Starting phenix.real_space_refine on Sat Mar 7 15:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pev_20333/03_2026/6pev_20333.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 Zn 24 6.06 5 S 252 5.16 5 C 29628 2.51 5 N 7848 2.21 5 O 8616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 299 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46368 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "C" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "D" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "E" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "F" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "G" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "H" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "I" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "J" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "K" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "L" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3862 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 11, 'TRANS': 466} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 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: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.22, per 1000 atoms: 0.20 Number of scatterers: 46368 At special positions: 0 Unit cell: (162.24, 156, 150.8, 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) Zn 24 29.99 S 252 16.00 O 8616 8.00 N 7848 7.00 C 29628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 58 " distance=2.03 Simple disulfide: pdb=" SG CYS J 26 " - pdb=" SG CYS J 58 " distance=2.03 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 58 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb="ZN ZN A1001 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 86 " pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb="ZN ZN B1001 " pdb="ZN ZN B1000 " - pdb=" NE2 HIS B 86 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb="ZN ZN C1001 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 86 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb="ZN ZN D1001 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 86 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb="ZN ZN E1001 " pdb="ZN ZN E1000 " - pdb=" NE2 HIS E 86 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb="ZN ZN F1001 " pdb="ZN ZN F1000 " - pdb=" NE2 HIS F 86 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb="ZN ZN G1001 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 86 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb="ZN ZN H1001 " pdb="ZN ZN H1000 " - pdb=" NE2 HIS H 86 " pdb=" ZN I1000 " pdb="ZN ZN I1000 " - pdb="ZN ZN I1001 " pdb="ZN ZN I1000 " - pdb=" NE2 HIS I 86 " pdb=" ZN J1000 " pdb="ZN ZN J1000 " - pdb="ZN ZN J1001 " pdb="ZN ZN J1000 " - pdb=" NE2 HIS J 86 " pdb=" ZN K1000 " pdb="ZN ZN K1000 " - pdb="ZN ZN K1001 " pdb="ZN ZN K1000 " - pdb=" NE2 HIS K 86 " pdb=" ZN L1000 " pdb="ZN ZN L1000 " - pdb="ZN ZN L1001 " pdb="ZN ZN L1000 " - pdb=" NE2 HIS L 86 " 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10824 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 35.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER A 170 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE A 381 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER B 170 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 327 through 345 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE B 381 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE B 479 " --> pdb=" O HIS B 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN B 561 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER C 170 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE C 381 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE C 479 " --> pdb=" O HIS C 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 520 Processing helix chain 'C' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER D 170 " --> pdb=" O TYR D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 327 through 345 Processing helix chain 'D' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE D 381 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE D 479 " --> pdb=" O HIS D 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 542 through 564 removed outlier: 3.515A pdb=" N TYR D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN D 561 " --> pdb=" O THR D 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER E 170 " --> pdb=" O TYR E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 277 through 289 Processing helix chain 'E' and resid 291 through 293 No H-bonds generated for 'chain 'E' and resid 291 through 293' Processing helix chain 'E' and resid 327 through 345 Processing helix chain 'E' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE E 381 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER E 403 " --> pdb=" O ASP E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN E 426 " --> pdb=" O GLY E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE E 479 " --> pdb=" O HIS E 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 489 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 520 Processing helix chain 'E' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN E 560 " --> pdb=" O TYR E 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN E 561 " --> pdb=" O THR E 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER F 170 " --> pdb=" O TYR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 277 through 289 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 327 through 345 Processing helix chain 'F' and resid 378 through 382 removed outlier: 3.607A pdb=" N ILE F 381 " --> pdb=" O HIS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE F 410 " --> pdb=" O PHE F 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS F 411 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN F 426 " --> pdb=" O GLY F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE F 479 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 489 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'F' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN F 560 " --> pdb=" O TYR F 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN F 561 " --> pdb=" O THR F 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 16 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER G 170 " --> pdb=" O TYR G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 192 Processing helix chain 'G' and resid 277 through 289 Processing helix chain 'G' and resid 291 through 293 No H-bonds generated for 'chain 'G' and resid 291 through 293' Processing helix chain 'G' and resid 327 through 345 Processing helix chain 'G' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE G 381 " --> pdb=" O HIS G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER G 403 " --> pdb=" O ASP G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE G 410 " --> pdb=" O PHE G 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU G 412 " --> pdb=" O LYS G 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS G 413 " --> pdb=" O GLU G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN G 426 " --> pdb=" O GLY G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE G 479 " --> pdb=" O HIS G 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 489 " --> pdb=" O LEU G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 520 Processing helix chain 'G' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN G 560 " --> pdb=" O TYR G 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN G 561 " --> pdb=" O THR G 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER H 170 " --> pdb=" O TYR H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 192 Processing helix chain 'H' and resid 277 through 289 Processing helix chain 'H' and resid 291 through 293 No H-bonds generated for 'chain 'H' and resid 291 through 293' Processing helix chain 'H' and resid 327 through 345 Processing helix chain 'H' and resid 378 through 382 removed outlier: 3.607A pdb=" N ILE H 381 " --> pdb=" O HIS H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER H 403 " --> pdb=" O ASP H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE H 410 " --> pdb=" O PHE H 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU H 412 " --> pdb=" O LYS H 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 413 " --> pdb=" O GLU H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN H 426 " --> pdb=" O GLY H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE H 479 " --> pdb=" O HIS H 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS H 489 " --> pdb=" O LEU H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 520 Processing helix chain 'H' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR H 559 " --> pdb=" O PHE H 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN H 560 " --> pdb=" O TYR H 556 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLN H 561 " --> pdb=" O THR H 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 16 Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER I 170 " --> pdb=" O TYR I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 192 Processing helix chain 'I' and resid 277 through 289 Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 327 through 345 Processing helix chain 'I' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE I 381 " --> pdb=" O HIS I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 406 removed outlier: 3.540A pdb=" N SER I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE I 410 " --> pdb=" O PHE I 406 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU I 412 " --> pdb=" O LYS I 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN I 426 " --> pdb=" O GLY I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE I 479 " --> pdb=" O HIS I 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS I 489 " --> pdb=" O LEU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 520 Processing helix chain 'I' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR I 559 " --> pdb=" O PHE I 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN I 560 " --> pdb=" O TYR I 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER J 170 " --> pdb=" O TYR J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 192 Processing helix chain 'J' and resid 277 through 289 Processing helix chain 'J' and resid 291 through 293 No H-bonds generated for 'chain 'J' and resid 291 through 293' Processing helix chain 'J' and resid 327 through 345 Processing helix chain 'J' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE J 381 " --> pdb=" O HIS J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER J 403 " --> pdb=" O ASP J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE J 410 " --> pdb=" O PHE J 406 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU J 412 " --> pdb=" O LYS J 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS J 413 " --> pdb=" O GLU J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN J 426 " --> pdb=" O GLY J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE J 479 " --> pdb=" O HIS J 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS J 489 " --> pdb=" O LEU J 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 520 Processing helix chain 'J' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR J 559 " --> pdb=" O PHE J 555 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN J 560 " --> pdb=" O TYR J 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN J 561 " --> pdb=" O THR J 557 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 166 through 171 removed outlier: 4.103A pdb=" N SER K 170 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 192 Processing helix chain 'K' and resid 277 through 289 Processing helix chain 'K' and resid 291 through 293 No H-bonds generated for 'chain 'K' and resid 291 through 293' Processing helix chain 'K' and resid 327 through 345 Processing helix chain 'K' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE K 381 " --> pdb=" O HIS K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER K 403 " --> pdb=" O ASP K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 414 removed outlier: 3.629A pdb=" N ILE K 410 " --> pdb=" O PHE K 406 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU K 412 " --> pdb=" O LYS K 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 426 removed outlier: 4.112A pdb=" N ASN K 426 " --> pdb=" O GLY K 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 491 removed outlier: 3.783A pdb=" N ILE K 479 " --> pdb=" O HIS K 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS