Starting phenix.real_space_refine on Sat Mar 7 07:28:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf7_25864/03_2026/7tf7_25864.cif" } resolution = 2.13 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= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 25530 2.51 5 N 6670 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 39976 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "B" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "C" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "D" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "E" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3328 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "G" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "H" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3328 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "J" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "K" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "L" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU A 250 " occ=0.97 residue: pdb=" N LEU B 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 250 " occ=0.97 residue: pdb=" N LEU C 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU C 250 " occ=0.97 residue: pdb=" N LEU D 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU D 250 " occ=0.97 residue: pdb=" N LEU E 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 250 " occ=0.97 residue: pdb=" N LEU F 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 250 " occ=0.97 residue: pdb=" N LEU G 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU G 250 " occ=0.97 residue: pdb=" N LEU H 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU H 250 " occ=0.97 residue: pdb=" N LEU I 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU I 250 " occ=0.97 residue: pdb=" N LEU J 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 250 " occ=0.97 residue: pdb=" N LEU K 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 250 " occ=0.97 residue: pdb=" N LEU L 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 250 " occ=0.97 Time building chain proxies: 9.47, per 1000 atoms: 0.24 Number of scatterers: 39976 At special positions: 0 Unit cell: (161.04, 154.88, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 7584 8.00 N 6670 7.00 C 25530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 36 sheets defined 41.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.570A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 204 through 225 removed outlier: 3.504A pdb=" N LYS A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.682A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.846A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 330 " --> pdb=" O GLY A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.636A pdb=" N GLU A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 430 removed outlier: 3.934A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.585A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 179 removed outlier: 3.509A pdb=" N MET B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.532A pdb=" N ARG B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.675A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.780A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 330 " --> pdb=" O GLY B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.630A pdb=" N GLU B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 430 removed outlier: 3.806A pdb=" N LYS B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N HIS B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.635A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 204 through 225 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.657A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.723A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.619A pdb=" N GLU C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 430 removed outlier: 4.013A pdb=" N LYS C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N HIS C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'D' and resid 5 through 17 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.582A pdb=" N ASP D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 204 through 225 Processing helix chain 'D' and resid 268 through 282 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.677A pdb=" N ARG D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 294 through 299' Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.741A pdb=" N SER D 329 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 330 " --> pdb=" O GLY D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 342 through 360 Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.572A pdb=" N GLU D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N HIS D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.577A pdb=" N ASP E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.522A pdb=" N MET E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 225 removed outlier: 3.504A pdb=" N ARG E 223 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 282 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.676A pdb=" N ARG E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 299' Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.777A pdb=" N SER E 329 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 330 " --> pdb=" O GLY E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 330' Processing helix chain 'E' and resid 342 through 361 Processing helix chain 'E' and resid 391 through 401 removed outlier: 3.632A pdb=" N GLU E 401 " --> pdb=" O LYS E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 430 removed outlier: 3.868A pdb=" N LYS E 406 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N HIS E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 440 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.581A pdb=" N ASP F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'F' and resid 204 through 225 removed outlier: 3.536A pdb=" N ARG F 223 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 224 " --> pdb=" O THR F 220 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS F 225 " --> pdb=" O ILE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.682A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.807A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 330 " --> pdb=" O GLY F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 330' Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.622A pdb=" N GLU F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 410 removed outlier: 3.846A pdb=" N LYS F 406 " --> pdb=" O ASN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 430 removed outlier: 3.796A pdb=" N THR F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.611A pdb=" N ASP G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 Processing helix chain 'G' and resid 204 through 225 Processing helix chain 'G' and resid 268 through 282 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.680A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.741A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR G 330 " --> pdb=" O GLY G 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 326 through 330' Processing helix chain 'G' and resid 342 through 360 Processing helix chain 'G' and resid 391 through 401 removed outlier: 3.576A pdb=" N GLU G 401 " --> pdb=" O LYS G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 430 removed outlier: 4.084A pdb=" N LYS G 406 " --> pdb=" O ASN G 402 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N HIS G 412 " --> pdb=" O ALA G 408 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE G 413 " --> pdb=" O LEU G 409 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 430 " --> pdb=" O ASP G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.601A pdb=" N ASP H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 179 Processing helix chain 'H' and resid 204 through 225 Processing helix chain 'H' and resid 268 through 282 Processing helix chain 'H' and resid 285 through 290 Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.650A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 294 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.798A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 330 " --> pdb=" O GLY H 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 326 through 330' Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.575A pdb=" N GLU H 401 " --> pdb=" O LYS H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 430 removed outlier: 4.012A pdb=" N LYS H 406 " --> pdb=" O ASN H 402 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N HIS H 412 " --> pdb=" O ALA H 408 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 440 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 107 through 121 removed outlier: 3.630A pdb=" N ASP I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 179 Processing helix chain 'I' and resid 204 through 225 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 285 through 290 Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.659A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.706A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 391 through 401 removed outlier: 3.602A pdb=" N GLU I 401 " --> pdb=" O LYS I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 430 removed outlier: 4.021A pdb=" N LYS I 406 " --> pdb=" O ASN I 402 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N HIS I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE I 413 " --> pdb=" O LEU I 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR I 430 " --> pdb=" O ASP I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.623A pdb=" N ASP J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 204 through 225 Processing helix chain 'J' and resid 268 through 281 Processing helix chain 'J' and resid 285 through 290 Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.676A pdb=" N ARG J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 294 through 299' Processing helix chain 'J' and resid 326 through 330 removed outlier: 3.688A pdb=" N SER J 329 " --> pdb=" O ARG J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 360 Processing helix chain 'J' and resid 391 through 401 removed outlier: 3.608A pdb=" N GLU J 401 " --> pdb=" O LYS J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS J 406 " --> pdb=" O ASN J 402 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N HIS J 412 " --> pdb=" O ALA J 408 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE J 413 " --> pdb=" O LEU J 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR J 430 " --> pdb=" O ASP J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'K' and resid 5 through 17 Processing helix chain 'K' and resid 41 through 47 Processing helix chain 'K' and resid 107 through 121 removed outlier: 3.623A pdb=" N ASP K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 179 Processing helix chain 'K' and resid 204 through 225 Processing helix chain 'K' and resid 268 through 281 Processing helix chain 'K' and resid 285 through 290 Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.674A pdb=" N ARG K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.682A pdb=" N SER K 329 " --> pdb=" O ARG K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 360 Processing helix chain 'K' and resid 391 through 401 removed outlier: 3.608A pdb=" N GLU K 401 " --> pdb=" O LYS K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS K 406 " --> pdb=" O ASN K 402 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N HIS K 412 " --> pdb=" O ALA K 408 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE K 413 " --> pdb=" O LEU K 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR K 430 " --> pdb=" O ASP K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 440 Processing helix chain 'L' and resid 5 through 17 Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 107 through 121 removed outlier: 3.614A pdb=" N ASP L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 179 Processing helix chain 'L' and resid 204 through 225 Processing helix chain 'L' and resid 268 through 281 Processing helix chain 'L' and resid 285 through 290 Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.657A pdb=" N ARG L 298 " --> pdb=" O ASN L 294 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU L 299 " --> pdb=" O SER L 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 294 through 299' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.799A pdb=" N SER L 329 " --> pdb=" O ARG L 326 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 330 " --> pdb=" O GLY L 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 326 through 330' Processing helix chain 'L' and resid 342 through 361 Processing helix chain 'L' and resid 391 through 401 removed outlier: 3.561A pdb=" N GLU L 401 " --> pdb=" O LYS L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 430 removed outlier: 4.022A pdb=" N LYS L 406 " --> pdb=" O ASN L 402 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N HIS L 412 " --> pdb=" O ALA L 408 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR L 430 " --> pdb=" O ASP L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 6.314A pdb=" N TYR A 20 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 92 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG A 22 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS A 94 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN A 24 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL A 96 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N THR A 26 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 11.906A pdb=" N VAL A 89 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N TRP A 77 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ARG A 91 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP A 75 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 93 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET A 50 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 140 removed outlier: 7.285A pdb=" N LEU A 137 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU A 149 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS A 139 " --> pdb=" O THR A 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 146 through 150 current: chain 'A' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 194 through 199 current: chain 'A' and resid 320 through 321 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.025A pdb=" N GLN A 386 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.471A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N VAL B 89 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N TRP B 77 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N ARG B 91 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP B 75 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 93 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 50 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 140 removed outlier: 7.375A pdb=" N