Starting phenix.real_space_refine on Sun Mar 24 04:38:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_25864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_25864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_25864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_25864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/03_2024/7tf7_25864.pdb" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.106 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 Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 21.81, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 17.09 Conformation dependent library (CDL) restraints added in 7.5 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: 4.00 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: 13.98 Time building geometry restraints manager: 18.21 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: 99.57 - 106.46: 1289 106.46 - 113.34: 21511 113.34 - 120.22: 15445 120.22 - 127.11: 16652 127.11 - 133.99: 463 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 2.440 nonbonded pdb=" OD2 ASP B 53 " pdb=" OG SER B 55 " model vdw 2.189 2.440 nonbonded pdb=" OD2 ASP A 53 " pdb=" OG SER A 55 " model vdw 2.189 2.440 nonbonded pdb=" OD2 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP F 53 " pdb=" OG SER F 55 " model vdw 2.202 2.440 ... (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 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.620 Check model and map are aligned: 0.600 Set scattering table: 0.420 Process input model: 105.030 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.490 ------------------------------------------------------------------------------- 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= 0.273 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (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 TRP 0.010 0.002 TRP B 425 HIS 0.005 0.001 HIS H 195 PHE 0.020 0.002 PHE G 285 TYR 0.019 0.002 TYR E 296 ARG 0.006 0.001 ARG C 321 *********************** 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 fitting. rotamer outliers: 62 poor density : 849 time to evaluate : 4.330 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: 0.7532 (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: 1.7500 time to fit residues: 1864.9417 Evaluate side-chains 714 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 671 time to evaluate : 4.111 ------------------------------------------------------------------------------- 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 415 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 385 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 C 443 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 HIS 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** F 212 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** 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 H 245 HIS I 111 ASN I 443 GLN ** J 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40900 Z= 0.278 Angle : 0.642 9.522 55360 Z= 0.343 Chirality : 0.045 0.164 5964 Planarity : 0.006 0.054 7260 Dihedral : 6.368 49.530 5421 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 3.98 % Allowed : 11.42 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.12), residues: 4884 helix: 1.76 (0.11), residues: 2028 sheet: 0.00 (0.17), residues: 912 loop : 0.13 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 425 HIS 0.008 0.002 HIS K 195 PHE 0.030 0.002 PHE H 285 TYR 0.031 0.003 TYR B 296 ARG 0.007 0.001 ARG K 114 *********************** 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 880 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 707 time to evaluate : 4.470 Fit side-chains REVERT: A 8 ASP cc_start: 0.5718 (m-30) cc_final: 0.5277 (m-30) REVERT: A 16 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6298 (mm-30) REVERT: A 19 ARG cc_start: 0.6264 (mmm160) cc_final: 0.4896 (mmm-85) REVERT: A 37 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6662 (m) REVERT: A 47 ASP cc_start: 0.6382 (m-30) cc_final: 0.5457 (t70) REVERT: A 50 MET cc_start: 0.6944 (tpp) cc_final: 0.6660 (tpt) REVERT: A 51 MET cc_start: 0.7344 (mtp) cc_final: 0.7092 (ttm) REVERT: A 105 GLU cc_start: 0.6432 (pm20) cc_final: 0.6163 (pm20) REVERT: A 142 GLU cc_start: 0.6537 (mm-30) cc_final: 0.5618 (mp0) REVERT: A 149 GLU cc_start: 0.6512 (pt0) cc_final: 0.6029 (tt0) REVERT: A 216 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6266 (tp) REVERT: A 269 GLU cc_start: 0.5593 (tp30) cc_final: 0.4896 (tp30) REVERT: A 321 ARG cc_start: 0.6430 (ttt90) cc_final: 0.5920 (ttt90) REVERT: A 370 GLN cc_start: 0.5177 (OUTLIER) cc_final: 0.4936 (pt0) REVERT: A 403 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5439 (mm-30) REVERT: A 407 LYS cc_start: 0.6559 (tttp) cc_final: 0.6198 (ttpp) REVERT: A 416 GLN cc_start: 0.6205 (mm110) cc_final: 0.6005 (mm110) REVERT: A 419 ASN cc_start: 0.6074 (m-40) cc_final: 0.4828 (t0) REVERT: A 429 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6615 (ptm-80) REVERT: A 434 GLU cc_start: 0.6603 (tp30) cc_final: 0.5361 (pm20) REVERT: A 438 ASP cc_start: 0.6500 (m-30) cc_final: 0.6093 (m-30) REVERT: B 8 ASP cc_start: 0.5846 (m-30) cc_final: 0.5367 (m-30) REVERT: B 17 ASN cc_start: 0.6191 (t0) cc_final: 0.5721 (t0) REVERT: B 22 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7299 (tpp80) REVERT: B 37 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6673 (m) REVERT: B 58 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4857 (mt-10) REVERT: B 269 GLU cc_start: 0.5707 (tp30) cc_final: 0.5224 (tp30) REVERT: B 321 ARG cc_start: 0.6356 (tmt-80) cc_final: 0.5702 (ttt90) REVERT: B 363 LYS cc_start: 0.6381 (tppt) cc_final: 0.6120 (mmmt) REVERT: B 407 LYS cc_start: 0.6511 (ttpp) cc_final: 0.6204 (ttpp) REVERT: B 419 ASN cc_start: 0.5967 (m-40) cc_final: 0.4580 (t0) REVERT: B 427 TYR cc_start: 0.6833 (m-80) cc_final: 0.5374 (t80) REVERT: C 11 LYS cc_start: 0.5930 (ttmm) cc_final: 0.4880 (tptt) REVERT: C 17 ASN cc_start: 0.6348 (t0) cc_final: 0.5929 (t0) REVERT: C 50 MET cc_start: 0.7010 (tpp) cc_final: 0.6766 (tpt) REVERT: C 142 GLU cc_start: 0.5275 (pm20) cc_final: 0.5017 (mp0) REVERT: C 149 GLU cc_start: 0.6493 (pt0) cc_final: 0.5999 (tt0) REVERT: C 153 ASP cc_start: 0.6628 (t0) cc_final: 0.6307 (t0) REVERT: C 184 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: C 216 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6317 (tp) REVERT: C 254 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6189 (mppt) REVERT: C 260 ASP cc_start: 0.5859 (t0) cc_final: 0.5563 (t0) REVERT: C 265 MET cc_start: 0.5683 (tpp) cc_final: 0.5394 (tpp) REVERT: C 269 GLU cc_start: 0.5412 (tp30) cc_final: 0.5017 (tp30) REVERT: C 321 ARG cc_start: 0.6503 (ttt90) cc_final: 0.6230 (ttt90) REVERT: C 363 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6138 (mmmm) REVERT: C 407 LYS cc_start: 0.6694 (tttp) cc_final: 0.6316 (tttp) REVERT: C 419 ASN cc_start: 0.5774 (m-40) cc_final: 0.4583 (t0) REVERT: C 434 GLU cc_start: 0.6433 (tp30) cc_final: 0.5576 (pm20) REVERT: D 8 ASP cc_start: 0.5859 (m-30) cc_final: 0.5347 (m-30) REVERT: D 22 ARG cc_start: 0.7551 (ttm170) cc_final: 0.6893 (tpp80) REVERT: D 37 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6603 (m) REVERT: D 223 ARG cc_start: 0.6649 (tpp-160) cc_final: 0.6053 (ttt180) REVERT: D 269 GLU cc_start: 0.5705 (tp30) cc_final: 0.5201 (tp30) REVERT: D 321 ARG cc_start: 0.6346 (tmt-80) cc_final: 0.5742 (ttt90) REVERT: D 363 LYS cc_start: 0.6438 (tppt) cc_final: 0.6058 (mmmt) REVERT: D 419 ASN cc_start: 0.5943 (m-40) cc_final: 0.4572 (t0) REVERT: D 427 TYR cc_start: 0.6887 (m-80) cc_final: 0.5394 (t80) REVERT: D 434 GLU cc_start: 0.6382 (tp30) cc_final: 0.5263 (pm20) REVERT: E 8 ASP cc_start: 0.5835 (m-30) cc_final: 0.5352 (m-30) REVERT: E 17 ASN cc_start: 0.6177 (t0) cc_final: 0.5722 (t0) REVERT: E 22 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7108 (tpp80) REVERT: E 