K 489 " --> pdb=" O LEU K 485 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 520 Processing helix chain 'K' and resid 542 through 564 removed outlier: 3.516A pdb=" N TYR K 559 " --> pdb=" O PHE K 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN K 560 " --> pdb=" O TYR K 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN K 561 " --> pdb=" O THR K 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 166 through 171 removed outlier: 4.104A pdb=" N SER L 170 " --> pdb=" O TYR L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 192 Processing helix chain 'L' and resid 277 through 289 Processing helix chain 'L' and resid 291 through 293 No H-bonds generated for 'chain 'L' and resid 291 through 293' Processing helix chain 'L' and resid 327 through 345 Processing helix chain 'L' and resid 378 through 382 removed outlier: 3.606A pdb=" N ILE L 381 " --> pdb=" O HIS L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 406 removed outlier: 3.539A pdb=" N SER L 403 " --> pdb=" O ASP L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 414 removed outlier: 3.630A pdb=" N ILE L 410 " --> pdb=" O PHE L 406 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU L 412 " --> pdb=" O LYS L 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS L 413 " --> pdb=" O GLU L 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 426 removed outlier: 4.111A pdb=" N ASN L 426 " --> pdb=" O GLY L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 491 removed outlier: 3.784A pdb=" N ILE L 479 " --> pdb=" O HIS L 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS L 489 " --> pdb=" O LEU L 485 " (cutoff:3.500A) Processing helix chain 'L' and resid 511 through 520 Processing helix chain 'L' and resid 542 through 564 removed outlier: 3.517A pdb=" N TYR L 559 " --> pdb=" O PHE L 555 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN L 560 " --> pdb=" O TYR L 556 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLN L 561 " --> pdb=" O THR L 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER A 79 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 372 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 81 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 374 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 83 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 80 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU A 431 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 82 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL A 433 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE A 84 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 430 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 526 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN A 432 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP A 525 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU A 92 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU A 300 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE A 295 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS A 135 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 297 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 126 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS A 149 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 140 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS A 106 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA A 541 " --> pdb=" O PRO A 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA A 436 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER B 79 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE B 372 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 81 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 374 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 83 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 80 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU B 431 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 82 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 433 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 84 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 430 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE B 526 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 432 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP B 525 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU B 92 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU B 300 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 295 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 135 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 297 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 149 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 140 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS B 106 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA B 541 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA B 436 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER C 79 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE C 372 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 81 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE C 374 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 83 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE C 80 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 431 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 82 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL C 433 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 84 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 430 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 526 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 432 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP C 525 " --> pdb=" O LYS C 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU C 92 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU C 300 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE C 295 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS C 135 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 297 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU C 126 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS C 149 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS C 106 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA C 541 " --> pdb=" O PRO C 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA C 436 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER D 79 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 372 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 81 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 374 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER D 83 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 80 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU D 431 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE D 82 " --> pdb=" O LEU D 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL D 433 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE D 84 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 430 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 526 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN D 432 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP D 525 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU D 92 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU D 300 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 295 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 135 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 297 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 126 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS D 149 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 140 " --> pdb=" O VAL L 567 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS D 106 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA D 541 " --> pdb=" O PRO D 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA D 436 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.587A pdb=" N LYS H 139 " --> pdb=" O LYS H 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS H 149 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP H 297 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS H 135 " --> pdb=" O ILE H 295 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE H 295 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU H 300 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU H 92 " --> pdb=" O LEU H 302 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER E 79 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 372 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 81 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE E 374 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 83 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 80 " --> pdb=" O PHE E 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU E 431 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 82 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL E 433 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE E 84 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 430 " --> pdb=" O ILE E 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE E 526 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN E 432 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP E 525 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU E 92 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU E 300 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE E 295 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS E 135 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 297 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 126 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS E 149 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 140 " --> pdb=" O VAL F 567 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS E 106 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA E 541 " --> pdb=" O PRO E 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA E 436 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 39 through 40 removed outlier: 6.706A pdb=" N SER F 79 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE F 372 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 81 " --> pdb=" O ILE F 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE F 374 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER F 83 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE F 80 " --> pdb=" O PHE F 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 431 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 82 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL F 433 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE F 84 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE F 430 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE F 526 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN F 432 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP F 525 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU F 92 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU F 300 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE F 295 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS F 135 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 297 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU F 126 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS F 149 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS F 139 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 140 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS F 106 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA F 541 " --> pdb=" O PRO F 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA F 436 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER G 79 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE G 372 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU G 81 " --> pdb=" O ILE G 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE G 374 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 83 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 80 " --> pdb=" O PHE G 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU G 431 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE G 82 " --> pdb=" O LEU G 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL G 433 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE G 84 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE G 430 " --> pdb=" O ILE G 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE G 526 " --> pdb=" O ILE G 