LEU B 137 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU B 149 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 139 " --> pdb=" O THR B 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 150 current: chain 'B' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 194 through 199 current: chain 'B' and resid 320 through 321 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 309 removed outlier: 4.106A pdb=" N GLN B 386 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.485A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N VAL C 89 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N TRP C 77 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 91 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP C 75 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 93 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET C 50 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 140 removed outlier: 7.349A pdb=" N LEU C 137 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 149 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS C 139 " --> pdb=" O THR C 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 146 through 150 current: chain 'C' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 194 through 199 current: chain 'C' and resid 320 through 321 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 309 removed outlier: 4.076A pdb=" N GLN C 386 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 38 removed outlier: 5.496A pdb=" N THR D 26 " --> pdb=" O CYS D 94 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 96 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N VAL D 89 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N TRP D 77 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG D 91 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP D 75 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 93 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N MET D 50 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 126 through 140 removed outlier: 7.347A pdb=" N LEU D 137 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU D 149 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS D 139 " --> pdb=" O THR D 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 146 through 150 current: chain 'D' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 194 through 199 current: chain 'D' and resid 320 through 321 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 309 removed outlier: 4.105A pdb=" N GLN D 386 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 38 removed outlier: 5.460A pdb=" N THR E 26 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL E 96 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N VAL E 89 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N TRP E 77 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG E 91 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP E 75 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE E 93 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET E 50 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 126 through 140 removed outlier: 7.367A pdb=" N LEU E 137 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU E 149 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS E 139 " --> pdb=" O THR E 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 146 through 150 current: chain 'E' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 194 through 199 current: chain 'E' and resid 320 through 321 Processing sheet with id=AB6, first strand: chain 'E' and resid 308 through 309 removed outlier: 4.079A pdb=" N GLN E 386 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 32 through 38 removed outlier: 6.293A pdb=" N TYR F 20 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU F 92 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG F 22 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS F 94 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN F 24 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL F 96 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N THR F 26 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N VAL F 89 " --> pdb=" O TRP F 77 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N TRP F 77 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG F 91 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASP F 75 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE F 93 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET F 50 " --> pdb=" O LEU F 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 126 through 140 removed outlier: 7.296A pdb=" N LEU F 137 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU F 149 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS F 139 " --> pdb=" O THR F 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 146 through 150 current: chain 'F' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 194 through 199 current: chain 'F' and resid 320 through 321 Processing sheet with id=AB9, first strand: chain 'F' and resid 308 through 309 removed outlier: 4.061A pdb=" N GLN F 386 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.478A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N VAL G 89 " --> pdb=" O TRP G 77 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N TRP G 77 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N ARG G 91 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP G 75 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE G 93 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET G 50 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 126 through 140 removed outlier: 5.410A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 146 through 150 current: chain 'G' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 194 through 199 current: chain 'G' and resid 320 through 321 Processing sheet with id=AC3, first strand: chain 'G' and resid 308 through 309 removed outlier: 4.113A pdb=" N GLN G 386 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.489A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N VAL H 89 " --> pdb=" O TRP H 77 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N TRP H 77 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N ARG H 91 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP H 75 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE H 93 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET H 50 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 140 removed outlier: 7.287A pdb=" N LEU H 137 " --> pdb=" O GLU H 149 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU H 149 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS H 139 " --> pdb=" O THR H 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 146 through 150 current: chain 'H' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 194 through 199 current: chain 'H' and resid 320 through 321 Processing sheet with id=AC6, first strand: chain 'H' and resid 308 through 309 removed outlier: 4.096A pdb=" N GLN H 386 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 38 removed outlier: 6.292A pdb=" N TYR I 20 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU I 92 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG I 22 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS I 94 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN I 24 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL I 96 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N THR I 26 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 11.884A pdb=" N VAL I 89 " --> pdb=" O TRP I 77 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N TRP I 77 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG I 91 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASP I 75 " --> pdb=" O ARG I 91 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE I 93 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET I 50 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 126 through 140 removed outlier: 7.358A pdb=" N LEU I 137 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU I 149 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS I 139 " --> pdb=" O THR I 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 146 through 150 current: chain 'I' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 199 current: chain 'I' and resid 320 through 321 Processing sheet with id=AC9, first strand: chain 'I' and resid 308 through 309 removed outlier: 4.055A pdb=" N GLN I 386 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 32 through 38 removed outlier: 5.484A pdb=" N THR J 26 " --> pdb=" O CYS J 94 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL J 96 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL J 89 " --> pdb=" O TRP J 77 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N TRP J 77 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG J 91 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP J 75 " --> pdb=" O ARG J 91 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE J 93 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET J 50 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 126 through 140 removed outlier: 7.323A pdb=" N LEU J 137 " --> pdb=" O GLU J 149 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU J 149 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS J 139 " --> pdb=" O THR J 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 146 through 150 current: chain 'J' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 194 through 199 current: chain 'J' and resid 320 through 321 Processing sheet with id=AD3, first strand: chain 'J' and resid 308 through 309 removed outlier: 4.055A pdb=" N GLN J 386 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 32 through 38 removed outlier: 6.299A pdb=" N TYR K 20 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU K 92 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG K 22 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS K 94 " --> pdb=" O ARG K 22 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN K 24 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL K 96 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N THR K 26 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N VAL K 89 " --> pdb=" O TRP K 77 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N TRP K 77 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N ARG K 91 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP K 75 " --> pdb=" O ARG K 91 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE K 93 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET K 50 " --> pdb=" O LEU K 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 126 through 140 removed outlier: 7.340A pdb=" N LEU K 137 " --> pdb=" O GLU K 149 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU K 149 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS K 139 " --> pdb=" O THR K 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 146 through 150 current: chain 'K' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 194 through 199 current: chain 'K' and resid 320 through 321 Processing sheet with id=AD6, first strand: chain 'K' and resid 308 through 309 removed outlier: 4.056A pdb=" N GLN K 386 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 32 through 38 removed outlier: 5.492A pdb=" N THR L 26 " --> pdb=" O CYS L 94 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL L 96 " --> pdb=" O THR L 26 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL L 89 " --> pdb=" O PHE L 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 78 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE L 93 " --> pdb=" O THR L 76 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR L 76 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N ASP L 95 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N LEU L 74 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 10.202A pdb=" N TYR L 97 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET L 50 " --> pdb=" O LEU L 70 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 126 through 140 removed outlier: 7.284A pdb=" N LEU L 137 " --> pdb=" O GLU L 149 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU L 149 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS L 139 " --> pdb=" O THR L 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 146 through 150 current: chain 'L' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 194 through 199 current: chain 'L' and resid 320 through 321 Processing sheet with id=AD9, first strand: chain 'L' and resid 308 through 309 removed outlier: 3.956A pdb=" N GLN L 386 " --> pdb=" O ILE L 309 " (cutoff:3.500A) 1557 hydrogen bonds defined for protein. 4623 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: 7.60 Time building geometry restraints manager: 4.82 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: 13141 1.34 - 1.46: 9152 1.46 - 1.58: 18283 1.58 - 1.70: 0 1.70 - 1.82: 324 Bond restraints: 40900 Sorted by residual: bond pdb=" N LYS H 254 " pdb=" CA LYS H 254 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.30e+00 bond pdb=" N LYS E 254 " pdb=" CA LYS E 254 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" N ILE G 32 " pdb=" CA ILE G 32 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.10e-02 8.26e+03 8.89e+00 bond pdb=" N VAL C 334 " pdb=" CA VAL C 334 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.84e+00 bond pdb=" N ARG C 335 " pdb=" CA ARG C 335 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.22e-02 6.72e+03 7.59e+00 ... (remaining 40895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 54556 2.03 - 4.06: 708 4.06 - 6.09: 83 6.09 - 8.12: 10 8.12 - 10.15: 3 Bond angle restraints: 55360 Sorted by residual: angle pdb=" N MET C 441 " pdb=" CA MET C 441 " pdb=" CB MET C 441 " ideal model delta sigma weight residual 114.17 109.75 4.42 1.14e+00 7.69e-01 1.50e+01 angle pdb=" CA LYS A 254 " pdb=" CB LYS A 254 " pdb=" CG LYS A 254 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA LYS B 254 " pdb=" CB LYS B 254 " pdb=" CG LYS B 254 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N MET I 441 " pdb=" CA MET I 441 " pdb=" CB MET I 441 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N MET L 441 " pdb=" CA MET L 441 " pdb=" CB MET L 441 " ideal model delta sigma weight residual 114.17 109.90 4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 55355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 22052 17.92 - 35.85: 1836 35.85 - 53.77: 534 53.77 - 71.70: 131 71.70 - 89.62: 51 Dihedral angle restraints: 24604 sinusoidal: 10144 harmonic: 14460 Sorted by residual: dihedral pdb=" CA SER E 317 " pdb=" C SER E 317 " pdb=" N PRO E 318 " pdb=" CA PRO E 318 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER A 317 " pdb=" C SER A 317 " pdb=" N PRO A 318 " pdb=" CA PRO A 318 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA SER L 317 " pdb=" C SER L 317 " pdb=" N PRO L 318 " pdb=" CA PRO L 318 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 