_start: 0.8353 (m-80) cc_final: 0.7725 (m-80) REVERT: I 594 TYR cc_start: 0.6257 (m-10) cc_final: 0.5940 (m-80) REVERT: J 444 MET cc_start: -0.0465 (OUTLIER) cc_final: -0.0667 (mmt) REVERT: J 594 TYR cc_start: 0.6257 (m-10) cc_final: 0.5941 (m-80) REVERT: K 594 TYR cc_start: 0.6258 (m-10) cc_final: 0.5941 (m-80) REVERT: L 444 MET cc_start: -0.0465 (OUTLIER) cc_final: -0.0678 (mmt) REVERT: L 594 TYR cc_start: 0.6257 (m-10) cc_final: 0.5941 (m-80) outliers start: 80 outliers final: 54 residues processed: 346 average time/residue: 0.5683 time to fit residues: 332.0248 Evaluate side-chains 324 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 5.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 712 GLU Chi-restraints excluded: chain F residue 304 HIS Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain H residue 304 HIS Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 465 GLU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 2.9990 chunk 683 optimal weight: 2.9990 chunk 417 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 475 optimal weight: 50.0000 chunk 717 optimal weight: 8.9990 chunk 660 optimal weight: 7.9990 chunk 571 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 441 optimal weight: 0.0050 chunk 350 optimal weight: 3.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN D 422 ASN F 422 ASN I 85 GLN ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 93 ASN ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 756 ASN L 85 GLN ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 58724 Z= 0.225 Angle : 0.553 8.399 79316 Z= 0.288 Chirality : 0.045 0.173 8888 Planarity : 0.004 0.042 10312 Dihedral : 4.350 27.631 7716 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.31 % Allowed : 18.07 % Favored : 80.61 % 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: 7136 helix: 0.92 (0.12), residues: 2044 sheet: -0.05 (0.16), residues: 1132 loop : -1.75 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 480 HIS 0.016 0.001 HIS J 220 PHE 0.015 0.001 PHE G 727 TYR 0.022 0.001 TYR I 594 ARG 0.008 0.000 ARG E 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14272 Ramachandran restraints generated. 7136 Oldfield, 0 Emsley, 7136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 244 time to evaluate : 5.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5884 (p0) REVERT: A 712 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6355 (pp20) REVERT: B 304 HIS cc_start: 0.0662 (OUTLIER) cc_final: -0.0154 (t70) REVERT: B 350 MET cc_start: 0.8474 (mtp) cc_final: 0.8123 (mtp) REVERT: B 436 TYR cc_start: 0.8829 (t80) cc_final: 0.8568 (t80) REVERT: B 465 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: B 662 MET cc_start: 0.7572 (mtp) cc_final: 0.7088 (ptp) REVERT: B 687 LEU cc_start: 0.8395 (tp) cc_final: 0.8178 (tt) REVERT: B 699 TYR cc_start: 0.8364 (m-80) cc_final: 0.7716 (m-80) REVERT: C 426 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5887 (p0) REVERT: C 712 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6354 (pp20) REVERT: D 304 HIS cc_start: 0.0662 (OUTLIER) cc_final: -0.0153 (t70) REVERT: D 350 MET cc_start: 0.8473 (mtp) cc_final: 0.8121 (mtp) REVERT: D 436 TYR cc_start: 0.8829 (t80) cc_final: 0.8568 (t80) REVERT: D 465 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: D 662 MET cc_start: 0.7602 (mtp) cc_final: 0.7108 (ptp) REVERT: D 687 LEU cc_start: 0.8396 (tp) cc_final: 0.8179 (tt) REVERT: D 699 TYR cc_start: 0.8367 (m-80) cc_final: 0.7725 (m-80) REVERT: E 426 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5886 (p0) REVERT: E 712 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6354 (pp20) REVERT: F 304 HIS cc_start: 0.0661 (OUTLIER) cc_final: -0.0153 (t70) REVERT: F 350 MET cc_start: 0.8474 (mtp) cc_final: 0.8122 (mtp) REVERT: F 436 TYR cc_start: 0.8829 (t80) cc_final: 0.8568 (t80) REVERT: F 465 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: F 662 MET cc_start: 0.7602 (mtp) cc_final: 0.7109 (ptp) REVERT: F 687 LEU cc_start: 0.8395 (tp) cc_final: 0.8178 (tt) REVERT: F 699 TYR cc_start: 0.8366 (m-80) cc_final: 0.7726 (m-80) REVERT: G 426 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5885 (p0) REVERT: G 712 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6354 (pp20) REVERT: H 304 HIS cc_start: 0.0663 (OUTLIER) cc_final: -0.0154 (t70) REVERT: H 350 MET cc_start: 0.8472 (mtp) cc_final: 0.8122 (mtp) REVERT: H 436 TYR cc_start: 0.8830 (t80) cc_final: 0.8567 (t80) REVERT: H 465 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: H 662 MET cc_start: 0.7600 (mtp) cc_final: 0.7106 (ptp) REVERT: H 687 LEU cc_start: 0.8395 (tp) cc_final: 0.8177 (tt) REVERT: H 699 TYR cc_start: 0.8367 (m-80) cc_final: 0.7724 (m-80) REVERT: I 85 GLN cc_start: 0.8197 (tm130) cc_final: 0.7882 (tm-30) REVERT: I 594 TYR cc_start: 0.6193 (m-10) cc_final: 0.5901 (m-80) REVERT: J 85 GLN cc_start: 0.8204 (tm130) cc_final: 0.7888 (tm-30) REVERT: J 444 MET cc_start: -0.0487 (OUTLIER) cc_final: -0.0718 (mmt) REVERT: J 594 TYR cc_start: 0.6193 (m-10) cc_final: 0.5900 (m-80) REVERT: K 85 GLN cc_start: 0.8199 (tm130) cc_final: 0.7885 (tm-30) REVERT: K 594 TYR cc_start: 0.6193 (m-10) cc_final: 0.5901 (m-80) REVERT: L 85 GLN cc_start: 0.8198 (tm130) cc_final: 0.7885 (tm-30) REVERT: L 444 MET cc_start: -0.0460 (OUTLIER) cc_final: -0.0700 (mmt) REVERT: L 594 TYR cc_start: 0.6194 (m-10) cc_final: 0.5901 (m-80) outliers start: 85 outliers final: 62 residues processed: 321 average time/residue: 0.5756 time to fit residues: 312.8255 Evaluate side-chains 320 residues out of total 6476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 401 LEU Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 712 GLU Chi-restraints excluded: chain F residue 304 HIS Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 465 GLU Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 725 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 646 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain H residue 304 HIS Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 465 GLU Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 725 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 444 MET Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 693 ILE Chi-restraints excluded: chain I residue 716 PHE Chi-restraints excluded: chain I residue 749 PHE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 444 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 693 ILE Chi-restraints excluded: chain J residue 716 PHE Chi-restraints excluded: chain J residue 749 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 693 ILE Chi-restraints excluded: chain K residue 716 PHE Chi-restraints excluded: chain K residue 749 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 444 MET Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 693 ILE Chi-restraints excluded: chain L residue 716 PHE Chi-restraints excluded: chain L residue 749 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 1.9990 chunk 608 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 526 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 572 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 587 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.0370 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN ** K 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098238 restraints weight = 104632.731| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.87 r_work: 0.2830 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 58724 Z= 0.211 Angle : 0.545 9.035 79316 Z= 0.283 Chirality : 0.044 0.166 8888 Planarity : 0.004 0.039 10312 Dihedral : 4.357 27.595 7716 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.36 % Allowed : 17.92 % Favored : 80.72 % 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: 7136 helix: 0.99 (0.12), residues: 2016 sheet: -0.02 (0.16), residues: 1140 loop : -1.68 (0.09), residues: 3980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 226 HIS 0.015 0.001 HIS J 220 PHE 0.015 0.001 PHE G 727 TYR 0.020 0.001 TYR J 594 ARG 0.008 0.000 ARG B 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8448.51 seconds wall clock time: 153 minutes 19.48 seconds (9199.48 seconds total)