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN G 432 " --> pdb=" O ILE G 526 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP G 525 " --> pdb=" O LYS G 462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 110 through 113 removed outlier: 4.298A pdb=" N LEU G 92 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU G 300 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE G 295 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS G 135 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 297 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU G 126 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS G 149 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 139 " --> pdb=" O LYS G 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS G 106 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA G 541 " --> pdb=" O PRO G 529 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA G 436 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER H 79 " --> pdb=" O LEU H 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE H 372 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU H 81 " --> pdb=" O ILE H 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE H 374 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER H 83 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE H 80 " --> pdb=" O PHE H 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU H 431 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE H 82 " --> pdb=" O LEU H 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL H 433 " --> pdb=" O ILE H 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE H 84 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 430 " --> pdb=" O ILE H 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE H 526 " --> pdb=" O ILE H 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN H 432 " --> pdb=" O ILE H 526 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP H 525 " --> pdb=" O LYS H 462 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS H 106 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA H 541 " --> pdb=" O PRO H 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA H 436 " --> pdb=" O GLN H 530 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER I 79 " --> pdb=" O LEU I 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE I 372 " --> pdb=" O SER I 79 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU I 81 " --> pdb=" O ILE I 372 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE I 374 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER I 83 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE I 80 " --> pdb=" O PHE I 429 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU I 431 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE I 82 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL I 433 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE I 84 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE I 430 " --> pdb=" O ILE I 524 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE I 526 " --> pdb=" O ILE I 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN I 432 " --> pdb=" O ILE I 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP I 525 " --> pdb=" O LYS I 462 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU I 92 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU I 300 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE I 295 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS I 135 " --> pdb=" O ILE I 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP I 297 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU I 126 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS I 149 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS I 139 " --> pdb=" O LYS I 136 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU I 140 " --> pdb=" O VAL J 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 100 through 102 removed outlier: 6.821A pdb=" N HIS I 106 " --> pdb=" O ILE I 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 309 through 311 removed outlier: 4.446A pdb=" N ALA I 541 " --> pdb=" O PRO I 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA I 436 " --> pdb=" O GLN I 530 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 566 through 567 removed outlier: 3.570A pdb=" N GLU K 142 " --> pdb=" O VAL I 567 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 139 " --> pdb=" O LYS K 136 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS K 149 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU K 126 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP K 297 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS K 135 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE K 295 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU K 300 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU K 92 " --> pdb=" O LEU K 302 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER J 79 " --> pdb=" O LEU J 370 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE J 372 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU J 81 " --> pdb=" O ILE J 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE J 374 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER J 83 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE J 80 " --> pdb=" O PHE J 429 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU J 431 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE J 82 " --> pdb=" O LEU J 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL J 433 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE J 84 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE J 430 " --> pdb=" O ILE J 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE J 526 " --> pdb=" O ILE J 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN J 432 " --> pdb=" O ILE J 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP J 525 " --> pdb=" O LYS J 462 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU J 92 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU J 300 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE J 295 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS J 135 " --> pdb=" O ILE J 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP J 297 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU J 126 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS J 149 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 139 " --> pdb=" O LYS J 136 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU J 140 " --> pdb=" O VAL K 567 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS J 106 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA J 541 " --> pdb=" O PRO J 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA J 436 " --> pdb=" O GLN J 530 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER K 79 " --> pdb=" O LEU K 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE K 372 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU K 81 " --> pdb=" O ILE K 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE K 374 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER K 83 " --> pdb=" O ILE K 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE K 80 " --> pdb=" O PHE K 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU K 431 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE K 82 " --> pdb=" O LEU K 431 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL K 433 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE K 84 " --> pdb=" O VAL K 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE K 430 " --> pdb=" O ILE K 524 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 526 " --> pdb=" O ILE K 430 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN K 432 " --> pdb=" O ILE K 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP K 525 " --> pdb=" O LYS K 462 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS K 106 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA K 541 " --> pdb=" O PRO K 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA K 436 " --> pdb=" O GLN K 530 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.707A pdb=" N SER L 79 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE L 372 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU L 81 " --> pdb=" O ILE L 372 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE L 374 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER L 83 " --> pdb=" O ILE L 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE L 80 " --> pdb=" O PHE L 429 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU L 431 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE L 82 " --> pdb=" O LEU L 431 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL L 433 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE L 84 " --> pdb=" O VAL L 433 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE L 430 " --> pdb=" O ILE L 524 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE L 526 " --> pdb=" O ILE L 430 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN L 432 " --> pdb=" O ILE L 526 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP L 525 " --> pdb=" O LYS L 462 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 110 through 113 removed outlier: 4.297A pdb=" N LEU L 92 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 300 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE L 295 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS L 135 " --> pdb=" O ILE L 295 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP L 297 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU L 126 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS L 149 " --> pdb=" O LEU L 126 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS L 139 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 100 through 102 removed outlier: 6.820A pdb=" N HIS L 106 " --> pdb=" O ILE L 183 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 309 through 311 removed outlier: 4.447A pdb=" N ALA L 541 " --> pdb=" O PRO L 529 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA L 436 " --> pdb=" O GLN L 530 " (cutoff:3.500A) 1900 hydrogen bonds defined for protein. 5304 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: 11.30 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14926 1.34 - 1.46: 11228 1.46 - 1.59: 20838 1.59 - 1.71: 0 1.71 - 1.84: 336 Bond restraints: 47328 Sorted by residual: bond pdb=" N THR E 165 " pdb=" CA THR E 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.82e+00 bond pdb=" N THR K 165 " pdb=" CA THR K 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.68e+00 bond pdb=" N THR G 165 " pdb=" CA THR G 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.60e+00 bond pdb=" N THR I 165 " pdb=" CA THR I 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.57e+00 bond pdb=" N THR J 165 " pdb=" CA THR J 165 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.56e+00 ... (remaining 47323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 60055 1.81 - 3.61: 3060 3.61 - 5.42: 497 5.42 - 7.23: 204 7.23 - 9.04: 72 Bond angle restraints: 63888 Sorted by residual: angle pdb=" C GLU F 319 " pdb=" N GLY F 320 " pdb=" CA GLY F 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU L 319 " pdb=" N GLY L 320 " pdb=" CA GLY L 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU E 319 " pdb=" N GLY E 320 " pdb=" CA GLY E 320 " ideal model delta sigma weight residual 121.41 113.54 7.87 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU J 319 " pdb=" N GLY J 320 " pdb=" CA GLY J 320 " ideal model delta sigma weight residual 121.41 113.55 7.86 1.96e+00 2.60e-01 1.61e+01 angle pdb=" C GLU H 319 " pdb=" N GLY H 320 " pdb=" CA GLY H 320 " ideal model delta sigma weight residual 121.41 113.56 7.85 1.96e+00 2.60e-01 1.60e+01 ... (remaining 63883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 24671 18.10 - 36.19: 2763 36.19 - 54.29: 562 54.29 - 72.39: 149 72.39 - 90.48: 91 Dihedral angle restraints: 28236 sinusoidal: 11436 harmonic: 16800 Sorted by residual: dihedral pdb=" CA GLU J 319 " pdb=" C GLU J 319 " pdb=" N GLY J 320 " pdb=" CA GLY J 320 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA GLU E 319 " pdb=" C GLU E 319 " pdb=" N GLY E 320 " pdb=" CA GLY E 320 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA GLU H 319 " pdb=" C GLU H 319 " pdb=" N GLY H 320 " pdb=" CA GLY H 320 " ideal model delta harmonic sigma weight residual 180.00 147.65 32.35 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 28233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4880 0.054 - 0.108: 1604 0.108 - 0.163: 440 0.163 - 0.217: 84 0.217 - 0.271: 12 Chirality restraints: 7020 Sorted by residual: chirality pdb=" CB VAL B 470 " pdb=" CA VAL B 470 " pdb=" CG1 VAL B 470 " pdb=" CG2 VAL B 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL C 470 " pdb=" CA VAL C 470 " pdb=" CG1 VAL C 470 " pdb=" CG2 VAL C 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL G 470 " pdb=" CA VAL G 470 " pdb=" CG1 VAL G 470 " pdb=" CG2 VAL G 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 7017 not shown) Planarity restraints: 8208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 278 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO I 279 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 279 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 279 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 278 " 0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO F 279 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 279 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 279 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 278 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO E 279 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " -0.036 5.00e-02 4.00e+02 ... (remaining 8205 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1187 2.66 - 3.22: 41854 3.22 - 3.78: 77168 3.78 - 4.34: 112422 4.34 - 4.90: 184553 Nonbonded interactions: 417184 Sorted by model distance: nonbonded pdb=" OD1 ASP B 324 " pdb="ZN ZN B1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP G 324 " pdb="ZN ZN G1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP K 324 " pdb="ZN ZN K1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP H 324 " pdb="ZN ZN H1000 " model vdw 2.103 2.230 nonbonded pdb=" OD1 ASP A 324 " pdb="ZN ZN A1000 " model vdw 2.104 2.230 ... (remaining 417179 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 46.650 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.018 0.995 47364 Z= 0.631 Angle : 0.995 9.036 63912 Z= 0.566 Chirality : 0.058 0.271 7020 Planarity : 0.006 0.064 8208 Dihedral : 16.571 90.485 17376 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.87 % Favored : 94.92 % Rotamer: Outliers : 1.84 % Allowed : 9.79 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.08), residues: 5664 helix: -4.09 (0.05), residues: 1836 sheet: -1.33 (0.15), residues: 1056 loop : -2.28 (0.09), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 164 TYR 0.025 0.003 TYR J 167 PHE 0.031 0.003 PHE B 188 TRP 0.005 0.002 TRP L 47 HIS 0.008 0.002 HIS K 543 Details of bonding type rmsd covalent geometry : bond 0.00764 (47328) covalent geometry : angle 0.99240 (63888) SS BOND : bond 0.00360 ( 12) SS BOND : angle 3.48389 ( 24) hydrogen bonds : bond 0.24929 ( 1900) hydrogen bonds : angle 11.04456 ( 5304) metal coordination : bond 0.70866 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1025 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: A 19 SER cc_start: 0.8677 (t) cc_final: 0.8335 (t) REVERT: A 338 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 408 LYS cc_start: 0.7350 (ptmm) cc_final: 0.6173 (ptmt) REVERT: A 535 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 338 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 2 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6829 (t70) REVERT: C 135 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7845 (mtpt) REVERT: C 439 SER cc_start: 0.8457 (t) cc_final: 0.8063 (m) REVERT: D 2 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6378 (t70) REVERT: D 19 SER cc_start: 0.8639 (t) cc_final: 0.8423 (t) REVERT: D 102 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8305 (mtmm) REVERT: D 338 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6823 (mt-10) REVERT: D 386 GLU cc_start: 0.7504 (pm20) cc_final: 0.7263 (pm20) REVERT: D 427 ARG cc_start: 0.8625 (mpp80) cc_final: 0.8367 (mpp-170) REVERT: D 435 MET cc_start: 0.8391 (mmm) cc_final: 0.8085 (mmm) REVERT: E 2 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6876 (t70) REVERT: E 19 SER cc_start: 0.8725 (t) cc_final: 0.8396 (t) REVERT: E 386 GLU cc_start: 0.7397 (pm20) cc_final: 0.7116 (pm20) REVERT: E 425 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8628 (t) REVERT: F 60 GLU cc_start: 0.7955 (pt0) cc_final: 0.7744 (pt0) REVERT: F 172 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6494 (tptp) REVERT: F 481 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7944 (mmm-85) REVERT: G 60 GLU cc_start: 0.7979 (pt0) cc_final: 0.7574 (pt0) REVERT: G 98 ASN cc_start: 0.7574 (p0) cc_final: 0.7145 (p0) REVERT: G 338 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7454 (mt-10) REVERT: H 19 SER cc_start: 0.8728 (t) cc_final: 0.8372 (t) REVERT: H 102 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8226 (mtmt) REVERT: H 172 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6802 (tptp) REVERT: H 426 ASN cc_start: 0.8426 (t0) cc_final: 0.8161 (t0) REVERT: H 428 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (t) REVERT: H 521 MET cc_start: 0.8768 (mtt) cc_final: 0.8504 (mtt) REVERT: I 338 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6974 (mt-10) REVERT: I 428 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (t) REVERT: J 19 SER cc_start: 0.8721 (t) cc_final: 0.8355 (t) REVERT: J 338 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6537 (mt-10) REVERT: K 408 LYS cc_start: 0.7319 (ptmm) cc_final: 0.6386 (ptmm) REVERT: K 428 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7531 (t) REVERT: K 500 MET cc_start: 0.8583 (ttp) cc_final: 0.8312 (ttp) REVERT: L 19 SER cc_start: 0.8730 (t) cc_final: 0.8382 (t) REVERT: L 172 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6824 (tptp) REVERT: L 289 ASN cc_start: 0.7171 (t0) cc_final: 0.6953 (t0) REVERT: L 428 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7843 (t) REVERT: L 439 SER cc_start: 0.8660 (t) cc_final: 0.8312 (m) REVERT: L 535 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (p) outliers start: 96 outliers final: 14 residues processed: 1090 average time/residue: 0.3043 time to fit residues: 528.8788 Evaluate side-chains 637 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 612 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 412 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain G residue 412 GLU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 428 SER Chi-restraints excluded: chain H residue 542 VAL Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain J residue 535 SER Chi-restraints excluded: chain K residue 428 SER Chi-restraints excluded: chain L residue 428 SER Chi-restraints excluded: chain L residue 535 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 35 ASN A 36 ASN A 119 HIS ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 411 HIS A 414 ASN ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN A 518 ASN B 36 ASN B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 411 HIS B 426 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN B 518 ASN C 35 ASN C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 ASN C 518 ASN D 36 ASN D 72 ASN D 119 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 426 ASN D 498 ASN D 518 ASN E 35 ASN E 36 ASN E 119 HIS ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 498 ASN E 518 ASN F 10 GLN F 35 ASN F 119 HIS F 131 GLN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN F 414 ASN F 426 ASN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 ASN F 518 ASN G 35 ASN G 36 ASN G 119 HIS G 131 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 ASN G 426 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 ASN G 518 ASN G 543 HIS G 560 ASN H 10 GLN H 119 HIS ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 ASN ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 ASN H 518 ASN H 560 ASN I 36 ASN I 119 HIS I 131 GLN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 363 ASN I 411 HIS I 414 ASN ** I 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 498 ASN I 518 ASN J 36 ASN J 72 ASN J 119 HIS ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 ASN J 411 HIS ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 498 ASN J 518 ASN J 560 ASN K 22 ASN K 35 ASN K 119 HIS ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN K 363 ASN K 426 ASN ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN K 498 ASN K 518 ASN L 22 ASN L 35 ASN L 36 ASN L 119 HIS ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 ASN L 437 HIS L 466 ASN L 498 ASN L 518 ASN ** L 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 HIS L 560 ASN Total number of N/Q/H flips: 98 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119718 restraints weight = 54109.590| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.17 r_work: 0.3134 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47364 Z= 0.154 Angle : 0.621 7.044 63912 Z= 0.341 Chirality : 0.046 0.181 7020 Planarity : 0.005 0.049 8208 Dihedral : 6.299 59.571 6165 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.05 % Allowed : 12.67 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.09), residues: 5664 helix: -1.90 (0.09), residues: 1956 sheet: -1.33 (0.15), residues: 1176 loop : -1.81 (0.10), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 6 TYR 0.018 0.001 TYR K 282 PHE 0.019 0.001 PHE K 330 TRP 0.005 0.001 TRP A 118 HIS 0.005 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00343 (47328) covalent geometry : angle 0.61934 (63888) SS BOND : bond 0.00500 ( 12) SS BOND : angle 2.60409 ( 24) hydrogen bonds : bond 0.04359 ( 1900) hydrogen bonds : angle 6.00325 ( 5304) metal coordination : bond 0.00984 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 711 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7634 (t70) REVERT: A 338 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 395 LYS cc_start: 0.8751 (tptp) cc_final: 0.8492 (tptp) REVERT: A 425 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8945 (t) REVERT: B 17 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7367 (tt0) REVERT: B 19 SER cc_start: 0.8962 (t) cc_final: 0.8694 (t) REVERT: B 191 LEU cc_start: 0.8611 (tt) cc_final: 0.8373 (tt) REVERT: B 390 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7706 (mtt180) REVERT: B 395 LYS cc_start: 0.8613 (tptp) cc_final: 0.8374 (tptp) REVERT: C 2 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7699 (t70) REVERT: C 19 SER cc_start: 0.9139 (m) cc_final: 0.8748 (p) REVERT: C 72 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7029 (p0) REVERT: C 135 LYS cc_start: 0.8605 (mtmt) cc_final: 0.7940 (mtpt) REVERT: C 172 LYS cc_start: 0.6830 (mmtm) cc_final: 0.6563 (tptp) REVERT: C 439 SER cc_start: 0.8827 (t) cc_final: 0.8524 (m) REVERT: C 457 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7844 (mt-10) REVERT: D 172 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7093 (tptp) REVERT: D 379 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 386 GLU cc_start: 0.7968 (pm20) cc_final: 0.7594 (pm20) REVERT: D 514 MET cc_start: 0.8543 (mtt) cc_final: 0.8264 (mtt) REVERT: E 2 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7476 (t70) REVERT: E 19 SER cc_start: 0.9038 (t) cc_final: 0.8749 (t) REVERT: E 135 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: E 172 LYS cc_start: 0.7425 (mmtm) cc_final: 0.6468 (tptp) REVERT: E 386 GLU cc_start: 0.7935 (pm20) cc_final: 0.7561 (pm20) REVERT: E 439 SER cc_start: 0.8764 (t) cc_final: 0.8410 (m) REVERT: F 140 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8325 (tp) REVERT: F 172 LYS cc_start: 0.6694 (mmtm) cc_final: 0.6408 (tptt) REVERT: F 286 LYS cc_start: 0.8178 (tppt) cc_final: 0.7814 (tptp) REVERT: F 291 LYS cc_start: 0.8210 (mptt) cc_final: 0.7969 (mmtt) REVERT: G 14 LYS cc_start: 0.8275 (mptt) cc_final: 0.7998 (mttm) REVERT: G 425 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9036 (t) REVERT: G 514 MET cc_start: 0.8700 (mtm) cc_final: 0.8263 (mtt) REVERT: H 19 SER cc_start: 0.8945 (t) cc_final: 0.8654 (t) REVERT: H 102 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8627 (mtmt) REVERT: H 172 LYS cc_start: 0.7316 (mmtm) cc_final: 0.6982 (tptt) REVERT: H 291 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7904 (mmtt) REVERT: H 457 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7551 (mt-10) REVERT: I 172 LYS cc_start: 0.7477 (mmtm) cc_final: 0.6940 (tptp) REVERT: I 428 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8674 (t) REVERT: J 19 SER cc_start: 0.9007 (t) cc_final: 0.8771 (t) REVERT: J 280 LEU cc_start: 0.9122 (tp) cc_final: 0.8891 (tp) REVERT: J 390 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7553 (mtt180) REVERT: K 6 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7506 (mmt180) REVERT: K 139 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8170 (ttmm) REVERT: K 500 MET cc_start: 0.9008 (ttp) cc_final: 0.8701 (ttp) REVERT: L 172 LYS cc_start: 0.7100 (mmtm) cc_final: 0.6760 (tptp) REVERT: L 190 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7478 (mm-40) REVERT: L 289 ASN cc_start: 0.7925 (t0) cc_final: 0.7679 (t0) REVERT: L 428 SER cc_start: 0.8652 (m) cc_final: 0.8236 (m) REVERT: L 439 SER cc_start: 0.8984 (t) cc_final: 0.8678 (m) outliers start: 107 outliers final: 33 residues processed: 784 average time/residue: 0.2890 time to fit residues: 368.7234 Evaluate side-chains 598 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 556 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 135 LYS Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain J residue 535 SER Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 319 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 414 optimal weight: 0.3980 chunk 556 optimal weight: 4.9990 chunk 550 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 509 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 486 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN D 432 ASN ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN G 560 ASN H 36 ASN ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN I 437 HIS J 35 ASN J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 190 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 426 ASN ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.110814 restraints weight = 54497.911| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.16 r_work: 0.2975 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 47364 Z= 0.250 Angle : 0.667 7.385 63912 Z= 0.358 Chirality : 0.049 0.193 7020 Planarity : 0.005 0.083 8208 Dihedral : 5.784 58.730 6147 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 15.00 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.10), residues: 5664 helix: -0.76 (0.10), residues: 1980 sheet: -1.36 (0.15), residues: 1140 loop : -1.56 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 390 TYR 0.016 0.002 TYR A 421 PHE 0.016 0.002 PHE B 330 TRP 0.008 0.002 TRP K 47 HIS 0.005 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00584 (47328) covalent geometry : angle 0.66563 (63888) SS BOND : bond 0.00274 ( 12) SS BOND : angle 2.30487 ( 24) hydrogen bonds : bond 0.04430 ( 1900) hydrogen bonds : angle 5.72070 ( 5304) metal coordination : bond 0.00676 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 613 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7930 (tt0) REVERT: A 136 LYS cc_start: 0.8233 (ptmm) cc_final: 0.7987 (tppt) REVERT: A 425 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9026 (t) REVERT: B 19 SER cc_start: 0.8983 (t) cc_final: 0.8710 (t) REVERT: B 191 LEU cc_start: 0.8501 (tt) cc_final: 0.8279 (tt) REVERT: B 395 LYS cc_start: 0.8615 (tptp) cc_final: 0.8385 (tptp) REVERT: C 139 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8059 (ttmt) REVERT: C 291 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8095 (mmtt) REVERT: C 435 MET cc_start: 0.8944 (mmm) cc_final: 0.8095 (mmm) REVERT: C 439 SER cc_start: 0.9021 (t) cc_final: 0.8647 (m) REVERT: C 457 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8114 (mt-10) REVERT: D 172 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7246 (tptp) REVERT: D 289 ASN cc_start: 0.7916 (t0) cc_final: 0.7652 (t0) REVERT: D 386 GLU cc_start: 0.8069 (pm20) cc_final: 0.7204 (pm20) REVERT: D 514 MET cc_start: 0.8539 (mtt) cc_final: 0.8276 (mtt) REVERT: E 19 SER cc_start: 0.9107 (t) cc_final: 0.8832 (t) REVERT: E 135 LYS cc_start: 0.8638 (mttp) cc_final: 0.8424 (mttp) REVERT: E 172 LYS cc_start: 0.7786 (mmtm) cc_final: 0.6874 (tptp) REVERT: E 428 SER cc_start: 0.8890 (t) cc_final: 0.8119 (t) REVERT: E 457 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7904 (mt-10) REVERT: E 481 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8144 (mmm160) REVERT: F 11 ASP cc_start: 0.8743 (t0) cc_final: 0.8487 (t0) REVERT: F 32 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7547 (ttm-80) REVERT: F 139 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8076 (ttmt) REVERT: F 172 LYS cc_start: 0.7145 (mmtm) cc_final: 0.6761 (tptp) REVERT: F 192 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7824 (t0) REVERT: F 286 LYS cc_start: 0.8483 (tppt) cc_final: 0.8110 (tptp) REVERT: F 291 LYS cc_start: 0.8228 (mptt) cc_final: 0.8012 (mmtt) REVERT: F 425 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9088 (t) REVERT: F 481 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8348 (mmm160) REVERT: G 14 LYS cc_start: 0.8340 (mptt) cc_final: 0.7890 (mttm) REVERT: G 26 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8045 (t) REVERT: G 53 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7565 (mt-10) REVERT: G 172 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6803 (tptp) REVERT: H 11 ASP cc_start: 0.8735 (t0) cc_final: 0.8205 (t0) REVERT: H 19 SER cc_start: 0.9020 (t) cc_final: 0.8730 (t) REVERT: H 32 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7389 (ttt-90) REVERT: H 131 GLN cc_start: 0.8662 (tt0) cc_final: 0.8233 (tt0) REVERT: H 136 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8279 (tppt) REVERT: H 172 LYS cc_start: 0.7435 (mmtm) cc_final: 0.7002 (tptt) REVERT: H 291 LYS cc_start: 0.8255 (mmtm) cc_final: 0.8008 (mmtt) REVERT: H 435 MET cc_start: 0.8835 (mmm) cc_final: 0.8112 (mmm) REVERT: H 457 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7752 (mt-10) REVERT: H 481 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8115 (mtp85) REVERT: H 560 ASN cc_start: 0.8188 (m110) cc_final: 0.7859 (m-40) REVERT: I 303 MET cc_start: 0.9107 (ptm) cc_final: 0.8898 (ptt) REVERT: J 19 SER cc_start: 0.9072 (t) cc_final: 0.8831 (t) REVERT: J 390 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7697 (mtt180) REVERT: J 435 MET cc_start: 0.9010 (mmm) cc_final: 0.8803 (mmm) REVERT: K 139 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8063 (ttmm) REVERT: K 172 LYS cc_start: 0.7691 (tppt) cc_final: 0.6991 (tptt) REVERT: K 293 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: K 390 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7683 (mtt180) REVERT: K 421 TYR cc_start: 0.9177 (t80) cc_final: 0.8950 (t80) REVERT: K 457 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8009 (mt-10) REVERT: L 172 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7225 (tptp) REVERT: L 428 SER cc_start: 0.8880 (m) cc_final: 0.8592 (m) REVERT: L 439 SER cc_start: 0.9126 (t) cc_final: 0.8789 (m) outliers start: 118 outliers final: 64 residues processed: 703 average time/residue: 0.2678 time to fit residues: 308.0922 Evaluate side-chains 605 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 536 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 567 VAL Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 293 GLU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 525 ASP Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 377 ASP Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain K residue 567 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 383 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 370 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 465 optimal weight: 0.9980 chunk 406 optimal weight: 0.8980 chunk 290 optimal weight: 0.7980 chunk 454 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 72 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 HIS J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 432 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS K 22 ASN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 396 ASN L 432 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.107560 restraints weight = 55810.206| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.38 r_work: 0.3058 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 47364 Z= 0.141 Angle : 0.582 15.656 63912 Z= 0.313 Chirality : 0.045 0.167 7020 Planarity : 0.004 0.042 8208 Dihedral : 5.436 58.438 6139 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.36 % Allowed : 16.38 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.10), residues: 5664 helix: -0.01 (0.11), residues: 1992 sheet: -1.21 (0.15), residues: 1128 loop : -1.38 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 390 TYR 0.015 0.001 TYR F 559 PHE 0.021 0.001 PHE L 73 TRP 0.004 0.001 TRP C 118 HIS 0.004 0.001 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.00327 (47328) covalent geometry : angle 0.57764 (63888) SS BOND : bond 0.00352 ( 12) SS BOND : angle 3.52864 ( 24) hydrogen bonds : bond 0.03734 ( 1900) hydrogen bonds : angle 5.35060 ( 5304) metal coordination : bond 0.00214 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 613 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 425 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8960 (t) REVERT: B 19 SER cc_start: 0.8926 (t) cc_final: 0.8713 (t) REVERT: B 136 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8497 (ptmm) REVERT: B 395 LYS cc_start: 0.8618 (tptp) cc_final: 0.8380 (tptp) REVERT: B 435 MET cc_start: 0.8957 (mmm) cc_final: 0.8688 (mmm) REVERT: C 123 ASP cc_start: 0.8482 (m-30) cc_final: 0.8229 (m-30) REVERT: C 135 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8282 (mtpt) REVERT: C 139 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8256 (ttmt) REVERT: C 172 LYS cc_start: 0.7186 (mmtm) cc_final: 0.6790 (tptp) REVERT: C 291 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8107 (mmtt) REVERT: C 428 SER cc_start: 0.8886 (t) cc_final: 0.8361 (t) REVERT: C 435 MET cc_start: 0.8883 (mmm) cc_final: 0.8115 (mmm) REVERT: C 439 SER cc_start: 0.9019 (t) cc_final: 0.8706 (m) REVERT: C 457 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8056 (mt-10) REVERT: D 172 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7243 (tptp) REVERT: D 514 MET cc_start: 0.8571 (mtt) cc_final: 0.8290 (mtt) REVERT: E 135 LYS cc_start: 0.8682 (mttp) cc_final: 0.8441 (mttp) REVERT: E 172 LYS cc_start: 0.7617 (mmtm) cc_final: 0.6956 (tptp) REVERT: E 457 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7913 (mt-10) REVERT: F 17 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (pp30) REVERT: F 135 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7841 (mtpt) REVERT: F 139 LYS cc_start: 0.8320 (mtpp) cc_final: 0.8097 (ttmt) REVERT: F 172 LYS cc_start: 0.6944 (mmtm) cc_final: 0.6672 (tptp) REVERT: F 192 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7903 (t0) REVERT: F 286 LYS cc_start: 0.8456 (tppt) cc_final: 0.8069 (tptp) REVERT: F 481 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8447 (mmm160) REVERT: G 14 LYS cc_start: 0.8342 (mptt) cc_final: 0.8127 (mttp) REVERT: G 53 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7602 (mt-10) REVERT: G 133 LEU cc_start: 0.8777 (tt) cc_final: 0.8313 (mp) REVERT: G 172 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6670 (tptp) REVERT: G 457 GLU cc_start: 0.8368 (tp30) cc_final: 0.8132 (mm-30) REVERT: H 11 ASP cc_start: 0.8790 (t0) cc_final: 0.8482 (t0) REVERT: H 139 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8066 (ttmt) REVERT: H 172 LYS cc_start: 0.7382 (mmtm) cc_final: 0.6974 (tptt) REVERT: H 191 LEU cc_start: 0.8576 (tt) cc_final: 0.8347 (tt) REVERT: H 291 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8110 (mmtt) REVERT: H 435 MET cc_start: 0.8795 (mmm) cc_final: 0.8136 (mmm) REVERT: H 457 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7820 (mt-10) REVERT: H 481 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8211 (mtp85) REVERT: I 338 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8191 (mt-10) REVERT: J 390 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7837 (mtt180) REVERT: K 139 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7991 (ttmm) REVERT: K 172 LYS cc_start: 0.7475 (tppt) cc_final: 0.6868 (tptt) REVERT: K 457 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8039 (mt-10) REVERT: L 172 LYS cc_start: 0.7447 (mmtm) cc_final: 0.7085 (tptp) REVERT: L 439 SER cc_start: 0.9093 (t) cc_final: 0.8781 (m) outliers start: 123 outliers final: 64 residues processed: 705 average time/residue: 0.2489 time to fit residues: 287.4730 Evaluate side-chains 616 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 547 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 293 GLU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 525 ASP Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 