24601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4265 0.043 - 0.086: 1306 0.086 - 0.129: 374 0.129 - 0.172: 18 0.172 - 0.215: 1 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CA VAL C 334 " pdb=" N VAL C 334 " pdb=" C VAL C 334 " pdb=" CB VAL C 334 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET J 51 " pdb=" N MET J 51 " pdb=" C MET J 51 " pdb=" CB MET J 51 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA MET G 51 " pdb=" N MET G 51 " pdb=" C MET G 51 " pdb=" CB MET G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 5961 not shown) Planarity restraints: 7260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 317 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO K 318 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO K 318 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 318 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 317 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO D 318 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 318 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 318 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 317 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO J 318 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 318 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 318 " -0.027 5.00e-02 4.00e+02 ... (remaining 7257 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2297 2.73 - 3.27: 39345 3.27 - 3.81: 68541 3.81 - 4.36: 87739 4.36 - 4.90: 146186 Nonbonded interactions: 344108 Sorted by model distance: nonbonded pdb=" OD2 ASP E 53 " pdb=" OG SER E 55 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP B 53 " pdb=" OG SER B 55 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP A 53 " pdb=" OG SER A 55 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP F 53 " pdb=" OG SER F 55 " model vdw 2.202 3.040 ... (remaining 344103 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'B' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'C' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'D' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = chain 'E' selection = (chain 'F' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'G' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = chain 'H' selection = (chain 'I' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'J' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'K' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'L' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.230 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.070 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40900 Z= 0.191 Angle : 0.611 10.151 55360 Z= 0.355 Chirality : 0.043 0.215 5964 Planarity : 0.004 0.048 7260 Dihedral : 15.424 89.620 15268 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 1.43 % Allowed : 15.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.01 (0.12), residues: 4884 helix: 1.66 (0.12), residues: 1992 sheet: 0.02 (0.18), residues: 912 loop : 0.10 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.019 0.002 TYR E 296 PHE 0.020 0.002 PHE G 285 TRP 0.010 0.002 TRP B 425 HIS 0.005 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00424 (40900) covalent geometry : angle 0.61115 (55360) hydrogen bonds : bond 0.15972 ( 1557) hydrogen bonds : angle 5.95068 ( 4623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 849 time to evaluate : 1.248 Fit side-chains REVERT: A 8 ASP cc_start: 0.5805 (m-30) cc_final: 0.5348 (m-30) REVERT: A 16 GLU cc_start: 0.6411 (mm-30) cc_final: 0.6153 (mm-30) REVERT: A 19 ARG cc_start: 0.6390 (mmm160) cc_final: 0.5037 (mmm-85) REVERT: A 37 VAL cc_start: 0.6543 (t) cc_final: 0.6186 (m) REVERT: A 50 MET cc_start: 0.6980 (tpp) cc_final: 0.6658 (tpt) REVERT: A 51 MET cc_start: 0.7252 (mtp) cc_final: 0.7044 (mtt) REVERT: A 105 GLU cc_start: 0.6485 (pm20) cc_final: 0.6176 (pm20) REVERT: A 149 GLU cc_start: 0.6535 (pt0) cc_final: 0.5931 (pt0) REVERT: A 269 GLU cc_start: 0.5697 (tp30) cc_final: 0.4958 (tp30) REVERT: A 307 CYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6128 (p) REVERT: A 321 ARG cc_start: 0.6397 (ttt90) cc_final: 0.5812 (ttt90) REVERT: A 352 GLU cc_start: 0.7134 (tp30) cc_final: 0.6903 (tp30) REVERT: A 394 THR cc_start: 0.6827 (m) cc_final: 0.6398 (p) REVERT: A 407 LYS cc_start: 0.6829 (tttp) cc_final: 0.6580 (tttm) REVERT: A 416 GLN cc_start: 0.6150 (mm110) cc_final: 0.5868 (mm110) REVERT: A 419 ASN cc_start: 0.6055 (m-40) cc_final: 0.4846 (t0) REVERT: A 429 ARG cc_start: 0.6732 (ttp80) cc_final: 0.6511 (ptm-80) REVERT: A 434 GLU cc_start: 0.6603 (tp30) cc_final: 0.5379 (pm20) REVERT: A 438 ASP cc_start: 0.6631 (m-30) cc_final: 0.6215 (m-30) REVERT: B 8 ASP cc_start: 0.5599 (m-30) cc_final: 0.5150 (m-30) REVERT: B 15 GLU cc_start: 0.6464 (pt0) cc_final: 0.6245 (pt0) REVERT: B 17 ASN cc_start: 0.6260 (t0) cc_final: 0.5811 (t0) REVERT: B 22 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7276 (tpp80) REVERT: B 37 VAL cc_start: 0.6668 (t) cc_final: 0.6345 (m) REVERT: B 50 MET cc_start: 0.6898 (tpp) cc_final: 0.6596 (tpt) REVERT: B 198 ASP cc_start: 0.7970 (m-30) cc_final: 0.7753 (m-30) REVERT: B 240 ASN cc_start: 0.6731 (t0) cc_final: 0.6461 (t0) REVERT: B 269 GLU cc_start: 0.5700 (tp30) cc_final: 0.5260 (tp30) REVERT: B 321 ARG cc_start: 0.6332 (tmt-80) cc_final: 0.5589 (ttt90) REVERT: B 329 SER cc_start: 0.7288 (p) cc_final: 0.6966 (p) REVERT: B 394 THR cc_start: 0.6729 (m) cc_final: 0.6313 (p) REVERT: B 407 LYS cc_start: 0.6845 (ttpp) cc_final: 0.6351 (tttp) REVERT: B 419 ASN cc_start: 0.5961 (m-40) cc_final: 0.4587 (t0) REVERT: B 427 TYR cc_start: 0.6828 (m-10) cc_final: 0.5392 (t80) REVERT: B 429 ARG cc_start: 0.6949 (ttp80) cc_final: 0.6730 (ptm-80) REVERT: B 434 GLU cc_start: 0.6429 (tp30) cc_final: 0.6064 (mm-30) REVERT: C 11 LYS cc_start: 0.6024 (ttmm) cc_final: 0.5681 (ttpp) REVERT: C 22 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7292 (tpp80) REVERT: C 37 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6382 (m) REVERT: C 50 MET cc_start: 0.7060 (tpp) cc_final: 0.6732 (tpt) REVERT: C 142 GLU cc_start: 0.5550 (pm20) cc_final: 0.5345 (mm-30) REVERT: C 149 GLU cc_start: 0.6604 (pt0) cc_final: 0.6153 (pt0) REVERT: C 153 ASP cc_start: 0.6737 (t0) cc_final: 0.6476 (t0) REVERT: C 265 MET cc_start: 0.5865 (tpp) cc_final: 0.5608 (tpp) REVERT: C 269 GLU cc_start: 0.5528 (tp30) cc_final: 0.5090 (tp30) REVERT: C 321 ARG cc_start: 0.6467 (ttt90) cc_final: 0.6123 (ttt90) REVERT: C 329 SER cc_start: 0.7349 (p) cc_final: 0.7020 (p) REVERT: C 345 MET cc_start: 0.7255 (mtp) cc_final: 0.6755 (mtp) REVERT: C 394 THR cc_start: 0.6530 (m) cc_final: 0.6167 (p) REVERT: C 407 LYS cc_start: 0.6757 (tttp) cc_final: 0.6272 (tttp) REVERT: C 419 ASN cc_start: 0.5743 (m-40) cc_final: 0.4509 (t0) REVERT: D 8 ASP cc_start: 0.5566 (m-30) cc_final: 0.5096 (m-30) REVERT: D 22 ARG cc_start: 0.7467 (ttm170) cc_final: 0.6939 (tpp80) REVERT: D 50 MET cc_start: 0.7008 (tpp) cc_final: 0.6770 (tpt) REVERT: D 69 TYR cc_start: 0.6954 (m-80) cc_final: 0.6389 (m-80) REVERT: D 198 ASP cc_start: 0.7595 (m-30) cc_final: 0.7371 (m-30) REVERT: D 223 ARG cc_start: 0.6622 (tpp-160) cc_final: 0.6007 (ttt180) REVERT: D 255 GLU cc_start: 0.6383 (tt0) cc_final: 0.5542 (pp20) REVERT: D 269 GLU cc_start: 0.5746 (tp30) cc_final: 0.5278 (tp30) REVERT: D 321 ARG cc_start: 0.6300 (tmt-80) cc_final: 0.5538 (ttt90) REVERT: D 329 SER cc_start: 0.7196 (p) cc_final: 0.6853 (p) REVERT: D 352 GLU cc_start: 0.7412 (tp30) cc_final: 0.7173 (tp30) REVERT: D 394 THR cc_start: 0.6686 (m) cc_final: 0.6278 (p) REVERT: D 407 LYS cc_start: 0.6699 (tttp) cc_final: 0.6151 (tttp) REVERT: D 419 ASN cc_start: 0.6011 (m-40) cc_final: 0.4634 (t0) REVERT: D 427 TYR cc_start: 0.6827 (m-10) cc_final: 0.5404 (t80) REVERT: D 429 ARG cc_start: 0.6908 (ttp80) cc_final: 0.6623 (ptm-80) REVERT: D 434 GLU cc_start: 0.6404 (tp30) cc_final: 0.6110 (mm-30) REVERT: D 441 MET cc_start: 0.6077 (ttt) cc_final: 0.5686 (tpt) REVERT: E 8 ASP cc_start: 0.5583 (m-30) cc_final: 0.5109 (m-30) REVERT: E 17 ASN cc_start: 0.6238 (t0) cc_final: 0.5763 (t0) REVERT: E 22 ARG cc_start: 0.7526 (ttm170) cc_final: 0.7169 (tpp80) REVERT: E 37 VAL cc_start: 0.6744 (t) cc_final: 0.6392 (m) REVERT: E 50 MET cc_start: 0.6952 (tpp) cc_final: 0.6580 (tpt) REVERT: E 69 TYR cc_start: 0.7148 (m-80) cc_final: 0.6588 (m-80) REVERT: E 149 GLU cc_start: 0.6722 (pt0) cc_final: 0.6160 (pt0) REVERT: E 223 ARG cc_start: 0.6811 (ttm-80) cc_final: 0.6609 (ttt90) REVERT: E 240 ASN cc_start: 0.6620 (t0) cc_final: 0.6344 (t0) REVERT: E 269 GLU cc_start: 0.5634 (tp30) cc_final: 0.5166 (tp30) REVERT: E 307 CYS cc_start: 0.6494 (m) cc_final: 0.6167 (m) REVERT: E 329 SER cc_start: 0.7359 (p) cc_final: 0.7057 (p) REVERT: E 366 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6725 (tp30) REVERT: E 386 GLN cc_start: 0.6504 (mt0) cc_final: 0.6279 (mt0) REVERT: E 394 THR cc_start: 0.6695 (m) cc_final: 0.6295 (p) REVERT: E 407 LYS cc_start: 0.6635 (ttpp) cc_final: 0.6222 (tttp) REVERT: E 419 ASN cc_start: 0.5916 (m-40) cc_final: 0.4554 (t0) REVERT: E 427 TYR cc_start: 0.6834 (m-10) cc_final: 0.5381 (t80) REVERT: E 429 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6738 (ptm-80) REVERT: E 434 GLU cc_start: 0.6414 (tp30) cc_final: 0.6138 (mm-30) REVERT: F 8 ASP cc_start: 0.5809 (m-30) cc_final: 0.5357 (m-30) REVERT: F 16 GLU cc_start: 0.6385 (mm-30) cc_final: 0.6145 (mm-30) REVERT: F 19 ARG cc_start: 0.6389 (mmm160) cc_final: 0.4960 (mmm-85) REVERT: F 22 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7325 (mmm-85) REVERT: F 32 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6503 (mm) REVERT: F 105 GLU cc_start: 0.6481 (pm20) cc_final: 0.6169 (pm20) REVERT: F 149 GLU cc_start: 0.6473 (pt0) cc_final: 0.6067 (pt0) REVERT: F 153 ASP cc_start: 0.6944 (t0) cc_final: 0.6713 (t70) REVERT: F 223 ARG cc_start: 0.6569 (mtp85) cc_final: 0.6267 (ttt90) REVERT: F 269 GLU cc_start: 0.5725 (tp30) cc_final: 0.5020 (tp30) REVERT: F 321 ARG cc_start: 0.6321 (ttt90) cc_final: 0.5657 (ttt90) REVERT: F 329 SER cc_start: 0.7531 (p) cc_final: 0.7207 (p) REVERT: F 352 GLU cc_start: 0.7126 (tp30) cc_final: 0.6845 (tp30) REVERT: F 394 THR cc_start: 0.6838 (m) cc_final: 0.6406 (p) REVERT: F 419 ASN cc_start: 0.6058 (m-40) cc_final: 0.4841 (t0) REVERT: F 429 ARG cc_start: 0.6729 (ttp80) cc_final: 0.6465 (ptm-80) REVERT: F 434 GLU cc_start: 0.6504 (tp30) cc_final: 0.5200 (pm20) REVERT: F 438 ASP cc_start: 0.6635 (m-30) cc_final: 0.6216 (m-30) REVERT: F 443 GLN cc_start: 0.7041 (tt0) cc_final: 0.6832 (tt0) REVERT: G 8 ASP cc_start: 0.5582 (m-30) cc_final: 0.5107 (m-30) REVERT: G 22 ARG cc_start: 0.7528 (ttm170) cc_final: 0.7144 (tpp80) REVERT: G 37 VAL cc_start: 0.6601 (t) cc_final: 0.6242 (m) REVERT: G 69 TYR cc_start: 0.6917 (m-80) cc_final: 0.6504 (m-80) REVERT: G 170 ARG cc_start: 0.6231 (tpp80) cc_final: 0.5759 (tpp80) REVERT: G 198 ASP cc_start: 0.7573 (m-30) cc_final: 0.7352 (m-30) REVERT: G 223 ARG cc_start: 0.6651 (tpp-160) cc_final: 0.6025 (ttt180) REVERT: G 240 ASN cc_start: 0.6615 (t0) cc_final: 0.6345 (t0) REVERT: G 255 GLU cc_start: 0.6443 (tt0) cc_final: 0.5594 (pp20) REVERT: G 269 GLU cc_start: 0.5386 (tp30) cc_final: 0.5022 (tp30) REVERT: G 321 ARG cc_start: 0.6305 (tmt-80) cc_final: 0.5543 (ttt90) REVERT: G 329 SER cc_start: 0.7211 (p) cc_final: 0.6863 (p) REVERT: G 352 GLU cc_start: 0.7416 (tp30) cc_final: 0.7173 (tp30) REVERT: G 386 GLN cc_start: 0.6726 (mt0) cc_final: 0.6484 (mt0) REVERT: G 394 THR cc_start: 0.6696 (m) cc_final: 0.6281 (p) REVERT: G 407 LYS cc_start: 0.6712 (tttp) cc_final: 0.6131 (tttp) REVERT: G 419 ASN cc_start: 0.6009 (m-40) cc_final: 0.4624 (t0) REVERT: G 429 ARG cc_start: 0.6889 (ttp80) cc_final: 0.6575 (ptm-80) REVERT: G 434 GLU cc_start: 0.6520 (tp30) cc_final: 0.6225 (mm-30) REVERT: H 8 ASP cc_start: 0.5763 (m-30) cc_final: 0.5331 (m-30) REVERT: H 16 GLU cc_start: 0.6343 (mm-30) cc_final: 0.6084 (mm-30) REVERT: H 19 ARG cc_start: 0.6420 (mmm160) cc_final: 0.4996 (mmm-85) REVERT: H 37 VAL cc_start: 0.6462 (OUTLIER) cc_final: 0.6131 (m) REVERT: H 105 GLU cc_start: 0.6512 (pm20) cc_final: 0.6233 (pm20) REVERT: H 126 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.7022 (t0) REVERT: H 149 GLU cc_start: 0.6496 (pt0) cc_final: 0.5906 (pt0) REVERT: H 167 ASN cc_start: 0.6449 (m-40) cc_final: 0.6198 (m-40) REVERT: H 224 LYS cc_start: 0.6796 (mttm) cc_final: 0.6447 (mttp) REVERT: H 269 GLU cc_start: 0.5724 (tp30) cc_final: 0.4984 (tp30) REVERT: H 321 ARG cc_start: 0.6311 (ttt90) cc_final: 0.5670 (ttt90) REVERT: H 329 SER cc_start: 0.7501 (p) cc_final: 0.7180 (p) REVERT: H 352 GLU cc_start: 0.7226 (tp30) cc_final: 0.6871 (tp30) REVERT: H 386 GLN cc_start: 0.6681 (tt0) cc_final: 0.6445 (mt0) REVERT: H 394 THR cc_start: 0.6847 (m) cc_final: 0.6426 (p) REVERT: H 407 LYS cc_start: 0.7026 (tttm) cc_final: 0.6697 (tttp) REVERT: H 419 ASN cc_start: 0.6005 (m-40) cc_final: 0.4815 (t0) REVERT: H 429 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6523 (ptm-80) REVERT: H 434 GLU cc_start: 0.6514 (tp30) cc_final: 0.5226 (pm20) REVERT: H 438 ASP cc_start: 0.6585 (m-30) cc_final: 0.6191 (m-30) REVERT: H 443 GLN cc_start: 0.7000 (tt0) cc_final: 0.6763 (tt0) REVERT: I 11 LYS cc_start: 0.5909 (ttmm) cc_final: 0.5610 (ttpp) REVERT: I 17 ASN cc_start: 0.6524 (t0) cc_final: 0.6097 (t0) REVERT: I 22 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7060 (tpp80) REVERT: I 37 VAL cc_start: 0.6771 (OUTLIER) cc_final: 0.6379 (m) REVERT: I 50 MET cc_start: 0.7026 (tpp) cc_final: 0.6646 (tpt) REVERT: I 51 MET cc_start: 0.7076 (mtp) cc_final: 0.6846 (ttm) REVERT: I 117 LYS cc_start: 0.5739 (tptp) cc_final: 0.5402 (tptp) REVERT: I 120 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6664 (mt-10) REVERT: I 149 GLU cc_start: 0.6638 (pt0) cc_final: 0.6222 (pt0) REVERT: I 153 ASP cc_start: 0.6754 (t0) cc_final: 0.6518 (t0) REVERT: I 269 GLU cc_start: 0.5445 (tp30) cc_final: 0.5035 (tp30) REVERT: I 321 ARG cc_start: 0.6480 (ttt90) cc_final: 0.6109 (ttt90) REVERT: I 329 SER cc_start: 0.7362 (p) cc_final: 0.6985 (p) REVERT: I 394 THR cc_start: 0.6581 (m) cc_final: 0.6214 (p) REVERT: I 407 LYS cc_start: 0.6777 (tttm) cc_final: 0.6290 (ttpp) REVERT: I 419 ASN cc_start: 0.5742 (m-40) cc_final: 0.4505 (t0) REVERT: J 11 LYS cc_start: 0.5874 (ttmm) cc_final: 0.5592 (ttpp) REVERT: J 17 ASN cc_start: 0.6501 (t0) cc_final: 0.6094 (t0) REVERT: J 22 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7136 (tpp80) REVERT: J 50 MET cc_start: 0.7143 (tpp) cc_final: 0.6783 (tpt) REVERT: J 120 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6614 (mt-10) REVERT: J 149 GLU cc_start: 0.6671 (pt0) cc_final: 0.6190 (pt0) REVERT: J 153 ASP cc_start: 0.6708 (t0) cc_final: 0.6463 (t70) REVERT: J 269 GLU cc_start: 0.5388 (tp30) cc_final: 0.4954 (tp30) REVERT: J 329 SER cc_start: 0.7363 (p) cc_final: 0.6969 (p) REVERT: J 394 THR cc_start: 0.6589 (m) cc_final: 0.6227 (p) REVERT: J 407 LYS cc_start: 0.6955 (tttm) cc_final: 0.6531 (ttpp) REVERT: J 419 ASN cc_start: 0.5631 (m-40) cc_final: 0.4505 (t0) REVERT: J 429 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6561 (ptm160) REVERT: J 434 GLU cc_start: 0.6545 (tp30) cc_final: 0.5570 (pm20) REVERT: K 11 LYS cc_start: 0.5849 (ttmm) cc_final: 0.5572 (ttpp) REVERT: K 50 MET cc_start: 0.7124 (tpp) cc_final: 0.6643 (tpt) REVERT: K 51 MET cc_start: 0.7054 (mtp) cc_final: 0.6746 (mtt) REVERT: K 120 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6607 (mt-10) REVERT: K 149 GLU cc_start: 0.6656 (pt0) cc_final: 0.6195 (pt0) REVERT: K 153 ASP cc_start: 0.6733 (t0) cc_final: 0.6458 (t0) REVERT: K 170 ARG cc_start: 0.6036 (tpp80) cc_final: 0.5680 (tpp80) REVERT: K 254 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6106 (mppt) REVERT: K 265 MET cc_start: 0.5754 (tpp) cc_final: 0.5531 (tpt) REVERT: K 269 GLU cc_start: 0.5401 (tp30) cc_final: 0.4970 (tp30) REVERT: K 329 SER cc_start: 0.7352 (p) cc_final: 0.6953 (p) REVERT: K 394 THR cc_start: 0.6588 (m) cc_final: 0.6226 (p) REVERT: K 407 LYS cc_start: 0.6953 (tttm) cc_final: 0.6528 (ttpp) REVERT: K 419 ASN cc_start: 0.5643 (m-40) cc_final: 0.4519 (t0) REVERT: K 429 ARG cc_start: 0.6802 (ttp80) cc_final: 0.6575 (ptm160) REVERT: K 434 GLU cc_start: 0.6550 (tp30) cc_final: 0.5564 (pm20) REVERT: L 8 ASP cc_start: 0.5774 (m-30) cc_final: 0.5336 (m-30) REVERT: L 16 GLU cc_start: 0.6349 (mm-30) cc_final: 0.6076 (mm-30) REVERT: L 19 ARG cc_start: 0.6348 (mmm160) cc_final: 0.4982 (mmm-85) REVERT: L 37 VAL cc_start: 0.6468 (OUTLIER) cc_final: 0.6119 (m) REVERT: L 50 MET cc_start: 0.6883 (tpp) cc_final: 0.6666 (tpt) REVERT: L 51 MET cc_start: 0.6859 (mtp) cc_final: 0.6569 (mtt) REVERT: L 105 GLU cc_start: 0.6498 (pm20) cc_final: 0.6217 (pm20) REVERT: L 126 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6950 (t0) REVERT: L 149 GLU cc_start: 0.6507 (pt0) cc_final: 0.5898 (pt0) REVERT: L 153 ASP cc_start: 0.6970 (t0) cc_final: 0.6724 (t0) REVERT: L 167 ASN cc_start: 0.6452 (m-40) cc_final: 0.6180 (m-40) REVERT: L 224 LYS cc_start: 0.6676 (mttm) cc_final: 0.6388 (mttp) REVERT: L 269 GLU cc_start: 0.5746 (tp30) cc_final: 0.5044 (tp30) REVERT: L 321 ARG cc_start: 0.6322 (ttt90) cc_final: 0.5708 (ttt90) REVERT: L 329 SER cc_start: 0.7511 (p) cc_final: 0.7197 (p) REVERT: L 352 GLU cc_start: 0.7302 (tp30) cc_final: 0.6982 (tp30) REVERT: L 394 THR cc_start: 0.6863 (m) cc_final: 0.6457 (p) REVERT: L 407 LYS cc_start: 0.7007 (tttm) cc_final: 0.6704 (tttp) REVERT: L 419 ASN cc_start: 0.6020 (m-40) cc_final: 0.4831 (t0) REVERT: L 429 ARG cc_start: 0.6750 (ttp80) cc_final: 0.6513 (ptm-80) REVERT: L 434 GLU cc_start: 0.6434 (tp30) cc_final: 0.5221 (pm20) REVERT: L 438 ASP cc_start: 0.6614 (m-30) cc_final: 0.6192 (m-30) REVERT: L 443 GLN cc_start: 0.7005 (tt0) cc_final: 0.6780 (tt0) outliers start: 62 outliers final: 34 residues processed: 900 average time/residue: 0.8344 time to fit residues: 883.8283 Evaluate side-chains 714 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 671 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 chunk 470 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN D 443 GLN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN J 443 GLN ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN K 443 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 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 = 0.3900 r_free = 0.3900 target = 0.167015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141252 restraints weight = 34527.196| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.09 r_work: 0.3498 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 40900 Z= 0.101 Angle : 0.503 7.859 55360 Z= 0.264 Chirality : 0.041 0.147 5964 Planarity : 0.004 0.053 7260 Dihedral : 5.408 52.602 5421 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.35 % Allowed : 13.63 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.42 (0.12), residues: 4884 helix: 1.97 (0.11), residues: 2028 sheet: 0.22 (0.18), residues: 852 loop : 0.31 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 19 TYR 0.019 0.001 TYR D 296 PHE 0.017 0.001 PHE D 285 TRP 0.010 0.001 TRP G 425 HIS 0.006 0.001 HIS L 195 Details of bonding type rmsd covalent geometry : bond 0.00214 (40900) covalent geometry : angle 0.50346 (55360) hydrogen bonds : bond 0.04072 ( 1557) hydrogen bonds : angle 4.52542 ( 4623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 752 time to evaluate : 1.564 Fit side-chains REVERT: A 8 ASP cc_start: 0.7747 (m-30) cc_final: 0.7520 (m-30) REVERT: A 19 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7246 (mmm-85) REVERT: A 47 ASP cc_start: 0.7988 (m-30) cc_final: 0.7545 (t70) REVERT: A 50 MET cc_start: 0.7975 (tpp) cc_final: 0.7732 (tpt) REVERT: A 149 GLU cc_start: 0.8337 (pt0) cc_final: 0.8107 (pt0) REVERT: A 269 GLU cc_start: 0.6979 (tp30) cc_final: 0.6471 (tp30) REVERT: A 321 ARG cc_start: 0.7941 (ttt90) cc_final: 0.7713 (ttt90) REVERT: A 335 ARG cc_start: 0.8469 (mtp-110) cc_final: 0.8255 (mtp85) REVERT: A 403 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 419 ASN cc_start: 0.8173 (m-40) cc_final: 0.7808 (t0) REVERT: A 434 GLU cc_start: 0.8207 (tp30) cc_final: 0.7828 (pm20) REVERT: A 438 ASP cc_start: 0.8488 (m-30) cc_final: 0.8273 (m-30) REVERT: B 8 ASP cc_start: 0.7716 (m-30) cc_final: 0.7478 (m-30) REVERT: B 17 ASN cc_start: 0.7881 (t0) cc_final: 0.7490 (t0) REVERT: B 119 MET cc_start: 0.8405 (ttp) cc_final: 0.8159 (ttp) REVERT: B 269 GLU cc_start: 0.7066 (tp30) cc_final: 0.6813 (tp30) REVERT: B 321 ARG cc_start: 0.7734 (tmt-80) cc_final: 0.7382 (ttt90) REVERT: B 419 ASN cc_start: 0.8213 (m-40) cc_final: 0.7768 (t0) REVERT: B 427 TYR cc_start: 0.8249 (m-10) cc_final: 0.7923 (t80) REVERT: C 11 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7253 (tptt) REVERT: C 50 MET cc_start: 0.7995 (tpp) cc_final: 0.7745 (tpt) REVERT: C 58 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6067 (mt-10) REVERT: C 254 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6563 (mppt) REVERT: C 269 GLU cc_start: 0.7028 (tp30) cc_final: 0.6766 (tp30) REVERT: C 345 MET cc_start: 0.8941 (mtp) cc_final: 0.8635 (mtp) REVERT: C 419 ASN cc_start: 0.8098 (m-40) cc_final: 0.7713 (t0) REVERT: C 426 ASP cc_start: 0.8569 (m-30) cc_final: 0.8317 (m-30) REVERT: D 11 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7424 (ttpp) REVERT: D 69 TYR cc_start: 0.8234 (m-80) cc_final: 0.8000 (m-80) REVERT: D 119 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8222 (ttp) REVERT: D 223 ARG cc_start: 0.8091 (tpp-160) cc_final: 0.7820 (ttt90) REVERT: D 255 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: D 269 GLU cc_start: 0.7060 (tp30) cc_final: 0.6819 (tp30) REVERT: D 321 ARG cc_start: 0.7760 (tmt-80) cc_final: 0.7432 (ttt90) REVERT: D 363 LYS cc_start: 0.6972 (tppt) cc_final: 0.6754 (mmmt) REVERT: D 419 ASN cc_start: 0.8203 (m-40) cc_final: 0.7753 (t0) REVERT: D 427 TYR cc_start: 0.8241 (m-80) cc_final: 0.7914 (t80) REVERT: E 11 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7473 (ttpp) REVERT: E 17 ASN cc_start: 0.7866 (t0) cc_final: 0.7472 (t0) REVERT: E 50 MET cc_start: 0.7949 (tpp) cc_final: 0.7350 (tpt) REVERT: E 269 GLU cc_start: 0.6996 (tp30) cc_final: 0.6769 (tp30) REVERT: E 363 LYS cc_start: 0.7006 (tppt) cc_final: 0.6786 (mmmt) REVERT: E 366 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7301 (tp30) REVERT: E 419 ASN cc_start: 0.8211 (m-40) cc_final: 0.7765 (t0) REVERT: E 427 TYR cc_start: 0.8225 (m-80) cc_final: 0.7912 (t80) REVERT: E 434 GLU cc_start: 0.8195 (tp30) cc_final: 0.7914 (pm20) REVERT: F 8 ASP cc_start: 0.7791 (m-30) cc_final: 0.7573 (m-30) REVERT: F 19 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7320 (mmm-85) REVERT: F 126 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7447 (t0) REVERT: F 269 GLU cc_start: 0.7004 (tp30) cc_final: 0.6516 (tp30) REVERT: F 321 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7589 (ttt90) REVERT: F 335 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.8217 (mtp85) REVERT: F 363 LYS cc_start: 0.6964 (mmmm) cc_final: 0.6731 (mmmt) REVERT: F 419 ASN cc_start: 0.8212 (m-40) cc_final: 0.7875 (t0) REVERT: F 434 GLU cc_start: 0.8175 (tp30) cc_final: 0.7922 (tp30) REVERT: F 438 ASP cc_start: 0.8473 (m-30) cc_final: 0.8263 (m-30) REVERT: G 8 ASP cc_start: 0.7703 (m-30) cc_final: 0.7479 (m-30) REVERT: G 51 MET cc_start: 0.7969 (ttm) cc_final: 0.7718 (ttm) REVERT: G 255 GLU cc_start: 0.7114 (tt0) cc_final: 0.6803 (pp20) REVERT: G 321 ARG cc_start: 0.7762 (tmt-80) cc_final: 0.7428 (ttt90) REVERT: G 370 GLN cc_start: 0.5445 (OUTLIER) cc_final: 0.5220 (pt0) REVERT: G 419 ASN cc_start: 0.8216 (m-40) cc_final: 0.7779 (t0) REVERT: G 434 GLU cc_start: 0.8217 (tp30) cc_final: 0.7905 (pm20) REVERT: H 8 ASP cc_start: 0.7730 (m-30) cc_final: 0.7512 (m-30) REVERT: H 19 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7259 (mmm-85) REVERT: H 47 ASP cc_start: 0.8016 (m-30) cc_final: 0.7512 (t70) REVERT: H 149 GLU cc_start: 0.8340 (pt0) cc_final: 0.8132 (pt0) REVERT: H 269 GLU cc_start: 0.7086 (tp30) cc_final: 0.6585 (tp30) REVERT: H 321 ARG cc_start: 0.7912 (ttt90) cc_final: 0.7655 (ttt90) REVERT: H 335 ARG cc_start: 0.8443 (mtp-110) cc_final: 0.8242 (mtp85) REVERT: H 419 ASN cc_start: 0.8146 (m-40) cc_final: 0.7836 (t0) REVERT: H 434 GLU cc_start: 0.8200 (tp30) cc_final: 0.7969 (tp30) REVERT: I 11 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7229 (tptt) REVERT: I 50 MET cc_start: 0.8051 (tpp) cc_final: 0.7838 (tpt) REVERT: I 51 MET cc_start: 0.8137 (mtp) cc_final: 0.7842 (ttm) REVERT: I 166 GLU cc_start: 0.8262 (tt0) cc_final: 0.8055 (tt0) REVERT: I 254 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6594 (mppt) REVERT: I 269 GLU cc_start: 0.7015 (tp30) cc_final: 0.6782 (tp30) REVERT: I 345 MET cc_start: 0.8881 (mtp) cc_final: 0.8576 (mtp) REVERT: I 370 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.5543 (pt0) REVERT: I 407 LYS cc_start: 0.8389 (tttm) cc_final: 0.8165 (ttpp) REVERT: I 419 ASN cc_start: 0.8088 (m-40) cc_final: 0.7715 (t0) REVERT: I 426 ASP cc_start: 0.8536 (m-30) cc_final: 0.8295 (m-30) REVERT: J 11 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7193 (tptt) REVERT: J 39 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7757 (t) REVERT: J 50 MET cc_start: 0.8037 (tpp) cc_final: 0.7803 (tpt) REVERT: J 58 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.6066 (mt-10) REVERT: J 159 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8453 (pt) REVERT: J 269 GLU cc_start: 0.6985 (tp30) cc_final: 0.6718 (tp30) REVERT: J 363 LYS cc_start: 0.7038 (mmmm) cc_final: 0.6821 (mmmm) REVERT: J 407 LYS cc_start: 0.8338 (tttm) cc_final: 0.8136 (ttpp) REVERT: J 419 ASN cc_start: 0.8129 (m-40) cc_final: 0.7710 (t0) REVERT: K 11 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7217 (tptt) REVERT: K 39 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7750 (t) REVERT: K 51 MET cc_start: 0.8146 (mtp) cc_final: 0.7896 (ttm) REVERT: K 58 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.6050 (mt-10) REVERT: K 269 GLU cc_start: 0.6977 (tp30) cc_final: 0.6722 (tp30) REVERT: K 363 LYS cc_start: 0.7058 (mmmm) cc_final: 0.6836 (mmmm) REVERT: K 407 LYS cc_start: 0.8351 (tttm) cc_final: 0.8149 (ttpp) REVERT: K 419 ASN cc_start: 0.8106 (m-40) cc_final: 0.7716 (t0) REVERT: L 8 ASP cc_start: 0.7754 (m-30) cc_final: 0.7537 (m-30) REVERT: L 19 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7225 (mmm-85) REVERT: L 47 ASP cc_start: 0.8002 (m-30) cc_final: 0.7519 (t70) REVERT: L 50 MET cc_start: 0.7962 (tpp) cc_final: 0.7749 (tpt) REVERT: L 51 MET cc_start: 0.8323 (mtp) cc_final: 0.8024 (ttm) REVERT: L 149 GLU cc_start: 0.8329 (pt0) cc_final: 0.8127 (pt0) REVERT: L 269 GLU cc_start: 0.7088 (tp30) cc_final: 0.6619 (tp30) REVERT: L 321 ARG cc_start: 0.7899 (ttt90) cc_final: 0.7662 (ttt90) REVERT: L 335 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8265 (mtp85) REVERT: L 419 ASN cc_start: 0.8150 (m-40) cc_final: 0.7816 (t0) REVERT: L 434 GLU cc_start: 0.8221 (tp30) cc_final: 0.7839 (pm20) REVERT: L 438 ASP cc_start: 0.8477 (m-30) cc_final: 0.8256 (m-30) outliers start: 102 outliers final: 34 residues processed: 835 average time/residue: 0.8407 time to fit residues: 826.8614 Evaluate side-chains 656 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 609 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 381 optimal weight: 0.0980 chunk 378 optimal weight: 0.6980 chunk 394 optimal weight: 7.9990 chunk 488 optimal weight: 0.3980 chunk 458 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 373 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 225 HIS D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS G 226 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 443 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137353 restraints weight = 34092.962| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.08 r_work: 0.3449 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40900 Z= 0.115 Angle : 0.506 7.076 55360 Z= 0.272 Chirality : 0.041 0.152 5964 Planarity : 0.004 0.073 7260 Dihedral : 5.097 44.570 5386 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 12.74 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.37 (0.12), residues: 4884 helix: 2.02 (0.11), residues: 2028 sheet: -0.03 (0.17), residues: 912 loop : 0.32 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 170 TYR 0.022 0.002 TYR G 296 PHE 0.020 0.002 PHE H 285 TRP 0.010 0.001 TRP E 425 HIS 0.006 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00251 (40900) covalent geometry : angle 0.50582 (55360) hydrogen bonds : bond 0.04408 ( 1557) hydrogen bonds : angle 4.41328 ( 4623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 623 time to evaluate : 1.273 Fit side-chains REVERT: A 8 ASP cc_start: 0.7770 (m-30) cc_final: 0.7549 (m-30) REVERT: A 19 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7265 (mmm-85) REVERT: A 47 ASP cc_start: 0.7999 (m-30) cc_final: 0.7597 (t70) REVERT: A 269 GLU cc_start: 0.6995 (tp30) cc_final: 0.6481 (tp30) REVERT: A 321 ARG cc_start: 0.7963 (ttt90) cc_final: 0.7729 (ttt90) REVERT: A 335 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.8231 (mtp85) REVERT: A 403 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 419 ASN cc_start: 0.8245 (m-40) cc_final: 0.7846 (t0) REVERT: A 434 GLU cc_start: 0.8318 (tp30) cc_final: 0.7993 (pm20) REVERT: B 8 ASP cc_start: 0.7787 (m-30) cc_final: 0.7556 (m-30) REVERT: B 269 GLU cc_start: 0.7084 (tp30) cc_final: 0.6835 (tp30) REVERT: B 321 ARG cc_start: 0.7896 (tmt-80) cc_final: 0.7574 (ttt90) REVERT: B 363 LYS cc_start: 0.7154 (tppt) cc_final: 0.6935 (mmmt) REVERT: B 419 ASN cc_start: 0.8217 (m-40) cc_final: 0.7730 (t0) REVERT: B 427 TYR cc_start: 0.8312 (m-80) cc_final: 0.7953 (t80) REVERT: C 11 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7257 (tptt) REVERT: C 17 ASN cc_start: 0.8042 (t0) cc_final: 0.7608 (t0) REVERT: C 58 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6136 (mt-10) REVERT: C 149 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: C 