383 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 12 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 526 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 534 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN E 368 ASN ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN H 119 HIS ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 HIS J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 GLN ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 560 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.113731 restraints weight = 54471.830| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.16 r_work: 0.3049 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 47364 Z= 0.162 Angle : 0.589 13.909 63912 Z= 0.316 Chirality : 0.046 0.174 7020 Planarity : 0.004 0.057 8208 Dihedral : 5.312 57.577 6137 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.90 % Allowed : 16.51 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.10), residues: 5664 helix: 0.36 (0.11), residues: 2004 sheet: -1.24 (0.15), residues: 1080 loop : -1.34 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 390 TYR 0.018 0.001 TYR A 421 PHE 0.014 0.001 PHE D 73 TRP 0.005 0.001 TRP A 118 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00383 (47328) covalent geometry : angle 0.58410 (63888) SS BOND : bond 0.00486 ( 12) SS BOND : angle 4.08526 ( 24) hydrogen bonds : bond 0.03713 ( 1900) hydrogen bonds : angle 5.24595 ( 5304) metal coordination : bond 0.00215 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 567 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9119 (pp) REVERT: A 425 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8993 (t) REVERT: B 14 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7989 (mttp) REVERT: B 19 SER cc_start: 0.8861 (t) cc_final: 0.8647 (t) REVERT: B 395 LYS cc_start: 0.8600 (tptp) cc_final: 0.8354 (tptp) REVERT: C 123 ASP cc_start: 0.8488 (m-30) cc_final: 0.8186 (m-30) REVERT: C 131 GLN cc_start: 0.8654 (tt0) cc_final: 0.8297 (tt0) REVERT: C 139 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8243 (ttmt) REVERT: C 172 LYS cc_start: 0.7127 (mmtm) cc_final: 0.6756 (tptp) REVERT: C 291 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8124 (mmtt) REVERT: C 435 MET cc_start: 0.8876 (mmm) cc_final: 0.8125 (mmm) REVERT: C 439 SER cc_start: 0.8998 (t) cc_final: 0.8662 (m) REVERT: C 457 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7959 (mt-10) REVERT: D 136 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8148 (ptmt) REVERT: D 481 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8210 (mmm-85) REVERT: D 514 MET cc_start: 0.8509 (mtt) cc_final: 0.8256 (mtt) REVERT: E 172 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6995 (tptp) REVERT: E 439 SER cc_start: 0.8820 (t) cc_final: 0.8311 (m) REVERT: E 457 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7802 (mt-10) REVERT: F 135 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: F 139 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8123 (ttmt) REVERT: F 172 LYS cc_start: 0.6968 (mmtm) cc_final: 0.6695 (tptp) REVERT: F 192 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7747 (t0) REVERT: F 286 LYS cc_start: 0.8419 (tppt) cc_final: 0.8058 (tptp) REVERT: F 425 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9014 (t) REVERT: F 457 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7970 (mt-10) REVERT: F 481 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8352 (mmm160) REVERT: G 14 LYS cc_start: 0.8344 (mptt) cc_final: 0.8087 (mttp) REVERT: G 133 LEU cc_start: 0.8823 (tt) cc_final: 0.8434 (mp) REVERT: G 172 LYS cc_start: 0.7148 (mmtm) cc_final: 0.6869 (tptp) REVERT: G 457 GLU cc_start: 0.8248 (tp30) cc_final: 0.8037 (mm-30) REVERT: H 11 ASP cc_start: 0.8822 (t0) cc_final: 0.8487 (t0) REVERT: H 24 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8863 (mt) REVERT: H 136 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8343 (tppt) REVERT: H 139 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8183 (ttmt) REVERT: H 172 LYS cc_start: 0.7404 (mmtm) cc_final: 0.6942 (tptt) REVERT: H 291 LYS cc_start: 0.8284 (mmtm) cc_final: 0.8062 (mmtt) REVERT: H 435 MET cc_start: 0.8791 (mmm) cc_final: 0.8124 (mmm) REVERT: H 457 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7755 (mt-10) REVERT: H 481 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8140 (mtp85) REVERT: H 525 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: I 73 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5140 (m-80) REVERT: I 338 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8070 (mt-10) REVERT: J 390 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7687 (mtt180) REVERT: K 139 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7972 (ttmm) REVERT: K 172 LYS cc_start: 0.7511 (tppt) cc_final: 0.6894 (tptt) REVERT: K 457 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7940 (mt-10) REVERT: L 172 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7115 (tptp) REVERT: L 190 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7561 (mm-40) REVERT: L 412 GLU cc_start: 0.5042 (OUTLIER) cc_final: 0.4771 (pt0) REVERT: L 439 SER cc_start: 0.9092 (t) cc_final: 0.8781 (m) outliers start: 151 outliers final: 88 residues processed: 687 average time/residue: 0.2352 time to fit residues: 264.6873 Evaluate side-chains 627 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 529 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 525 ASP Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 525 ASP Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 412 GLU Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 227 optimal weight: 1.9990 chunk 508 optimal weight: 0.9990 chunk 504 optimal weight: 4.9990 chunk 539 optimal weight: 4.9990 chunk 351 optimal weight: 0.9990 chunk 334 optimal weight: 4.9990 chunk 392 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN H 28 ASN ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 HIS J 28 ASN J 72 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110850 restraints weight = 55336.104| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.08 r_work: 0.3056 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 47364 Z= 0.179 Angle : 0.602 12.269 63912 Z= 0.323 Chirality : 0.047 0.180 7020 Planarity : 0.004 0.061 8208 Dihedral : 5.324 54.494 6137 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.03 % Allowed : 16.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.10), residues: 5664 helix: 0.49 (0.11), residues: 2016 sheet: -1.44 (0.15), residues: 1116 loop : -1.20 (0.11), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 390 TYR 0.019 0.001 TYR A 421 PHE 0.015 0.001 PHE D 73 TRP 0.006 0.001 TRP A 118 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00425 (47328) covalent geometry : angle 0.59721 (63888) SS BOND : bond 0.00305 ( 12) SS BOND : angle 4.07087 ( 24) hydrogen bonds : bond 0.03716 ( 1900) hydrogen bonds : angle 5.23568 ( 5304) metal coordination : bond 0.00201 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 564 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8039 (mttm) REVERT: A 87 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 136 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8186 (ptpt) REVERT: A 425 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.8993 (t) REVERT: B 14 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: B 19 SER cc_start: 0.8812 (t) cc_final: 0.8608 (t) REVERT: B 395 LYS cc_start: 0.8576 (tptp) cc_final: 0.8349 (tptp) REVERT: C 17 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8088 (pp30) REVERT: C 123 ASP cc_start: 0.8421 (m-30) cc_final: 0.8066 (m-30) REVERT: C 139 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8311 (ttmt) REVERT: C 172 LYS cc_start: 0.7139 (mmtm) cc_final: 0.6794 (tptp) REVERT: C 291 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8150 (mmtt) REVERT: C 435 MET cc_start: 0.8874 (mmm) cc_final: 0.8152 (mmm) REVERT: C 439 SER cc_start: 0.8987 (t) cc_final: 0.8621 (m) REVERT: C 457 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8001 (mt-10) REVERT: D 14 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8102 (mttm) REVERT: D 481 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8161 (mmm-85) REVERT: D 514 MET cc_start: 0.8514 (mtt) cc_final: 0.8258 (mtt) REVERT: E 14 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: E 172 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7099 (tptp) REVERT: E 439 SER cc_start: 0.8888 (t) cc_final: 0.8392 (m) REVERT: F 14 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8203 (mttt) REVERT: F 172 LYS cc_start: 0.6951 (mmtm) cc_final: 0.6748 (tptp) REVERT: F 192 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7756 (t0) REVERT: F 286 LYS cc_start: 0.8438 (tppt) cc_final: 0.8122 (tptp) REVERT: F 425 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9032 (t) REVERT: F 457 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8010 (mt-10) REVERT: F 481 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8237 (mmm160) REVERT: G 14 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (mttp) REVERT: G 26 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7637 (t) REVERT: G 133 LEU cc_start: 0.8835 (tt) cc_final: 0.8497 (mp) REVERT: G 172 LYS cc_start: 0.7159 (mmtm) cc_final: 0.6927 (tptp) REVERT: G 457 GLU cc_start: 0.8174 (tp30) cc_final: 0.7961 (mm-30) REVERT: H 11 ASP cc_start: 0.8759 (t0) cc_final: 0.8475 (t0) REVERT: H 14 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: H 24 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8947 (mp) REVERT: H 136 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8402 (tppt) REVERT: H 139 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8144 (ttmt) REVERT: H 192 ASN cc_start: 0.7936 (t0) cc_final: 0.7556 (t0) REVERT: H 390 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7828 (mmm-85) REVERT: H 435 MET cc_start: 0.8796 (mmm) cc_final: 0.8153 (mmm) REVERT: H 439 SER cc_start: 0.9114 (t) cc_final: 0.8903 (p) REVERT: H 457 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7790 (mt-10) REVERT: H 481 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8106 (mtp85) REVERT: H 525 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: I 14 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8167 (mttt) REVERT: I 73 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: I 172 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7373 (tttp) REVERT: I 338 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7925 (mt-10) REVERT: J 14 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8001 (mttm) REVERT: J 390 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7635 (mtt180) REVERT: K 139 LYS cc_start: 0.8280 (mtpp) cc_final: 0.7993 (ttmm) REVERT: K 172 LYS cc_start: 0.7511 (tppt) cc_final: 0.6963 (tptt) REVERT: K 457 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7898 (mt-10) REVERT: L 14 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8157 (mttp) REVERT: L 172 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7145 (tptp) REVERT: L 439 SER cc_start: 0.9099 (t) cc_final: 0.8783 (m) outliers start: 158 outliers final: 103 residues processed: 694 average time/residue: 0.2144 time to fit residues: 244.9304 Evaluate side-chains 660 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 538 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 415 LEU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 525 ASP Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 525 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 373 optimal weight: 0.9990 chunk 511 optimal weight: 1.9990 chunk 527 optimal weight: 0.9980 chunk 402 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 508 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 470 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 486 optimal weight: 5.9990 chunk 447 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN G 543 HIS ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 289 ASN ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.113807 restraints weight = 54656.558| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.12 r_work: 0.3042 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 47364 Z= 0.144 Angle : 0.579 12.066 63912 Z= 0.310 Chirality : 0.046 0.178 7020 Planarity : 0.004 0.063 8208 Dihedral : 5.222 54.292 6135 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.96 % Allowed : 16.86 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.11), residues: 5664 helix: 0.71 (0.11), residues: 2016 