254 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6593 (mppt) REVERT: C 269 GLU cc_start: 0.7013 (tp30) cc_final: 0.6761 (tp30) REVERT: C 363 LYS cc_start: 0.7445 (mmmt) cc_final: 0.6987 (mmmm) REVERT: C 419 ASN cc_start: 0.8099 (m-40) cc_final: 0.7683 (t0) REVERT: D 39 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7866 (m) REVERT: D 69 TYR cc_start: 0.8385 (m-80) cc_final: 0.8156 (m-80) REVERT: D 255 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6803 (pp20) REVERT: D 269 GLU cc_start: 0.7030 (tp30) cc_final: 0.6762 (tp30) REVERT: D 321 ARG cc_start: 0.7855 (tmt-80) cc_final: 0.7608 (ttt90) REVERT: D 363 LYS cc_start: 0.7092 (tppt) cc_final: 0.6865 (mmmt) REVERT: D 419 ASN cc_start: 0.8217 (m-40) cc_final: 0.7737 (t0) REVERT: D 427 TYR cc_start: 0.8336 (m-80) cc_final: 0.7950 (t80) REVERT: D 434 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7973 (pm20) REVERT: E 39 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7880 (m) REVERT: E 50 MET cc_start: 0.8049 (tpp) cc_final: 0.7390 (tpt) REVERT: E 269 GLU cc_start: 0.6962 (tp30) cc_final: 0.6748 (tp30) REVERT: E 363 LYS cc_start: 0.7156 (tppt) cc_final: 0.6944 (mmmt) REVERT: E 366 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7345 (tp30) REVERT: E 419 ASN cc_start: 0.8216 (m-40) cc_final: 0.7738 (t0) REVERT: E 427 TYR cc_start: 0.8311 (m-80) cc_final: 0.7955 (t80) REVERT: E 434 GLU cc_start: 0.8189 (tp30) cc_final: 0.7950 (pm20) REVERT: F 8 ASP cc_start: 0.7800 (m-30) cc_final: 0.7576 (m-30) REVERT: F 19 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7317 (mmm-85) REVERT: F 47 ASP cc_start: 0.8013 (m-30) cc_final: 0.7520 (t70) REVERT: F 126 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7491 (t0) REVERT: F 184 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: F 269 GLU cc_start: 0.6976 (tp30) cc_final: 0.6489 (tp30) REVERT: F 307 CYS cc_start: 0.7669 (m) cc_final: 0.7352 (m) REVERT: F 321 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7750 (ttt90) REVERT: F 335 ARG cc_start: 0.8449 (mtp-110) cc_final: 0.8228 (mtp85) REVERT: F 419 ASN cc_start: 0.8248 (m-40) cc_final: 0.7853 (t0) REVERT: G 8 ASP cc_start: 0.7821 (m-30) cc_final: 0.7588 (m-30) REVERT: G 39 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7904 (m) REVERT: G 51 MET cc_start: 0.7951 (ttm) cc_final: 0.7737 (ttm) REVERT: G 254 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6868 (mttp) REVERT: G 255 GLU cc_start: 0.7106 (tt0) cc_final: 0.6799 (pp20) REVERT: G 321 ARG cc_start: 0.7855 (tmt-80) cc_final: 0.7608 (ttt90) REVERT: G 370 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.5338 (pt0) REVERT: G 419 ASN cc_start: 0.8224 (m-40) cc_final: 0.7779 (t0) REVERT: G 434 GLU cc_start: 0.8216 (tp30) cc_final: 0.7958 (pm20) REVERT: H 8 ASP cc_start: 0.7713 (m-30) cc_final: 0.7495 (m-30) REVERT: H 19 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7228 (mmm-85) REVERT: H 47 ASP cc_start: 0.8023 (m-30) cc_final: 0.7606 (t70) REVERT: H 269 GLU cc_start: 0.7114 (tp30) cc_final: 0.6596 (tp30) REVERT: H 321 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7739 (ttt90) REVERT: H 335 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8197 (mtp85) REVERT: H 419 ASN cc_start: 0.8235 (m-40) cc_final: 0.7867 (t0) REVERT: I 11 LYS cc_start: 0.7941 (ttmm) cc_final: 0.7260 (tptt) REVERT: I 51 MET cc_start: 0.8162 (mtp) cc_final: 0.7827 (ttm) REVERT: I 254 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6599 (mppt) REVERT: I 363 LYS cc_start: 0.7388 (mmmt) cc_final: 0.6967 (mmmm) REVERT: I 419 ASN cc_start: 0.8101 (m-40) cc_final: 0.7681 (t0) REVERT: J 11 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7271 (tptt) REVERT: J 17 ASN cc_start: 0.8052 (t0) cc_final: 0.7627 (t0) REVERT: J 58 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6139 (mt-10) REVERT: J 149 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: J 269 GLU cc_start: 0.7009 (tp30) cc_final: 0.6736 (tp30) REVERT: J 370 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.5528 (pt0) REVERT: J 407 LYS cc_start: 0.8398 (tttm) cc_final: 0.8186 (ttpp) REVERT: J 419 ASN cc_start: 0.8159 (m-40) cc_final: 0.7712 (t0) REVERT: K 11 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7264 (tptt) REVERT: K 51 MET cc_start: 0.8161 (mtp) cc_final: 0.7888 (ttm) REVERT: K 58 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6089 (mt-10) REVERT: K 149 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: K 269 GLU cc_start: 0.7036 (tp30) cc_final: 0.6752 (tp30) REVERT: K 370 GLN cc_start: 0.5790 (OUTLIER) cc_final: 0.5539 (pt0) REVERT: K 407 LYS cc_start: 0.8397 (tttm) cc_final: 0.8186 (ttpp) REVERT: K 419 ASN cc_start: 0.8127 (m-40) cc_final: 0.7692 (t0) REVERT: L 8 ASP cc_start: 0.7787 (m-30) cc_final: 0.7570 (m-30) REVERT: L 19 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7268 (mmm-85) REVERT: L 47 ASP cc_start: 0.8010 (m-30) cc_final: 0.7569 (t70) REVERT: L 50 MET cc_start: 0.8023 (tpp) cc_final: 0.7778 (tpt) REVERT: L 51 MET cc_start: 0.8293 (mtp) cc_final: 0.7958 (ttm) REVERT: L 269 GLU cc_start: 0.7149 (tp30) cc_final: 0.6630 (tp30) REVERT: L 321 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7743 (ttt90) REVERT: L 335 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8216 (mtp85) REVERT: L 419 ASN cc_start: 0.8236 (m-40) cc_final: 0.7852 (t0) outliers start: 124 outliers final: 40 residues processed: 721 average time/residue: 0.8200 time to fit residues: 698.8550 Evaluate side-chains 669 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 611 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 319 LEU Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 370 GLN Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 200 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 443 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 399 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 452 optimal weight: 9.9990 chunk 411 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 111 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 111 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 111 ASN E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 212 GLN F 225 HIS F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 111 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN K 443 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN L 443 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132380 restraints weight = 33683.687| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.06 r_work: 0.3387 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 40900 Z= 0.204 Angle : 0.635 7.959 55360 Z= 0.348 Chirality : 0.046 0.167 5964 Planarity : 0.006 0.058 7260 Dihedral : 5.916 57.762 5384 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.04 % Allowed : 11.86 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.05 (0.12), residues: 4884 helix: 1.68 (0.11), residues: 2028 sheet: -0.12 (0.17), residues: 912 loop : 0.20 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 114 TYR 0.033 0.003 TYR E 296 PHE 0.031 0.002 PHE C 285 TRP 0.015 0.002 TRP E 425 HIS 0.007 0.002 HIS H 71 Details of bonding type rmsd covalent geometry : bond 0.00464 (40900) covalent geometry : angle 0.63486 (55360) hydrogen bonds : bond 0.05744 ( 1557) hydrogen bonds : angle 4.67834 ( 4623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 636 time to evaluate : 1.503 Fit side-chains REVERT: A 8 ASP cc_start: 0.7943 (m-30) cc_final: 0.7722 (m-30) REVERT: A 19 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7356 (mmm-85) REVERT: A 47 ASP cc_start: 0.8016 (m-30) cc_final: 0.7622 (t70) REVERT: A 178 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7955 (t70) REVERT: A 254 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6789 (mppt) REVERT: A 269 GLU cc_start: 0.7084 (tp30) cc_final: 0.6527 (tp30) REVERT: A 321 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7804 (ttt90) REVERT: A 335 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8246 (mtp85) REVERT: A 403 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 419 ASN cc_start: 0.8240 (m-40) cc_final: 0.7809 (t0) REVERT: A 434 GLU cc_start: 0.8181 (tp30) cc_final: 0.7934 (pm20) REVERT: B 8 ASP cc_start: 0.8036 (m-30) cc_final: 0.7772 (m-30) REVERT: B 17 ASN cc_start: 0.7965 (t0) cc_final: 0.7521 (t0) REVERT: B 269 GLU cc_start: 0.7191 (tp30) cc_final: 0.6843 (tp30) REVERT: B 321 ARG cc_start: 0.7996 (tmt-80) cc_final: 0.7703 (ttp80) REVERT: B 363 LYS cc_start: 0.7379 (tppt) cc_final: 0.6829 (mmmm) REVERT: B 370 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.5319 (pt0) REVERT: B 386 GLN cc_start: 0.7713 (mt0) cc_final: 0.7202 (mt0) REVERT: B 419 ASN cc_start: 0.8254 (m-40) cc_final: 0.7774 (t0) REVERT: B 427 TYR cc_start: 0.8390 (m-80) cc_final: 0.7997 (t80) REVERT: C 11 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7289 (tptt) REVERT: C 142 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7198 (mp0) REVERT: C 149 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8435 (pt0) REVERT: C 184 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: C 254 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6600 (mppt) REVERT: C 269 GLU cc_start: 0.7094 (tp30) cc_final: 0.6685 (mm-30) REVERT: C 363 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7193 (mmmm) REVERT: C 419 ASN cc_start: 0.8158 (m-40) cc_final: 0.7720 (t0) REVERT: D 269 GLU cc_start: 0.7131 (tp30) cc_final: 0.6801 (tp30) REVERT: D 419 ASN cc_start: 0.8282 (m-40) cc_final: 0.7789 (t0) REVERT: D 427 TYR cc_start: 0.8379 (m-80) cc_final: 0.7985 (t80) REVERT: D 434 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8022 (pm20) REVERT: E 8 ASP cc_start: 0.8104 (m-30) cc_final: 0.7812 (m-30) REVERT: E 17 ASN cc_start: 0.7960 (t0) cc_final: 0.7482 (t0) REVERT: E 269 GLU cc_start: 0.7027 (tp30) cc_final: 0.6756 (tp30) REVERT: E 366 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7465 (tp30) REVERT: E 419 ASN cc_start: 0.8266 (m-40) cc_final: 0.7791 (t0) REVERT: E 427 TYR cc_start: 0.8384 (m-80) cc_final: 0.7995 (t80) REVERT: E 434 GLU cc_start: 0.8306 (tp30) cc_final: 0.7991 (pm20) REVERT: F 8 ASP cc_start: 0.7943 (m-30) cc_final: 0.7731 (m-30) REVERT: F 19 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7327 (mmm-85) REVERT: F 22 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8203 (mmt-90) REVERT: F 47 ASP cc_start: 0.8061 (m-30) cc_final: 0.7560 (t70) REVERT: F 178 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7947 (t70) REVERT: F 184 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: F 269 GLU cc_start: 0.7061 (tp30) cc_final: 0.6505 (tp30) REVERT: F 321 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7769 (ttt90) REVERT: F 335 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8218 (mtp85) REVERT: F 403 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7424 (mm-30) REVERT: F 419 ASN cc_start: 0.8251 (m-40) cc_final: 0.7836 (t0) REVERT: G 8 ASP cc_start: 0.8038 (m-30) cc_final: 0.7773 (m-30) REVERT: G 370 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5482 (pt0) REVERT: G 419 ASN cc_start: 0.8263 (m-40) cc_final: 0.7798 (t0) REVERT: G 434 GLU cc_start: 0.8292 (tp30) cc_final: 0.7981 (pm20) REVERT: H 8 ASP cc_start: 0.7914 (m-30) cc_final: 0.7683 (m-30) REVERT: H 19 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7304 (mmm-85) REVERT: H 47 ASP cc_start: 0.8076 (m-30) cc_final: 0.7665 (t70) REVERT: H 269 GLU cc_start: 0.7055 (tp30) cc_final: 0.6510 (tp30) REVERT: H 321 ARG cc_start: 0.8047 (ttt90) cc_final: 0.7787 (ttt90) REVERT: H 335 ARG cc_start: 0.8453 (mtp-110) cc_final: 0.8203 (mtp85) REVERT: H 403 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7402 (mm-30) REVERT: H 419 ASN cc_start: 0.8214 (m-40) cc_final: 0.7817 (t0) REVERT: I 11 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7291 (tptt) REVERT: I 51 MET cc_start: 0.8048 (mtp) cc_final: 0.7736 (ttm) REVERT: I 142 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7221 (mp0) REVERT: I 254 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6503 (mppt) REVERT: I 363 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7097 (mmmm) REVERT: I 419 ASN cc_start: 0.8168 (m-40) cc_final: 0.7721 (t0) REVERT: J 11 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7279 (tptt) REVERT: J 58 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: J 149 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: J 269 GLU cc_start: 0.6998 (tp30) cc_final: 0.6797 (tp30) REVERT: J 419 ASN cc_start: 0.8189 (m-40) cc_final: 0.7729 (t0) REVERT: K 11 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7281 (tptt) REVERT: K 17 ASN cc_start: 0.8097 (t0) cc_final: 0.7672 (t0) REVERT: K 51 MET cc_start: 0.7990 (mtp) cc_final: 0.7786 (ttm) REVERT: K 58 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: K 149 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: K 254 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6636 (mppt) REVERT: K 269 GLU cc_start: 0.6993 (tp30) cc_final: 0.6789 (tp30) REVERT: K 419 ASN cc_start: 0.8157 (m-40) cc_final: 0.7701 (t0) REVERT: L 8 ASP cc_start: 0.7914 (m-30) cc_final: 0.7692 (m-30) REVERT: L 19 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7344 (mmm-85) REVERT: L 47 ASP cc_start: 0.8006 (m-30) cc_final: 0.7593 (t70) REVERT: L 51 MET cc_start: 0.8191 (mtp) cc_final: 0.7902 (ttm) REVERT: L 269 GLU cc_start: 0.7104 (tp30) cc_final: 0.6537 (tp30) REVERT: L 321 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7807 (ttt90) REVERT: L 335 ARG cc_start: 0.8463 (mtp-110) cc_final: 0.8210 (mtp85) REVERT: L 403 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7423 (mm-30) REVERT: L 419 ASN cc_start: 0.8215 (m-40) cc_final: 0.7812 (t0) outliers start: 132 outliers final: 56 residues processed: 751 average time/residue: 0.8086 time to fit residues: 720.9597 Evaluate side-chains 683 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 611 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 483 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 335 optimal weight: 0.2980 chunk 152 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 412 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 467 optimal weight: 0.9990 chunk 186 optimal weight: 0.0020 chunk 91 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 443 GLN C 17 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 402 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN I 17 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 443 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137377 restraints weight = 33924.164| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.07 r_work: 0.3449 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 40900 Z= 0.097 Angle : 0.475 6.226 55360 Z= 0.257 Chirality : 0.040 0.147 5964 Planarity : 0.004 0.055 7260 Dihedral : 5.420 57.153 5384 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.84 % Allowed : 13.17 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.50 (0.12), residues: 4884 helix: 2.04 (0.12), residues: 2028 sheet: 0.27 (0.17), residues: 852 loop : 0.36 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 170 TYR 0.020 0.001 TYR I 296 PHE 0.015 0.001 PHE H 285 TRP 0.010 0.001 TRP G 425 HIS 0.005 0.001 HIS L 195 Details of bonding type rmsd covalent geometry : bond 0.00212 (40900) covalent geometry : angle 0.47524 (55360) hydrogen bonds : bond 0.03830 ( 1557) hydrogen bonds : angle 4.27750 ( 4623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 612 time to evaluate : 1.547 Fit side-chains REVERT: A 8 ASP cc_start: 0.7875 (m-30) cc_final: 0.7637 (m-30) REVERT: A 19 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7288 (mmm-85) REVERT: A 47 ASP cc_start: 0.7988 (m-30) cc_final: 0.7506 (t70) REVERT: A 178 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 269 GLU cc_start: 0.6976 (tp30) cc_final: 0.6380 (tp30) REVERT: A 321 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7731 (ttt90) REVERT: A 335 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.8234 (mtp85) REVERT: A 403 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 419 ASN cc_start: 0.8302 (m-40) cc_final: 0.7841 (t0) REVERT: A 434 GLU cc_start: 0.8125 (tp30) cc_final: 0.7890 (pm20) REVERT: B 8 ASP cc_start: 0.7910 (m-30) cc_final: 0.7651 (m-30) REVERT: B 69 TYR cc_start: 0.8437 (m-80) cc_final: 0.8170 (m-80) REVERT: B 269 GLU cc_start: 0.7068 (tp30) cc_final: 0.6743 (tp30) REVERT: B 321 ARG cc_start: 0.7922 (tmt-80) cc_final: 0.7694 (ttp80) REVERT: B 419 ASN cc_start: 0.8199 (m-40) cc_final: 0.7706 (t0) REVERT: B 427 TYR cc_start: 0.8317 (m-80) cc_final: 0.7956 (t80) REVERT: C 11 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7182 (tptt) REVERT: C 17 ASN cc_start: 0.8074 (t0) cc_final: 0.7651 (t0) REVERT: C 254 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6577 (mppt) REVERT: C 269 GLU cc_start: 0.6978 (tp30) cc_final: 0.6689 (tp30) REVERT: C 345 MET cc_start: 0.8932 (mtp) cc_final: 0.8639 (mtp) REVERT: C 363 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7174 (mmmm) REVERT: C 419 ASN cc_start: 0.8086 (m-40) cc_final: 0.7658 (t0) REVERT: D 69 TYR cc_start: 0.8509 (m-80) cc_final: 0.8305 (m-80) REVERT: D 269 GLU cc_start: 0.7054 (tp30) cc_final: 0.6743 (tp30) REVERT: D 419 ASN cc_start: 0.8221 (m-40) cc_final: 0.7719 (t0) REVERT: D 427 TYR cc_start: 0.8320 (m-80) cc_final: 0.7947 (t80) REVERT: D 434 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7898 (pm20) REVERT: E 8 ASP cc_start: 0.8019 (m-30) cc_final: 0.7745 (m-30) REVERT: E 269 GLU cc_start: 0.6888 (tp30) cc_final: 0.6652 (tp30) REVERT: E 419 ASN cc_start: 0.8208 (m-40) cc_final: 0.7718 (t0) REVERT: E 427 TYR cc_start: 0.8297 (m-80) cc_final: 0.7945 (t80) REVERT: E 434 GLU cc_start: 0.8187 (tp30) cc_final: 0.7931 (pm20) REVERT: F 8 ASP cc_start: 0.7843 (m-30) cc_final: 0.7613 (m-30) REVERT: F 19 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7259 (mmm-85) REVERT: F 22 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7953 (mmt-90) REVERT: F 47 ASP cc_start: 0.8023 (m-30) cc_final: 0.7500 (t70) REVERT: F 126 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7475 (t0) REVERT: F 178 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: F 184 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: F 269 GLU cc_start: 0.6987 (tp30) cc_final: 0.6465 (tp30) REVERT: F 321 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7701 (ttt90) REVERT: F 335 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8241 (mtp85) REVERT: F 403 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7305 (mm-30) REVERT: F 419 ASN cc_start: 0.8276 (m-40) cc_final: 0.7846 (t0) REVERT: G 8 ASP cc_start: 0.7938 (m-30) cc_final: 0.7670 (m-30) REVERT: G 255 GLU cc_start: 0.7164 (tt0) cc_final: 0.6755 (pp20) REVERT: G 419 ASN cc_start: 0.8219 (m-40) cc_final: 0.7741 (t0) REVERT: G 434 GLU cc_start: 0.8192 (tp30) cc_final: 0.7918 (pm20) REVERT: H 8 ASP cc_start: 0.7824 (m-30) cc_final: 0.7568 (m-30) REVERT: H 19 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7246 (mmm-85) REVERT: H 47 ASP cc_start: 0.8046 (m-30) cc_final: 0.7566 (t70) REVERT: H 269 GLU cc_start: 0.7016 (tp30) cc_final: 0.6476 (tp30) REVERT: H 321 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7705 (ttt90) REVERT: H 335 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8238 (mtp85) REVERT: H 403 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7247 (mm-30) REVERT: H 419 ASN cc_start: 0.8230 (m-40) cc_final: 0.7823 (t0) REVERT: I 11 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7185 (tptt) REVERT: I 17 ASN cc_start: 0.8076 (t0) cc_final: 0.7675 (t0) REVERT: I 51 MET cc_start: 0.8136 (mtp) cc_final: 0.7811 (ttm) REVERT: I 149 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: I 254 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6590 (mppt) REVERT: I 345 MET cc_start: 0.8928 (mtp) cc_final: 0.8635 (mtp) REVERT: I 363 LYS cc_start: 0.7506 (mmmt) cc_final: 0.7073 (mmmm) REVERT: I 419 ASN cc_start: 0.8073 (m-40) cc_final: 0.7640 (t0) REVERT: J 11 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7201 (tptt) REVERT: J 17 ASN cc_start: 0.8070 (t0) cc_final: 0.7648 (t0) REVERT: J 345 MET cc_start: 0.8917 (mtp) cc_final: 0.8610 (mtp) REVERT: J 419 ASN cc_start: 0.8148 (m-40) cc_final: 0.7692 (t0) REVERT: K 11 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7189 (tptt) REVERT: K 17 ASN cc_start: 0.8092 (t0) cc_final: 0.7683 (t0) REVERT: K 51 MET cc_start: 0.7980 (mtp) cc_final: 0.7780 (ttm) REVERT: K 254 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6588 (mppt) REVERT: K 345 MET cc_start: 0.8923 (mtp) cc_final: 0.8615 (mtp) REVERT: K 419 ASN cc_start: 0.8118 (m-40) cc_final: 0.7671 (t0) REVERT: L 8 ASP cc_start: 0.7869 (m-30) cc_final: 0.7627 (m-30) REVERT: L 19 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7224 (mmm-85) REVERT: L 47 ASP cc_start: 0.7982 (m-30) cc_final: 0.7545 (t70) REVERT: L 51 MET cc_start: 0.8184 (mtp) cc_final: 0.7840 (ttm) REVERT: L 269 GLU cc_start: 0.7069 (tp30) cc_final: 0.6508 (tp30) REVERT: L 321 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7727 (ttt90) REVERT: L 335 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.8243 (mtp85) REVERT: L 403 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7299 (mm-30) REVERT: L 419 ASN cc_start: 0.8249 (m-40) cc_final: 0.7827 (t0) outliers start: 80 outliers final: 44 residues processed: 683 average time/residue: 0.8225 time to fit residues: 665.7344 Evaluate side-chains 655 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 602 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 149 GLU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 129 optimal weight: 0.2980 chunk 213 optimal weight: 7.9990 chunk 469 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 486 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 360 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 225 HIS B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 24 GLN H 245 HIS H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN L 443 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131255 restraints weight = 33758.634| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.06 r_work: 0.3373 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40900 Z= 0.237 Angle : 0.663 8.160 55360 Z= 0.365 Chirality : 0.047 0.171 5964 Planarity : 0.007 0.063 7260 Dihedral : 6.028 58.760 5382 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.49 % Allowed : 12.34 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.96 (0.12), residues: 4884 helix: 1.62 (0.11), residues: 2028 sheet: -0.23 (0.17), residues: 912 loop : 0.18 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 114 TYR 0.035 0.003 TYR D 296 PHE 0.032 0.002 PHE C 285 TRP 0.016 0.003 TRP E 425 HIS 0.007 0.002 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00546 (40900) covalent geometry : angle 0.66331 (55360) hydrogen bonds : bond 0.06029 ( 1557) hydrogen bonds : angle 4.69909 ( 4623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 624 time to evaluate : 1.637 Fit side-chains REVERT: A 8 ASP cc_start: 0.7945 (m-30) cc_final: 0.7723 (m-30) REVERT: A 19 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7353 (mmm-85) REVERT: A 47 ASP cc_start: 0.8026 (m-30) cc_final: 0.7539 (t70) REVERT: A 178 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7960 (t70) REVERT: A 269 GLU cc_start: 0.7083 (tp30) cc_final: 0.6450 (tp30) REVERT: A 321 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7771 (ttt90) REVERT: A 335 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8255 (mtp85) REVERT: A 403 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 419 ASN cc_start: 0.8215 (m-40) cc_final: 0.7790 (t0) REVERT: B 8 ASP cc_start: 0.8051 (m-30) cc_final: 0.7828 (m-30) REVERT: B 17 ASN cc_start: 0.7961 (t0) cc_final: 0.7478 (t0) REVERT: B 269 GLU cc_start: 0.7161 (tp30) cc_final: 0.6767 (tp30) REVERT: B 321 ARG cc_start: 0.8001 (tmt-80) cc_final: 0.7780 (ttp80) REVERT: B 370 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5622 (pt0) REVERT: B 386 GLN cc_start: 0.7746 (mt0) cc_final: 0.7258 (mt0) REVERT: B 419 ASN cc_start: 0.8258 (m-40) cc_final: 0.7772 (t0) REVERT: B 427 TYR cc_start: 0.8421 (m-80) cc_final: 0.8002 (t80) REVERT: C 11 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7312 (tptt) REVERT: C 142 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7238 (mp0) REVERT: C 149 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: C 254 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6624 (mppt) REVERT: C 269 GLU cc_start: 0.7133 (tp30) cc_final: 0.6740 (mm-30) REVERT: C 363 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7234 (mmmm) REVERT: C 419 ASN cc_start: 0.8162 (m-40) cc_final: 0.7721 (t0) REVERT: D 269 GLU cc_start: 0.7117 (tp30) cc_final: 0.6745 (tp30) REVERT: D 386 GLN cc_start: 0.7743 (mt0) cc_final: 0.7255 (mt0) REVERT: D 419 ASN cc_start: 0.8262 (m-40) cc_final: 0.7786 (t0) REVERT: D 427 TYR cc_start: 0.8414 (m-80) cc_final: 0.7992 (t80) REVERT: D 434 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8025 (pm20) REVERT: E 8 ASP cc_start: 0.8135 (m-30) cc_final: 0.7863 (m-30) REVERT: E 17 ASN cc_start: 0.7963 (t0) cc_final: 0.7477 (t0) REVERT: E 269 GLU cc_start: 0.7072 (tp30) cc_final: 0.6784 (tp30) REVERT: E 321 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7555 (ttt90) REVERT: E 386 GLN cc_start: 0.7760 (mt0) cc_final: 0.7260 (mt0) REVERT: E 419 ASN cc_start: 0.8270 (m-40) cc_final: 0.7796 (t0) REVERT: E 427 TYR cc_start: 0.8405 (m-80) cc_final: 0.7985 (t80) REVERT: E 434 GLU cc_start: 0.8351 (tp30) cc_final: 0.8063 (pm20) REVERT: F 8 ASP cc_start: 0.7923 (m-30) cc_final: 0.7717 (m-30) REVERT: F 19 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7322 (mmm-85) REVERT: F 22 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8191 (mmt-90) REVERT: F 47 ASP cc_start: 0.8078 (m-30) cc_final: 0.7577 (t70) REVERT: F 178 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (t70) REVERT: F 184 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: F 269 GLU cc_start: 0.7114 (tp30) cc_final: 0.6524 (tp30) REVERT: F 321 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7751 (ttt90) REVERT: F 335 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8267 (mtp85) REVERT: F 403 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7440 (mm-30) REVERT: F 419 ASN cc_start: 0.8262 (m-40) cc_final: 0.7840 (t0) REVERT: G 8 ASP cc_start: 0.7997 (m-30) cc_final: 0.7768 (m-30) REVERT: G 386 GLN cc_start: 0.7749 (mt0) cc_final: 0.7264 (mt0) REVERT: G 419 ASN cc_start: 0.8252 (m-40) cc_final: 0.7787 (t0) REVERT: G 434 GLU cc_start: 0.8318 (tp30) cc_final: 0.8062 (pm20) REVERT: H 8 ASP cc_start: 0.7915 (m-30) cc_final: 0.7685 (m-30) REVERT: H 19 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7314 (mmm-85) REVERT: H 22 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8217 (mtm-85) REVERT: H 47 ASP cc_start: 0.8027 (m-30) cc_final: 0.7571 (t70) REVERT: H 269 GLU cc_start: 0.7058 (tp30) cc_final: 0.6546 (tp30) REVERT: H 321 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7748 (ttt90) REVERT: H 403 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7415 (mm-30) REVERT: H 419 ASN cc_start: 0.8257 (m-40) cc_final: 0.7851 (t0) REVERT: I 11 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7292 (tptt) REVERT: I 51 MET cc_start: 0.7988 (mtp) cc_final: 0.7705 (ttm) REVERT: I 142 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7268 (mp0) REVERT: I 254 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6514 (mppt) REVERT: I 363 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7222 (mmmm) REVERT: I 419 ASN cc_start: 0.8166 (m-40) cc_final: 0.7713 (t0) REVERT: J 11 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7306 (tptt) REVERT: J 149 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: J 419 ASN cc_start: 0.8208 (m-40) cc_final: 0.7737 (t0) REVERT: K 11 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7282 (tptt) REVERT: K 149 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: K 254 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6629 (mppt) REVERT: K 419 ASN cc_start: 0.8180 (m-40) cc_final: 0.7722 (t0) REVERT: L 8 ASP cc_start: 0.7919 (m-30) cc_final: 0.7696 (m-30) REVERT: L 19 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7350 (mmm-85) REVERT: L 47 ASP cc_start: 0.8023 (m-30) cc_final: 0.7557 (t70) REVERT: L 269 GLU cc_start: 0.7106 (tp30) cc_final: 0.6572 (tp30) REVERT: L 321 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7778 (ttt90) REVERT: L 403 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7441 (mm-30) REVERT: L 419 ASN cc_start: 0.8257 (m-40) cc_final: 0.7842 (t0) outliers start: 108 outliers final: 66 residues processed: 714 average time/residue: 0.8077 time to fit residues: 685.3411 Evaluate side-chains 693 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 614 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 319 LEU Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 137 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 489 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 422 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 490 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 443 GLN C 17 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 443 GLN H 24 GLN H 443 GLN I 17 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN J 17 ASN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 24 GLN L 443 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135938 restraints weight = 34114.854| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.06 r_work: 0.3432 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40900 Z= 0.104 Angle : 0.488 5.696 55360 Z= 0.265 Chirality : 0.041 0.147 5964 Planarity : 0.004 0.052 7260 Dihedral : 5.560 59.853 5382 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.84 % Allowed : 12.94 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.35 (0.12), residues: 4884 helix: 1.99 (0.12), residues: 2028 sheet: -0.19 (0.17), residues: 912 loop : 0.41 