sheet: -1.21 (0.15), residues: 1104 loop : -1.25 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 390 TYR 0.014 0.001 TYR A 421 PHE 0.014 0.001 PHE D 73 TRP 0.005 0.001 TRP A 118 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00340 (47328) covalent geometry : angle 0.57319 (63888) SS BOND : bond 0.00449 ( 12) SS BOND : angle 4.33031 ( 24) hydrogen bonds : bond 0.03574 ( 1900) hydrogen bonds : angle 5.13910 ( 5304) metal coordination : bond 0.00200 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 569 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8065 (mttm) REVERT: A 87 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9141 (pp) REVERT: A 415 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 425 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.8980 (t) REVERT: B 395 LYS cc_start: 0.8619 (tptp) cc_final: 0.8360 (tptp) REVERT: C 14 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8144 (mttt) REVERT: C 71 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8187 (tttm) REVERT: C 139 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8314 (ttmt) REVERT: C 172 LYS cc_start: 0.7067 (mmtm) cc_final: 0.6730 (tptp) REVERT: C 291 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8117 (mmtt) REVERT: C 435 MET cc_start: 0.8843 (mmm) cc_final: 0.8120 (mmm) REVERT: C 439 SER cc_start: 0.8999 (t) cc_final: 0.8682 (m) REVERT: C 457 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7995 (mt-10) REVERT: D 14 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8089 (mttm) REVERT: D 297 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7848 (t0) REVERT: D 514 MET cc_start: 0.8501 (mtt) cc_final: 0.8233 (mtt) REVERT: E 14 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: E 172 LYS cc_start: 0.7582 (mmtm) cc_final: 0.6980 (tptp) REVERT: E 439 SER cc_start: 0.8796 (t) cc_final: 0.8325 (m) REVERT: F 14 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8169 (mttt) REVERT: F 192 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7681 (t0) REVERT: F 286 LYS cc_start: 0.8441 (tppt) cc_final: 0.8148 (tptp) REVERT: F 425 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9001 (t) REVERT: F 457 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8059 (mt-10) REVERT: F 481 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8234 (mmm160) REVERT: G 14 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7868 (mttm) REVERT: G 22 ASN cc_start: 0.8668 (p0) cc_final: 0.8438 (p0) REVERT: G 26 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7641 (t) REVERT: G 133 LEU cc_start: 0.8861 (tt) cc_final: 0.8591 (mp) REVERT: G 140 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8556 (tt) REVERT: G 172 LYS cc_start: 0.7124 (mmtm) cc_final: 0.6880 (tptp) REVERT: G 390 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7607 (mtt180) REVERT: G 457 GLU cc_start: 0.8214 (tp30) cc_final: 0.8006 (mm-30) REVERT: H 11 ASP cc_start: 0.8762 (t0) cc_final: 0.8448 (t0) REVERT: H 14 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (mttp) REVERT: H 24 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8841 (mt) REVERT: H 131 GLN cc_start: 0.8613 (tt0) cc_final: 0.8397 (tt0) REVERT: H 139 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8032 (ttmt) REVERT: H 172 LYS cc_start: 0.7388 (mmtm) cc_final: 0.6892 (tptt) REVERT: H 192 ASN cc_start: 0.7904 (t0) cc_final: 0.7677 (t0) REVERT: H 390 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7803 (mmm-85) REVERT: H 435 MET cc_start: 0.8752 (mmm) cc_final: 0.8095 (mmm) REVERT: H 457 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7784 (mt-10) REVERT: H 481 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8090 (mtp85) REVERT: I 14 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (mttt) REVERT: I 73 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.5062 (m-80) REVERT: I 172 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7296 (tttp) REVERT: I 338 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8012 (mt-10) REVERT: J 390 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7651 (mtt180) REVERT: K 139 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7942 (ttmt) REVERT: K 172 LYS cc_start: 0.7475 (tppt) cc_final: 0.6919 (tptt) REVERT: K 457 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7913 (mt-10) REVERT: L 172 LYS cc_start: 0.7443 (mmtm) cc_final: 0.7112 (tptp) REVERT: L 439 SER cc_start: 0.9094 (t) cc_final: 0.8787 (m) outliers start: 154 outliers final: 104 residues processed: 693 average time/residue: 0.1910 time to fit residues: 218.2490 Evaluate side-chains 663 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 541 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 58 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 415 LEU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 26 CYS Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 268 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 473 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 292 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 478 optimal weight: 0.9980 chunk 397 optimal weight: 0.9990 chunk 439 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 HIS ** L 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115000 restraints weight = 54633.619| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.12 r_work: 0.3086 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 47364 Z= 0.130 Angle : 0.569 10.899 63912 Z= 0.304 Chirality : 0.045 0.171 7020 Planarity : 0.003 0.037 8208 Dihedral : 5.146 53.148 6135 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.78 % Allowed : 17.22 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.11), residues: 5664 helix: 0.91 (0.11), residues: 2016 sheet: -1.26 (0.16), residues: 972 loop : -1.20 (0.10), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 390 TYR 0.017 0.001 TYR A 421 PHE 0.014 0.001 PHE D 73 TRP 0.004 0.001 TRP A 118 HIS 0.003 0.001 HIS J 86 Details of bonding type rmsd covalent geometry : bond 0.00305 (47328) covalent geometry : angle 0.56335 (63888) SS BOND : bond 0.00351 ( 12) SS BOND : angle 4.06186 ( 24) hydrogen bonds : bond 0.03474 ( 1900) hydrogen bonds : angle 5.06127 ( 5304) metal coordination : bond 0.00114 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 569 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7993 (mttm) REVERT: A 87 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9040 (pp) REVERT: A 425 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8938 (t) REVERT: A 457 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7775 (mt-10) REVERT: B 14 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7940 (mttp) REVERT: B 390 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7628 (mtm-85) REVERT: B 395 LYS cc_start: 0.8627 (tptp) cc_final: 0.8367 (tptp) REVERT: C 13 LEU cc_start: 0.9100 (mt) cc_final: 0.8786 (mt) REVERT: C 14 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (mttt) REVERT: C 19 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8762 (p) REVERT: C 71 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8237 (tttm) REVERT: C 139 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8329 (ttmt) REVERT: C 172 LYS cc_start: 0.7027 (mmtm) cc_final: 0.6722 (tptp) REVERT: C 291 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8135 (mmtt) REVERT: C 435 MET cc_start: 0.8841 (mmm) cc_final: 0.8158 (mmm) REVERT: C 439 SER cc_start: 0.8986 (t) cc_final: 0.8671 (m) REVERT: C 457 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7922 (mt-10) REVERT: D 14 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8111 (mttm) REVERT: D 297 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7759 (t0) REVERT: D 514 MET cc_start: 0.8513 (mtt) cc_final: 0.8239 (mtt) REVERT: E 14 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: E 89 SER cc_start: 0.8540 (p) cc_final: 0.7987 (t) REVERT: E 172 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7086 (tptp) REVERT: E 439 SER cc_start: 0.8782 (t) cc_final: 0.8306 (m) REVERT: E 481 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8462 (mmm-85) REVERT: F 14 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8097 (mttt) REVERT: F 71 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8545 (tttm) REVERT: F 89 SER cc_start: 0.8489 (p) cc_final: 0.7955 (t) REVERT: F 192 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7661 (t0) REVERT: F 286 LYS cc_start: 0.8421 (tppt) cc_final: 0.8165 (tptp) REVERT: F 425 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8992 (t) REVERT: F 457 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7984 (mt-10) REVERT: G 14 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7853 (mttm) REVERT: G 22 ASN cc_start: 0.8586 (p0) cc_final: 0.8383 (p0) REVERT: G 26 CYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7575 (t) REVERT: G 140 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8581 (tt) REVERT: G 172 LYS cc_start: 0.7114 (mmtm) cc_final: 0.6884 (tptp) REVERT: G 390 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7618 (mtt180) REVERT: H 11 ASP cc_start: 0.8770 (t0) cc_final: 0.8470 (t0) REVERT: H 14 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7940 (mttp) REVERT: H 24 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8849 (mt) REVERT: H 131 GLN cc_start: 0.8614 (tt0) cc_final: 0.8405 (tt0) REVERT: H 139 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8036 (ttmt) REVERT: H 172 LYS cc_start: 0.7402 (mmtm) cc_final: 0.6893 (tptt) REVERT: H 191 LEU cc_start: 0.8643 (mt) cc_final: 0.8384 (mt) REVERT: H 192 ASN cc_start: 0.7835 (t0) cc_final: 0.7486 (t0) REVERT: H 435 MET cc_start: 0.8714 (mmm) cc_final: 0.8093 (mmm) REVERT: H 457 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7742 (mt-10) REVERT: H 481 ARG cc_start: 0.8455 (mmm160) cc_final: 0.8105 (mtp85) REVERT: I 14 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8157 (mttt) REVERT: I 89 SER cc_start: 0.8507 (p) cc_final: 0.7853 (t) REVERT: I 172 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7267 (tttp) REVERT: I 338 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7994 (mt-10) REVERT: I 439 SER cc_start: 0.9038 (t) cc_final: 0.8553 (p) REVERT: J 14 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7927 (mttm) REVERT: J 172 LYS cc_start: 0.7081 (tppt) cc_final: 0.6192 (tptp) REVERT: J 390 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7620 (mtt180) REVERT: K 139 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7963 (ttmt) REVERT: K 142 GLU cc_start: 0.6831 (tp30) cc_final: 0.6537 (tp30) REVERT: K 172 LYS cc_start: 0.7388 (tppt) cc_final: 0.6782 (tptt) REVERT: K 457 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7864 (mt-10) REVERT: L 172 LYS cc_start: 0.7420 (mmtm) cc_final: 0.7114 (tptp) REVERT: L 439 SER cc_start: 0.9073 (t) cc_final: 0.8787 (m) outliers start: 145 outliers final: 99 residues processed: 687 average time/residue: 0.1743 time to fit residues: 197.3239 Evaluate side-chains 663 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 544 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 415 LEU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 428 SER Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 26 CYS Chi-restraints excluded: chain J residue 46 THR Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 525 ASP Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 36 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 358 optimal weight: 0.7980 chunk 285 optimal weight: 0.0010 chunk 260 optimal weight: 2.9990 chunk 420 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 ASN ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 HIS ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN G 325 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.117123 restraints weight = 54270.844| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.19 r_work: 0.3083 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 47364 Z= 0.115 Angle : 0.558 11.480 63912 Z= 0.298 Chirality : 0.045 0.177 7020 Planarity : 0.003 0.034 8208 Dihedral : 5.055 51.945 6135 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.63 % Allowed : 17.59 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.11), residues: 5664 helix: 1.11 (0.12), residues: 2016 sheet: -1.20 (0.16), residues: 1020 loop : -1.17 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 390 TYR 0.012 0.001 TYR H 559 PHE 0.014 0.001 PHE D 73 TRP 0.007 0.001 TRP I 47 HIS 0.004 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00267 (47328) covalent geometry : angle 0.55225 (63888) SS BOND : bond 0.00342 ( 