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 170 TYR 0.022 0.002 TYR I 296 PHE 0.016 0.001 PHE G 285 TRP 0.011 0.001 TRP G 425 HIS 0.005 0.001 HIS L 195 Details of bonding type rmsd covalent geometry : bond 0.00229 (40900) covalent geometry : angle 0.48777 (55360) hydrogen bonds : bond 0.04030 ( 1557) hydrogen bonds : angle 4.29578 ( 4623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 607 time to evaluate : 1.563 Fit side-chains REVERT: A 8 ASP cc_start: 0.7882 (m-30) cc_final: 0.7628 (m-30) REVERT: A 19 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7333 (mmm-85) REVERT: A 47 ASP cc_start: 0.7981 (m-30) cc_final: 0.7538 (t70) REVERT: A 159 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 178 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: A 269 GLU cc_start: 0.6976 (tp30) cc_final: 0.6382 (tp30) REVERT: A 321 ARG cc_start: 0.7974 (ttt90) cc_final: 0.7723 (ttt90) REVERT: A 335 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.8186 (mtp85) REVERT: A 403 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 419 ASN cc_start: 0.8279 (m-40) cc_final: 0.7825 (t0) REVERT: B 8 ASP cc_start: 0.7917 (m-30) cc_final: 0.7622 (m-30) REVERT: B 69 TYR cc_start: 0.8431 (m-80) cc_final: 0.8193 (m-80) REVERT: B 269 GLU cc_start: 0.7080 (tp30) cc_final: 0.6726 (tp30) REVERT: B 321 ARG cc_start: 0.7931 (tmt-80) cc_final: 0.7709 (ttp80) REVERT: B 386 GLN cc_start: 0.7768 (mt0) cc_final: 0.7274 (mt0) REVERT: B 419 ASN cc_start: 0.8236 (m-40) cc_final: 0.7733 (t0) REVERT: B 427 TYR cc_start: 0.8337 (m-80) cc_final: 0.7963 (t80) REVERT: C 11 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7208 (tptt) REVERT: C 17 ASN cc_start: 0.8077 (t0) cc_final: 0.7642 (t0) REVERT: C 254 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6586 (mppt) REVERT: C 269 GLU cc_start: 0.7018 (tp30) cc_final: 0.6798 (tp30) REVERT: C 345 MET cc_start: 0.8959 (mtp) cc_final: 0.8708 (mtp) REVERT: C 363 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7233 (mmmm) REVERT: C 419 ASN cc_start: 0.8119 (m-40) cc_final: 0.7671 (t0) REVERT: D 69 TYR cc_start: 0.8532 (m-80) cc_final: 0.8315 (m-80) REVERT: D 269 GLU cc_start: 0.7050 (tp30) cc_final: 0.6717 (tp30) REVERT: D 386 GLN cc_start: 0.7798 (mt0) cc_final: 0.7301 (mt0) REVERT: D 419 ASN cc_start: 0.8251 (m-40) cc_final: 0.7744 (t0) REVERT: D 427 TYR cc_start: 0.8353 (m-80) cc_final: 0.7959 (t80) REVERT: D 434 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7939 (pm20) REVERT: E 8 ASP cc_start: 0.8016 (m-30) cc_final: 0.7734 (m-30) REVERT: E 269 GLU cc_start: 0.6912 (tp30) cc_final: 0.6689 (tp30) REVERT: E 386 GLN cc_start: 0.7816 (mt0) cc_final: 0.7320 (mt0) REVERT: E 419 ASN cc_start: 0.8241 (m-40) cc_final: 0.7751 (t0) REVERT: E 427 TYR cc_start: 0.8342 (m-80) cc_final: 0.7954 (t80) REVERT: E 434 GLU cc_start: 0.8237 (tp30) cc_final: 0.8002 (pm20) REVERT: F 8 ASP cc_start: 0.7869 (m-30) cc_final: 0.7607 (m-30) REVERT: F 19 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7277 (mmm-85) REVERT: F 22 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7900 (mmt-90) REVERT: F 47 ASP cc_start: 0.8029 (m-30) cc_final: 0.7499 (t70) REVERT: F 159 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8518 (pp) REVERT: F 178 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: F 184 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: F 269 GLU cc_start: 0.7003 (tp30) cc_final: 0.6471 (tp30) REVERT: F 321 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7684 (ttt90) REVERT: F 335 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8263 (mtp85) REVERT: F 403 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7297 (mm-30) REVERT: F 419 ASN cc_start: 0.8264 (m-40) cc_final: 0.7828 (t0) REVERT: G 8 ASP cc_start: 0.7958 (m-30) cc_final: 0.7675 (m-30) REVERT: G 386 GLN cc_start: 0.7782 (mt0) cc_final: 0.7288 (mt0) REVERT: G 419 ASN cc_start: 0.8261 (m-40) cc_final: 0.7767 (t0) REVERT: G 434 GLU cc_start: 0.8257 (tp30) cc_final: 0.8001 (pm20) REVERT: H 8 ASP cc_start: 0.7874 (m-30) cc_final: 0.7611 (m-30) REVERT: H 19 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7333 (mmm-85) REVERT: H 47 ASP cc_start: 0.8037 (m-30) cc_final: 0.7562 (t70) REVERT: H 269 GLU cc_start: 0.6935 (tp30) cc_final: 0.6409 (tp30) REVERT: H 321 ARG cc_start: 0.7970 (ttt90) cc_final: 0.7675 (ttt90) REVERT: H 335 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.8188 (mtp85) REVERT: H 403 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7233 (mm-30) REVERT: H 419 ASN cc_start: 0.8256 (m-40) cc_final: 0.7825 (t0) REVERT: I 11 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7186 (tptt) REVERT: I 17 ASN cc_start: 0.8078 (t0) cc_final: 0.7668 (t0) REVERT: I 51 MET cc_start: 0.8008 (mtp) cc_final: 0.7740 (ttm) REVERT: I 254 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6504 (mppt) REVERT: I 363 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7202 (mmmm) REVERT: I 419 ASN cc_start: 0.8125 (m-40) cc_final: 0.7661 (t0) REVERT: J 11 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7176 (tptt) REVERT: J 17 ASN cc_start: 0.8080 (t0) cc_final: 0.7676 (t0) REVERT: J 419 ASN cc_start: 0.8165 (m-40) cc_final: 0.7712 (t0) REVERT: K 11 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7189 (tptt) REVERT: K 17 ASN cc_start: 0.8093 (t0) cc_final: 0.7686 (t0) REVERT: K 254 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6592 (mppt) REVERT: K 419 ASN cc_start: 0.8141 (m-40) cc_final: 0.7674 (t0) REVERT: L 8 ASP cc_start: 0.7877 (m-30) cc_final: 0.7611 (m-30) REVERT: L 19 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7306 (mmm-85) REVERT: L 47 ASP cc_start: 0.7979 (m-30) cc_final: 0.7496 (t70) REVERT: L 51 MET cc_start: 0.8205 (mtp) cc_final: 0.7886 (ttm) REVERT: L 159 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8533 (pp) REVERT: L 269 GLU cc_start: 0.7102 (tp30) cc_final: 0.6558 (tp30) REVERT: L 321 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7719 (ttt90) REVERT: L 335 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8256 (mtp85) REVERT: L 403 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7311 (mm-30) REVERT: L 419 ASN cc_start: 0.8260 (m-40) cc_final: 0.7824 (t0) outliers start: 80 outliers final: 53 residues processed: 678 average time/residue: 0.8250 time to fit residues: 662.4525 Evaluate side-chains 664 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 601 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 470 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 316 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 379 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 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 226 ASN E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 443 GLN H 24 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 24 GLN L 245 HIS L 443 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132597 restraints weight = 33739.947| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.16 r_work: 0.3385 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 40900 Z= 0.166 Angle : 0.575 6.644 55360 Z= 0.315 Chirality : 0.043 0.160 5964 Planarity : 0.005 0.056 7260 Dihedral : 5.860 59.842 5382 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 12.97 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.16 (0.12), residues: 4884 helix: 1.81 (0.11), residues: 2028 sheet: -0.26 (0.17), residues: 912 loop : 0.32 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 170 TYR 0.029 0.002 TYR G 296 PHE 0.024 0.002 PHE C 285 TRP 0.014 0.002 TRP B 425 HIS 0.006 0.002 HIS H 228 Details of bonding type rmsd covalent geometry : bond 0.00376 (40900) covalent geometry : angle 0.57498 (55360) hydrogen bonds : bond 0.05227 ( 1557) hydrogen bonds : angle 4.50826 ( 4623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 607 time to evaluate : 1.542 Fit side-chains REVERT: A 8 ASP cc_start: 0.7908 (m-30) cc_final: 0.7676 (m-30) REVERT: A 19 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7312 (mmm-85) REVERT: A 159 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8564 (pp) REVERT: A 178 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7959 (t70) REVERT: A 269 GLU cc_start: 0.7028 (tp30) cc_final: 0.6417 (tp30) REVERT: A 321 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7706 (ttt90) REVERT: A 335 ARG cc_start: 0.8454 (mtp-110) cc_final: 0.8207 (mtp85) REVERT: A 403 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7378 (mm-30) REVERT: A 419 ASN cc_start: 0.8243 (m-40) cc_final: 0.7782 (t0) REVERT: B 8 ASP cc_start: 0.8022 (m-30) cc_final: 0.7760 (m-30) REVERT: B 269 GLU cc_start: 0.7076 (tp30) cc_final: 0.6677 (tp30) REVERT: B 321 ARG cc_start: 0.7925 (tmt-80) cc_final: 0.7702 (ttp80) REVERT: B 386 GLN cc_start: 0.7735 (mt0) cc_final: 0.7229 (mt0) REVERT: B 419 ASN cc_start: 0.8280 (m-40) cc_final: 0.7748 (t0) REVERT: B 427 TYR cc_start: 0.8382 (m-80) cc_final: 0.7967 (t80) REVERT: C 11 LYS cc_start: 0.7919 (ttmm) cc_final: 0.7237 (tptt) REVERT: C 149 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: C 254 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6631 (mppt) REVERT: C 269 GLU cc_start: 0.7058 (tp30) cc_final: 0.6855 (tp30) REVERT: C 363 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7246 (mmmm) REVERT: C 419 ASN cc_start: 0.8148 (m-40) cc_final: 0.7673 (t0) REVERT: D 269 GLU cc_start: 0.7058 (tp30) cc_final: 0.6698 (tp30) REVERT: D 386 GLN cc_start: 0.7745 (mt0) cc_final: 0.7238 (mt0) REVERT: D 419 ASN cc_start: 0.8287 (m-40) cc_final: 0.7755 (t0) REVERT: D 427 TYR cc_start: 0.8396 (m-80) cc_final: 0.7965 (t80) REVERT: D 434 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7972 (pm20) REVERT: E 8 ASP cc_start: 0.8095 (m-30) cc_final: 0.7799 (m-30) REVERT: E 269 GLU cc_start: 0.6983 (tp30) cc_final: 0.6708 (tp30) REVERT: E 386 GLN cc_start: 0.7759 (mt0) cc_final: 0.7251 (mt0) REVERT: E 419 ASN cc_start: 0.8290 (m-40) cc_final: 0.7765 (t0) REVERT: E 427 TYR cc_start: 0.8394 (m-80) cc_final: 0.7960 (t80) REVERT: E 434 GLU cc_start: 0.8292 (tp30) cc_final: 0.7999 (pm20) REVERT: F 8 ASP cc_start: 0.7892 (m-30) cc_final: 0.7654 (m-30) REVERT: F 19 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7284 (mmm-85) REVERT: F 22 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8150 (mmt-90) REVERT: F 47 ASP cc_start: 0.8064 (m-30) cc_final: 0.7502 (t70) REVERT: F 159 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8587 (pp) REVERT: F 178 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7961 (t70) REVERT: F 184 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: F 269 GLU cc_start: 0.7025 (tp30) cc_final: 0.6450 (tp30) REVERT: F 321 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7678 (ttt90) REVERT: F 335 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8223 (mtp85) REVERT: F 403 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7365 (mm-30) REVERT: F 419 ASN cc_start: 0.8253 (m-40) cc_final: 0.7803 (t0) REVERT: G 8 ASP cc_start: 0.8031 (m-30) cc_final: 0.7778 (m-30) REVERT: G 69 TYR cc_start: 0.8482 (m-80) cc_final: 0.8175 (m-80) REVERT: G 386 GLN cc_start: 0.7739 (mt0) cc_final: 0.7236 (mt0) REVERT: G 419 ASN cc_start: 0.8287 (m-40) cc_final: 0.7770 (t0) REVERT: G 434 GLU cc_start: 0.8289 (tp30) cc_final: 0.8011 (pm20) REVERT: H 8 ASP cc_start: 0.7894 (m-30) cc_final: 0.7651 (m-30) REVERT: H 19 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7273 (mmm-85) REVERT: H 47 ASP cc_start: 0.7976 (m-30) cc_final: 0.7499 (t70) REVERT: H 159 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8620 (pp) REVERT: H 269 GLU cc_start: 0.6889 (tp30) cc_final: 0.6376 (tp30) REVERT: H 321 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7686 (ttt90) REVERT: H 335 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8201 (mtp85) REVERT: H 403 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7314 (mm-30) REVERT: H 419 ASN cc_start: 0.8245 (m-40) cc_final: 0.7797 (t0) REVERT: I 11 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7227 (tptt) REVERT: I 51 MET cc_start: 0.8023 (mtp) cc_final: 0.7744 (ttm) REVERT: I 254 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6491 (mppt) REVERT: I 363 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7197 (mmmm) REVERT: I 419 ASN cc_start: 0.8143 (m-40) cc_final: 0.7661 (t0) REVERT: J 11 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7229 (tptt) REVERT: J 149 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: J 419 ASN cc_start: 0.8187 (m-40) cc_final: 0.7698 (t0) REVERT: K 11 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7222 (tptt) REVERT: K 120 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: K 149 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: K 254 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6621 (mppt) REVERT: K 419 ASN cc_start: 0.8162 (m-40) cc_final: 0.7676 (t0) REVERT: L 8 ASP cc_start: 0.7880 (m-30) cc_final: 0.7657 (m-30) REVERT: L 19 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7305 (mmm-85) REVERT: L 47 ASP cc_start: 0.8002 (m-30) cc_final: 0.7514 (t70) REVERT: L 51 MET cc_start: 0.8198 (mtp) cc_final: 0.7892 (ttm) REVERT: L 159 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8561 (pp) REVERT: L 254 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6622 (mptt) REVERT: L 269 GLU cc_start: 0.7048 (tp30) cc_final: 0.6522 (tp30) REVERT: L 321 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7718 (ttt90) REVERT: L 403 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7369 (mm-30) REVERT: L 419 ASN cc_start: 0.8248 (m-40) cc_final: 0.7800 (t0) outliers start: 90 outliers final: 62 residues processed: 682 average time/residue: 0.8107 time to fit residues: 655.9735 Evaluate side-chains 683 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 605 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 319 LEU Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 254 LYS Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 60 optimal weight: 3.9990 chunk 412 optimal weight: 1.9990 chunk 409 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 366 optimal weight: 7.9990 chunk 441 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 17 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN J 17 ASN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133564 restraints weight = 33878.374| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.07 r_work: 0.3402 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40900 Z= 0.139 Angle : 0.539 5.820 55360 Z= 0.295 Chirality : 0.042 0.154 5964 Planarity : 0.005 0.057 7260 Dihedral : 5.785 59.815 5382 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.98 % Allowed : 13.01 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.21 (0.12), residues: 4884 helix: 1.87 (0.11), residues: 2028 sheet: -0.26 (0.17), residues: 912 loop : 0.35 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 170 TYR 0.026 0.002 TYR J 296 PHE 0.022 0.002 PHE C 285 TRP 0.013 0.002 TRP B 425 HIS 0.005 0.001 HIS L 228 Details of bonding type rmsd covalent geometry : bond 