12) SS BOND : angle 4.15758 ( 24) hydrogen bonds : bond 0.03388 ( 1900) hydrogen bonds : angle 4.99029 ( 5304) metal coordination : bond 0.00082 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 568 time to evaluate : 0.957 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 14 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8023 (mttm) REVERT: A 87 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9132 (pp) REVERT: A 425 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8916 (t) REVERT: A 457 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7825 (mt-10) REVERT: B 14 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7937 (mttt) REVERT: B 390 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7458 (mtm-85) REVERT: B 395 LYS cc_start: 0.8618 (tptp) cc_final: 0.8371 (tptp) REVERT: B 435 MET cc_start: 0.8881 (mmm) cc_final: 0.8657 (mmm) REVERT: C 13 LEU cc_start: 0.9071 (mt) cc_final: 0.8748 (mt) REVERT: C 14 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8176 (mttt) REVERT: C 71 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8215 (tttm) REVERT: C 139 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8306 (ttmt) REVERT: C 172 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6664 (tptp) REVERT: C 291 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8125 (mmtt) REVERT: C 435 MET cc_start: 0.8830 (mmm) cc_final: 0.8116 (mmm) REVERT: C 439 SER cc_start: 0.8988 (t) cc_final: 0.8700 (m) REVERT: C 457 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7942 (mt-10) REVERT: D 14 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (mttm) REVERT: D 89 SER cc_start: 0.8489 (p) cc_final: 0.7911 (t) REVERT: D 297 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7755 (t0) REVERT: D 514 MET cc_start: 0.8518 (mtt) cc_final: 0.8220 (mtt) REVERT: E 89 SER cc_start: 0.8527 (p) cc_final: 0.7930 (t) REVERT: E 172 LYS cc_start: 0.7469 (mmtm) cc_final: 0.7069 (tptp) REVERT: E 439 SER cc_start: 0.8758 (t) cc_final: 0.8325 (m) REVERT: F 71 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8541 (tttm) REVERT: F 192 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7687 (t0) REVERT: F 425 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8948 (t) REVERT: F 457 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7992 (mt-10) REVERT: G 14 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7919 (mttm) REVERT: G 71 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8184 (ttpp) REVERT: G 140 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8630 (tp) REVERT: G 172 LYS cc_start: 0.7063 (mmtm) cc_final: 0.6798 (tptp) REVERT: G 390 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7630 (mtt180) REVERT: G 435 MET cc_start: 0.8850 (mmm) cc_final: 0.8256 (mmm) REVERT: H 11 ASP cc_start: 0.8809 (t0) cc_final: 0.8499 (t0) REVERT: H 14 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7888 (mttp) REVERT: H 24 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8866 (mt) REVERT: H 131 GLN cc_start: 0.8654 (tt0) cc_final: 0.8428 (tt0) REVERT: H 191 LEU cc_start: 0.8609 (mt) cc_final: 0.8358 (mt) REVERT: H 192 ASN cc_start: 0.7755 (t0) cc_final: 0.7445 (t0) REVERT: H 435 MET cc_start: 0.8693 (mmm) cc_final: 0.8029 (mmm) REVERT: H 457 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7783 (mt-10) REVERT: H 481 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8083 (mtp85) REVERT: I 89 SER cc_start: 0.8496 (p) cc_final: 0.7835 (t) REVERT: I 172 LYS cc_start: 0.7549 (mmtm) cc_final: 0.7273 (tttp) REVERT: I 338 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8059 (mt-10) REVERT: I 439 SER cc_start: 0.9028 (t) cc_final: 0.8564 (p) REVERT: J 14 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7838 (mttm) REVERT: J 172 LYS cc_start: 0.7033 (tppt) cc_final: 0.6157 (tptp) REVERT: J 390 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7745 (mtt180) REVERT: K 139 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7946 (ttmt) REVERT: K 172 LYS cc_start: 0.7350 (tppt) cc_final: 0.6736 (tptt) REVERT: K 457 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7868 (mt-10) REVERT: L 172 LYS cc_start: 0.7384 (mmtm) cc_final: 0.7111 (tptp) REVERT: L 439 SER cc_start: 0.9063 (t) cc_final: 0.8795 (m) outliers start: 137 outliers final: 94 residues processed: 684 average time/residue: 0.1697 time to fit residues: 192.3823 Evaluate side-chains 646 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 537 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 58 CYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 415 LEU Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 26 CYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 525 ASP Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 325 ASN Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 502 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 568 HIS C 28 ASN C 119 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 ASN G 568 HIS ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 HIS ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN I 432 ASN ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 426 ASN ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 568 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN K 368 ASN ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 466 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107914 restraints weight = 55715.189| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.11 r_work: 0.2998 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 47364 Z= 0.289 Angle : 0.701 14.336 63912 Z= 0.370 Chirality : 0.050 0.287 7020 Planarity : 0.005 0.079 8208 Dihedral : 5.448 48.312 6135 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.38 % Allowed : 17.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.10), residues: 5664 helix: 0.66 (0.11), residues: 2004 sheet: -1.60 (0.15), residues: 1032 loop : -1.10 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 537 TYR 0.021 0.002 TYR A 421 PHE 0.016 0.002 PHE D 73 TRP 0.015 0.002 TRP D 47 HIS 0.005 0.001 HIS L 437 Details of bonding type rmsd covalent geometry : bond 0.00691 (47328) covalent geometry : angle 0.69355 (63888) SS BOND : bond 0.00591 ( 12) SS BOND : angle 5.38565 ( 24) hydrogen bonds : bond 0.04061 ( 1900) hydrogen bonds : angle 5.37802 ( 5304) metal coordination : bond 0.00400 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 527 time to evaluate : 0.975 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: A 14 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7998 (mttm) REVERT: A 87 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9111 (pp) REVERT: A 136 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8132 (ptpt) REVERT: A 425 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9032 (t) REVERT: B 17 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7490 (pt0) REVERT: B 435 MET cc_start: 0.8989 (mmm) cc_final: 0.8754 (mmm) REVERT: C 14 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8250 (mttp) REVERT: C 71 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8232 (tttm) REVERT: C 131 GLN cc_start: 0.8285 (tt0) cc_final: 0.8003 (tp40) REVERT: C 139 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8295 (ttmt) REVERT: C 172 LYS cc_start: 0.7351 (mmtm) cc_final: 0.6966 (tttt) REVERT: C 291 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8099 (mmtt) REVERT: C 435 MET cc_start: 0.8960 (mmm) cc_final: 0.8216 (mmm) REVERT: C 457 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8042 (mt-10) REVERT: D 14 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8075 (mttm) REVERT: D 297 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7775 (t0) REVERT: D 514 MET cc_start: 0.8519 (mtt) cc_final: 0.8280 (mtt) REVERT: E 439 SER cc_start: 0.8900 (t) cc_final: 0.8379 (m) REVERT: F 14 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8205 (mttt) REVERT: F 71 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8254 (tptt) REVERT: F 192 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7759 (t0) REVERT: F 425 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9098 (t) REVERT: F 457 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8011 (mt-10) REVERT: G 14 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8199 (mttp) REVERT: G 17 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7561 (pt0) REVERT: G 136 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8308 (ptmt) REVERT: G 140 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (tp) REVERT: G 172 LYS cc_start: 0.7456 (mmtm) cc_final: 0.7038 (tptp) REVERT: H 11 ASP cc_start: 0.8813 (t0) cc_final: 0.8516 (t0) REVERT: H 14 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7914 (mttp) REVERT: H 24 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8897 (mp) REVERT: H 192 ASN cc_start: 0.8047 (t0) cc_final: 0.7653 (t0) REVERT: H 435 MET cc_start: 0.8898 (mmm) cc_final: 0.8185 (mmm) REVERT: H 457 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7708 (mt-10) REVERT: H 481 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8178 (mtp85) REVERT: I 73 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: I 172 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7407 (tttt) REVERT: J 14 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7885 (mttm) REVERT: J 172 LYS cc_start: 0.7390 (tppt) cc_final: 0.6623 (tptp) REVERT: J 390 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7794 (mtt180) REVERT: K 139 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8062 (ttmt) REVERT: K 142 GLU cc_start: 0.6888 (tp30) cc_final: 0.6495 (tp30) REVERT: L 172 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7330 (tptp) outliers start: 124 outliers final: 84 residues processed: 627 average time/residue: 0.1720 time to fit residues: 177.5722 Evaluate side-chains 607 residues out of total 5208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 508 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 58 CYS Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 409 GLU Chi-restraints excluded: chain G residue 501 VAL Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 293 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 394 THR Chi-restraints excluded: chain H residue 409 GLU Chi-restraints excluded: chain H residue 524 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 58 CYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 409 GLU Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 14 LYS Chi-restraints excluded: chain J residue 26 CYS Chi-restraints excluded: chain J residue 73 PHE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 58 CYS Chi-restraints excluded: chain K residue 73 PHE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 409 GLU Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain L residue 58 CYS Chi-restraints excluded: chain L residue 73 PHE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 129 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 476 optimal weight: 0.7980 chunk 460 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 400 optimal weight: 0.5980 chunk 281 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS B 28 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 190 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 HIS G 119 HIS ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN G 414 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 568 HIS I 131 GLN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.106967 restraints weight = 55938.723| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.50 r_work: 0.3004 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 47364 Z= 0.133 Angle : 0.593 12.185 63912 Z= 0.314 Chirality : 0.045 0.209 7020 Planarity : 0.003 0.045 8208 Dihedral : 5.212 47.561 6135 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.04 % Allowed : 18.36 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.11), residues: 5664 helix: 0.93 (0.11), residues: 2028 sheet: -1.32 (0.16), residues: 996 loop : -1.16 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 537 TYR 0.013 0.001 TYR E 278 PHE 0.015 0.001 PHE D 73 TRP 0.006 0.001 TRP I 47 HIS 0.003 0.001 HIS G 475 Details of bonding type rmsd covalent geometry : bond 0.00311 (47328) covalent geometry : angle 0.58429 (63888) SS BOND : bond 0.00423 ( 12) SS BOND : angle 5.17958 ( 24) hydrogen bonds : bond 0.03503 ( 1900) hydrogen bonds : angle 5.12227 ( 5304) metal coordination : bond 0.00124 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8522.52 seconds wall clock time: 148 minutes 0.43 seconds (8880.43 seconds total)