0.00312 (40900) covalent geometry : angle 0.53856 (55360) hydrogen bonds : bond 0.04781 ( 1557) hydrogen bonds : angle 4.43526 ( 4623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 601 time to evaluate : 1.529 Fit side-chains REVERT: A 8 ASP cc_start: 0.7880 (m-30) cc_final: 0.7641 (m-30) REVERT: A 19 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7366 (mmm-85) REVERT: A 159 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8569 (pp) REVERT: A 269 GLU cc_start: 0.6981 (tp30) cc_final: 0.6395 (tp30) REVERT: A 321 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7724 (ttt90) REVERT: A 335 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8210 (mtp85) REVERT: A 403 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 419 ASN cc_start: 0.8264 (m-40) cc_final: 0.7821 (t0) REVERT: B 8 ASP cc_start: 0.8008 (m-30) cc_final: 0.7768 (m-30) REVERT: B 69 TYR cc_start: 0.8486 (m-80) cc_final: 0.8240 (m-80) REVERT: B 269 GLU cc_start: 0.7060 (tp30) cc_final: 0.6676 (tp30) REVERT: B 321 ARG cc_start: 0.7944 (tmt-80) cc_final: 0.7725 (ttp80) REVERT: B 386 GLN cc_start: 0.7751 (mt0) cc_final: 0.7252 (mt0) REVERT: B 419 ASN cc_start: 0.8268 (m-40) cc_final: 0.7765 (t0) REVERT: B 427 TYR cc_start: 0.8359 (m-80) cc_final: 0.7978 (t80) REVERT: C 11 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7277 (tptt) REVERT: C 149 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: C 184 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: C 254 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6626 (mppt) REVERT: C 269 GLU cc_start: 0.7034 (tp30) cc_final: 0.6810 (tp30) REVERT: C 363 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7261 (mmmm) REVERT: C 419 ASN cc_start: 0.8134 (m-40) cc_final: 0.7682 (t0) REVERT: D 269 GLU cc_start: 0.7094 (tp30) cc_final: 0.6703 (tp30) REVERT: D 386 GLN cc_start: 0.7765 (mt0) cc_final: 0.7263 (mt0) REVERT: D 419 ASN cc_start: 0.8285 (m-40) cc_final: 0.7771 (t0) REVERT: D 427 TYR cc_start: 0.8383 (m-80) cc_final: 0.7976 (t80) REVERT: D 434 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8001 (pm20) REVERT: E 8 ASP cc_start: 0.8107 (m-30) cc_final: 0.7823 (m-30) REVERT: E 269 GLU cc_start: 0.6990 (tp30) cc_final: 0.6736 (tp30) REVERT: E 386 GLN cc_start: 0.7770 (mt0) cc_final: 0.7263 (mt0) REVERT: E 419 ASN cc_start: 0.8279 (m-40) cc_final: 0.7784 (t0) REVERT: E 427 TYR cc_start: 0.8375 (m-80) cc_final: 0.7973 (t80) REVERT: E 434 GLU cc_start: 0.8276 (tp30) cc_final: 0.8035 (pm20) REVERT: F 8 ASP cc_start: 0.7897 (m-30) cc_final: 0.7688 (m-30) REVERT: F 19 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7294 (mmm-85) REVERT: F 22 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8115 (mmt-90) REVERT: F 47 ASP cc_start: 0.8112 (m-30) cc_final: 0.7551 (t70) REVERT: F 159 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (pp) REVERT: F 178 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7941 (t70) REVERT: F 184 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: F 269 GLU cc_start: 0.6985 (tp30) cc_final: 0.6443 (tp30) REVERT: F 321 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7682 (ttt90) REVERT: F 335 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8229 (mtp85) REVERT: F 403 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7365 (mm-30) REVERT: F 419 ASN cc_start: 0.8292 (m-40) cc_final: 0.7846 (t0) REVERT: G 8 ASP cc_start: 0.8028 (m-30) cc_final: 0.7774 (m-30) REVERT: G 386 GLN cc_start: 0.7754 (mt0) cc_final: 0.7256 (mt0) REVERT: G 419 ASN cc_start: 0.8284 (m-40) cc_final: 0.7789 (t0) REVERT: G 434 GLU cc_start: 0.8274 (tp30) cc_final: 0.8026 (pm20) REVERT: H 8 ASP cc_start: 0.7885 (m-30) cc_final: 0.7671 (m-30) REVERT: H 19 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7354 (mmm-85) REVERT: H 47 ASP cc_start: 0.7977 (m-30) cc_final: 0.7512 (t70) REVERT: H 159 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8615 (pp) REVERT: H 269 GLU cc_start: 0.6890 (tp30) cc_final: 0.6401 (tp30) REVERT: H 321 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7690 (ttt90) REVERT: H 403 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7319 (mm-30) REVERT: H 419 ASN cc_start: 0.8279 (m-40) cc_final: 0.7839 (t0) REVERT: I 11 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7237 (tptt) REVERT: I 51 MET cc_start: 0.8022 (mtp) cc_final: 0.7776 (ttm) REVERT: I 254 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6464 (mppt) REVERT: I 363 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7202 (mmmm) REVERT: I 419 ASN cc_start: 0.8117 (m-40) cc_final: 0.7664 (t0) REVERT: J 11 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7250 (tptt) REVERT: J 149 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: J 419 ASN cc_start: 0.8171 (m-40) cc_final: 0.7712 (t0) REVERT: K 11 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7248 (tptt) REVERT: K 120 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: K 149 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: K 254 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6621 (mppt) REVERT: K 419 ASN cc_start: 0.8131 (m-40) cc_final: 0.7669 (t0) REVERT: L 8 ASP cc_start: 0.7893 (m-30) cc_final: 0.7652 (m-30) REVERT: L 19 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7338 (mmm-85) REVERT: L 47 ASP cc_start: 0.8010 (m-30) cc_final: 0.7535 (t70) REVERT: L 51 MET cc_start: 0.8197 (mtp) cc_final: 0.7895 (ttm) REVERT: L 159 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8566 (pp) REVERT: L 269 GLU cc_start: 0.7067 (tp30) cc_final: 0.6565 (tp30) REVERT: L 321 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7717 (ttt90) REVERT: L 335 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8198 (mtp-110) REVERT: L 403 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7359 (mm-30) REVERT: L 419 ASN cc_start: 0.8285 (m-40) cc_final: 0.7843 (t0) outliers start: 86 outliers final: 59 residues processed: 675 average time/residue: 0.8055 time to fit residues: 645.9984 Evaluate side-chains 675 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 601 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 481 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 485 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 412 optimal weight: 0.8980 chunk 327 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 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 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 443 GLN C 17 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN J 17 ASN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135465 restraints weight = 33854.343| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.06 r_work: 0.3425 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40900 Z= 0.111 Angle : 0.499 5.572 55360 Z= 0.272 Chirality : 0.041 0.150 5964 Planarity : 0.004 0.052 7260 Dihedral : 5.593 59.857 5382 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.91 % Allowed : 13.08 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.38 (0.12), residues: 4884 helix: 2.02 (0.11), residues: 2028 sheet: -0.20 (0.17), residues: 912 loop : 0.45 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 170 TYR 0.023 0.002 TYR C 296 PHE 0.016 0.001 PHE H 285 TRP 0.011 0.001 TRP B 425 HIS 0.005 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00246 (40900) covalent geometry : angle 0.49948 (55360) hydrogen bonds : bond 0.04208 ( 1557) hydrogen bonds : angle 4.29763 ( 4623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 615 time to evaluate : 1.607 Fit side-chains REVERT: A 8 ASP cc_start: 0.7896 (m-30) cc_final: 0.7650 (m-30) REVERT: A 19 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7340 (mmm-85) REVERT: A 159 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8533 (pp) REVERT: A 269 GLU cc_start: 0.6972 (tp30) cc_final: 0.6396 (tp30) REVERT: A 321 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7705 (ttt90) REVERT: A 335 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.8234 (mtp85) REVERT: A 403 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 419 ASN cc_start: 0.8248 (m-40) cc_final: 0.7812 (t0) REVERT: B 8 ASP cc_start: 0.7940 (m-30) cc_final: 0.7650 (m-30) REVERT: B 69 TYR cc_start: 0.8466 (m-80) cc_final: 0.8215 (m-80) REVERT: B 170 ARG cc_start: 0.8326 (tpp80) cc_final: 0.8100 (tpp80) REVERT: B 269 GLU cc_start: 0.7010 (tp30) cc_final: 0.6669 (tp30) REVERT: B 321 ARG cc_start: 0.7937 (tmt-80) cc_final: 0.7703 (ttp80) REVERT: B 386 GLN cc_start: 0.7756 (mt0) cc_final: 0.7244 (mt0) REVERT: B 419 ASN cc_start: 0.8241 (m-40) cc_final: 0.7742 (t0) REVERT: B 427 TYR cc_start: 0.8353 (m-80) cc_final: 0.7971 (t80) REVERT: C 11 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7292 (tptt) REVERT: C 17 ASN cc_start: 0.8119 (t0) cc_final: 0.7692 (t0) REVERT: C 149 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (pt0) REVERT: C 254 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6576 (mppt) REVERT: C 269 GLU cc_start: 0.6988 (tp30) cc_final: 0.6695 (tp30) REVERT: C 363 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7216 (mmmm) REVERT: C 419 ASN cc_start: 0.8118 (m-40) cc_final: 0.7670 (t0) REVERT: D 69 TYR cc_start: 0.8556 (m-80) cc_final: 0.8321 (m-80) REVERT: D 269 GLU cc_start: 0.7022 (tp30) cc_final: 0.6696 (tp30) REVERT: D 419 ASN cc_start: 0.8267 (m-40) cc_final: 0.7754 (t0) REVERT: D 427 TYR cc_start: 0.8356 (m-80) cc_final: 0.7967 (t80) REVERT: D 434 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7974 (pm20) REVERT: E 8 ASP cc_start: 0.8026 (m-30) cc_final: 0.7752 (m-30) REVERT: E 11 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7507 (ttpp) REVERT: E 269 GLU cc_start: 0.6891 (tp30) cc_final: 0.6663 (tp30) REVERT: E 419 ASN cc_start: 0.8258 (m-40) cc_final: 0.7762 (t0) REVERT: E 427 TYR cc_start: 0.8354 (m-80) cc_final: 0.7973 (t80) REVERT: E 434 GLU cc_start: 0.8247 (tp30) cc_final: 0.8009 (pm20) REVERT: F 8 ASP cc_start: 0.7857 (m-30) cc_final: 0.7625 (m-30) REVERT: F 19 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7299 (mmm-85) REVERT: F 47 ASP cc_start: 0.8071 (m-30) cc_final: 0.7582 (t70) REVERT: F 159 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8530 (pp) REVERT: F 178 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: F 184 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: F 269 GLU cc_start: 0.6936 (tp30) cc_final: 0.6419 (tp30) REVERT: F 321 ARG cc_start: 0.8002 (ttt90) cc_final: 0.7680 (ttt90) REVERT: F 335 ARG cc_start: 0.8472 (mtp-110) cc_final: 0.8257 (mtp85) REVERT: F 403 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7362 (mm-30) REVERT: F 419 ASN cc_start: 0.8283 (m-40) cc_final: 0.7840 (t0) REVERT: G 8 ASP cc_start: 0.7965 (m-30) cc_final: 0.7688 (m-30) REVERT: G 170 ARG cc_start: 0.8288 (tpp80) cc_final: 0.8055 (tpp80) REVERT: G 419 ASN cc_start: 0.8270 (m-40) cc_final: 0.7769 (t0) REVERT: G 434 GLU cc_start: 0.8227 (tp30) cc_final: 0.7973 (pm20) REVERT: H 8 ASP cc_start: 0.7902 (m-30) cc_final: 0.7664 (m-30) REVERT: H 19 ARG cc_start: 0.8109 (mmm160) cc_final: 0.7300 (mmm-85) REVERT: H 47 ASP cc_start: 0.7976 (m-30) cc_final: 0.7485 (t70) REVERT: H 159 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8553 (pp) REVERT: H 269 GLU cc_start: 0.6909 (tp30) cc_final: 0.6438 (tp30) REVERT: H 321 ARG cc_start: 0.7991 (ttt90) cc_final: 0.7690 (ttt90) REVERT: H 335 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.8229 (mtp85) REVERT: H 403 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7244 (mm-30) REVERT: H 419 ASN cc_start: 0.8305 (m-40) cc_final: 0.7852 (t0) REVERT: I 11 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7231 (tptt) REVERT: I 17 ASN cc_start: 0.8082 (t0) cc_final: 0.7664 (t0) REVERT: I 51 MET cc_start: 0.7999 (mtp) cc_final: 0.7770 (ttm) REVERT: I 254 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6493 (mppt) REVERT: I 363 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7131 (mmmm) REVERT: I 419 ASN cc_start: 0.8124 (m-40) cc_final: 0.7668 (t0) REVERT: J 11 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7209 (tptt) REVERT: J 17 ASN cc_start: 0.8103 (t0) cc_final: 0.7701 (t0) REVERT: J 149 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: J 419 ASN cc_start: 0.8172 (m-40) cc_final: 0.7708 (t0) REVERT: K 11 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7265 (tptt) REVERT: K 17 ASN cc_start: 0.8122 (t0) cc_final: 0.7710 (t0) REVERT: K 120 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: K 149 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: K 254 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6607 (mppt) REVERT: K 419 ASN cc_start: 0.8122 (m-40) cc_final: 0.7662 (t0) REVERT: L 8 ASP cc_start: 0.7916 (m-30) cc_final: 0.7663 (m-30) REVERT: L 19 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7318 (mmm-85) REVERT: L 51 MET cc_start: 0.8187 (mtp) cc_final: 0.7871 (ttm) REVERT: L 159 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8534 (pp) REVERT: L 269 GLU cc_start: 0.7085 (tp30) cc_final: 0.6534 (tp30) REVERT: L 321 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7693 (ttt90) REVERT: L 335 ARG cc_start: 0.8445 (mtp-110) cc_final: 0.8221 (mtp85) REVERT: L 403 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7295 (mm-30) REVERT: L 419 ASN cc_start: 0.8297 (m-40) cc_final: 0.7843 (t0) outliers start: 83 outliers final: 57 residues processed: 687 average time/residue: 0.7993 time to fit residues: 652.2577 Evaluate side-chains 677 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 607 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 149 GLU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 254 LYS Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 77 optimal weight: 0.9990 chunk 473 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 428 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 465 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 431 optimal weight: 10.0000 chunk 396 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 HIS F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133530 restraints weight = 33908.812| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.12 r_work: 0.3402 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40900 Z= 0.149 Angle : 0.555 6.028 55360 Z= 0.304 Chirality : 0.043 0.157 5964 Planarity : 0.005 0.064 7260 Dihedral : 5.812 59.993 5382 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.77 % Allowed : 13.27 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.23 (0.12), residues: 4884 helix: 1.86 (0.11), residues: 2028 sheet: -0.26 (0.17), residues: 912 loop : 0.38 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 170 TYR 0.027 0.002 TYR G 296 PHE 0.022 0.002 PHE H 285 TRP 0.013 0.002 TRP B 425 HIS 0.006 0.002 HIS H 228 Details of bonding type rmsd covalent geometry : bond 0.00335 (40900) covalent geometry : angle 0.55452 (55360) hydrogen bonds : bond 0.04969 ( 1557) hydrogen bonds : angle 4.45223 ( 4623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19091.02 seconds wall clock time: 323 minutes 59.32 seconds (19439.32 seconds total)