37 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6662 (m) REVERT: E 58 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4843 (mt-10) REVERT: E 67 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.5065 (t0) REVERT: E 149 GLU cc_start: 0.6564 (pt0) cc_final: 0.5944 (tt0) REVERT: E 269 GLU cc_start: 0.5523 (tp30) cc_final: 0.5078 (tp30) REVERT: E 363 LYS cc_start: 0.6409 (tppt) cc_final: 0.6098 (mmmt) REVERT: E 366 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6882 (tp30) REVERT: E 370 GLN cc_start: 0.5054 (OUTLIER) cc_final: 0.4800 (pt0) REVERT: E 407 LYS cc_start: 0.6492 (ttpp) cc_final: 0.6177 (ttpp) REVERT: E 419 ASN cc_start: 0.5944 (m-40) cc_final: 0.4559 (t0) REVERT: E 427 TYR cc_start: 0.6840 (m-80) cc_final: 0.5355 (t80) REVERT: E 434 GLU cc_start: 0.6468 (tp30) cc_final: 0.5359 (pm20) REVERT: E 441 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5915 (tpt) REVERT: F 8 ASP cc_start: 0.5719 (m-30) cc_final: 0.5283 (m-30) REVERT: F 16 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6271 (mm-30) REVERT: F 19 ARG cc_start: 0.6316 (mmm160) cc_final: 0.4877 (mmm-85) REVERT: F 22 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7274 (mmm-85) REVERT: F 37 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6582 (m) REVERT: F 126 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6876 (t0) REVERT: F 149 GLU cc_start: 0.6547 (pt0) cc_final: 0.5965 (pt0) REVERT: F 153 ASP cc_start: 0.6896 (t0) cc_final: 0.6635 (t0) REVERT: F 184 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6264 (mm-30) REVERT: F 216 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6291 (tp) REVERT: F 223 ARG cc_start: 0.6764 (mtp85) cc_final: 0.6399 (ttt90) REVERT: F 269 GLU cc_start: 0.5565 (tp30) cc_final: 0.4855 (tp30) REVERT: F 321 ARG cc_start: 0.6427 (ttt90) cc_final: 0.5878 (ttt90) REVERT: F 419 ASN cc_start: 0.6005 (m-40) cc_final: 0.4839 (t0) REVERT: F 429 ARG cc_start: 0.6951 (ttp80) cc_final: 0.6525 (ptm-80) REVERT: F 438 ASP cc_start: 0.6509 (m-30) cc_final: 0.6103 (m-30) REVERT: G 8 ASP cc_start: 0.5877 (m-30) cc_final: 0.5358 (m-30) REVERT: G 17 ASN cc_start: 0.6260 (t0) cc_final: 0.5838 (t0) REVERT: G 22 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7069 (tpp80) REVERT: G 37 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6646 (m) REVERT: G 67 ASP cc_start: 0.5458 (t70) cc_final: 0.5112 (t0) REVERT: G 223 ARG cc_start: 0.6644 (tpp-160) cc_final: 0.6045 (ttt180) REVERT: G 252 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6319 (mtpt) REVERT: G 254 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6202 (mppt) REVERT: G 255 GLU cc_start: 0.6455 (tt0) cc_final: 0.5503 (pp20) REVERT: G 269 GLU cc_start: 0.5583 (tp30) cc_final: 0.5221 (tp30) REVERT: G 321 ARG cc_start: 0.6352 (tmt-80) cc_final: 0.5752 (ttt90) REVERT: G 363 LYS cc_start: 0.6398 (tppt) cc_final: 0.5746 (mmmm) REVERT: G 370 GLN cc_start: 0.4924 (OUTLIER) cc_final: 0.4559 (pt0) REVERT: G 419 ASN cc_start: 0.5949 (m-40) cc_final: 0.4579 (t0) REVERT: G 434 GLU cc_start: 0.6390 (tp30) cc_final: 0.5233 (pm20) REVERT: G 441 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.5919 (tpt) REVERT: H 8 ASP cc_start: 0.5716 (m-30) cc_final: 0.5295 (m-30) REVERT: H 16 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6186 (mm-30) REVERT: H 19 ARG cc_start: 0.6256 (mmm160) cc_final: 0.4810 (mmm-85) REVERT: H 47 ASP cc_start: 0.6408 (m-30) cc_final: 0.5488 (t70) REVERT: H 105 GLU cc_start: 0.6466 (pm20) cc_final: 0.6214 (pm20) REVERT: H 142 GLU cc_start: 0.6689 (mm-30) cc_final: 0.5816 (mp0) REVERT: H 149 GLU cc_start: 0.6492 (pt0) cc_final: 0.6009 (tt0) REVERT: H 216 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6315 (tp) REVERT: H 224 LYS cc_start: 0.6489 (mttm) cc_final: 0.6189 (mttp) REVERT: H 269 GLU cc_start: 0.5677 (tp30) cc_final: 0.4940 (tp30) REVERT: H 321 ARG cc_start: 0.6458 (ttt90) cc_final: 0.5925 (ttt90) REVERT: H 386 GLN cc_start: 0.6307 (tt0) cc_final: 0.6029 (mt0) REVERT: H 419 ASN cc_start: 0.6056 (m-40) cc_final: 0.4811 (t0) REVERT: H 429 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6573 (ptm-80) REVERT: H 438 ASP cc_start: 0.6471 (m-30) cc_final: 0.6053 (m-30) REVERT: I 11 LYS cc_start: 0.5807 (ttmm) cc_final: 0.4802 (tptt) REVERT: I 50 MET cc_start: 0.7030 (tpp) cc_final: 0.6732 (tpt) REVERT: I 51 MET cc_start: 0.7261 (mtp) cc_final: 0.6986 (ttm) REVERT: I 117 LYS cc_start: 0.5821 (tptp) cc_final: 0.5471 (tptp) REVERT: I 120 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: I 142 GLU cc_start: 0.6370 (mm-30) cc_final: 0.5618 (mp0) REVERT: I 149 GLU cc_start: 0.6588 (pt0) cc_final: 0.6126 (tt0) REVERT: I 153 ASP cc_start: 0.6609 (t0) cc_final: 0.6299 (t0) REVERT: I 216 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6346 (tp) REVERT: I 254 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6194 (mppt) REVERT: I 269 GLU cc_start: 0.5290 (tp30) cc_final: 0.4802 (tp30) REVERT: I 321 ARG cc_start: 0.6475 (ttt90) cc_final: 0.6067 (ttt90) REVERT: I 363 LYS cc_start: 0.6662 (mmmt) cc_final: 0.6075 (mmmm) REVERT: I 370 GLN cc_start: 0.5247 (OUTLIER) cc_final: 0.4958 (pt0) REVERT: I 407 LYS cc_start: 0.6590 (tttm) cc_final: 0.6190 (ttpp) REVERT: I 419 ASN cc_start: 0.5772 (m-40) cc_final: 0.4583 (t0) REVERT: I 434 GLU cc_start: 0.6501 (tp30) cc_final: 0.5597 (pm20) REVERT: J 11 LYS cc_start: 0.5823 (ttmm) cc_final: 0.4822 (tptt) REVERT: J 37 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6669 (m) REVERT: J 50 MET cc_start: 0.7095 (tpp) cc_final: 0.6809 (tpt) REVERT: J 142 GLU cc_start: 0.6388 (mm-30) cc_final: 0.5586 (mp0) REVERT: J 149 GLU cc_start: 0.6509 (pt0) cc_final: 0.6001 (tt0) REVERT: J 153 ASP cc_start: 0.6605 (t0) cc_final: 0.6299 (t0) REVERT: J 216 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6338 (tp) REVERT: J 269 GLU cc_start: 0.5247 (tp30) cc_final: 0.4943 (tp30) REVERT: J 370 GLN cc_start: 0.5337 (OUTLIER) cc_final: 0.4988 (pt0) REVERT: J 419 ASN cc_start: 0.5777 (m-40) cc_final: 0.4561 (t0) REVERT: J 429 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6699 (ptm160) REVERT: J 441 MET cc_start: 0.6397 (ttt) cc_final: 0.6037 (tpt) REVERT: K 11 LYS cc_start: 0.5809 (ttmm) cc_final: 0.4816 (tptt) REVERT: K 17 ASN cc_start: 0.6363 (t0) cc_final: 0.5952 (t0) REVERT: K 22 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: K 50 MET cc_start: 0.7136 (tpp) cc_final: 0.6919 (tpt) REVERT: K 142 GLU cc_start: 0.6344 (mm-30) cc_final: 0.5564 (mp0) REVERT: K 149 GLU cc_start: 0.6514 (pt0) cc_final: 0.6012 (tt0) REVERT: K 153 ASP cc_start: 0.6597 (t0) cc_final: 0.6285 (t70) REVERT: K 216 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6326 (tp) REVERT: K 254 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6183 (mppt) REVERT: K 265 MET cc_start: 0.5799 (tpp) cc_final: 0.5557 (tpp) REVERT: K 269 GLU cc_start: 0.5253 (tp30) cc_final: 0.4947 (tp30) REVERT: K 363 LYS cc_start: 0.6422 (mmmm) cc_final: 0.6197 (mmmm) REVERT: K 370 GLN cc_start: 0.5307 (OUTLIER) cc_final: 0.4936 (pt0) REVERT: K 419 ASN cc_start: 0.5793 (m-40) cc_final: 0.4577 (t0) REVERT: K 429 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6715 (ptm160) REVERT: K 441 MET cc_start: 0.6395 (ttt) cc_final: 0.6035 (tpt) REVERT: L 8 ASP cc_start: 0.5675 (m-30) cc_final: 0.5273 (m-30) REVERT: L 16 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6237 (mm-30) REVERT: L 19 ARG cc_start: 0.6262 (mmm160) cc_final: 0.4820 (mmm-85) REVERT: L 37 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6626 (m) REVERT: L 47 ASP cc_start: 0.6386 (m-30) cc_final: 0.5478 (t70) REVERT: L 50 MET cc_start: 0.6962 (tpp) cc_final: 0.6671 (tpt) REVERT: L 51 MET cc_start: 0.7472 (mtp) cc_final: 0.7195 (ttm) REVERT: L 105 GLU cc_start: 0.6466 (pm20) cc_final: 0.6212 (pm20) REVERT: L 142 GLU cc_start: 0.6697 (mm-30) cc_final: 0.5825 (mp0) REVERT: L 149 GLU cc_start: 0.6501 (pt0) cc_final: 0.6024 (tt0) REVERT: L 153 ASP cc_start: 0.7024 (t0) cc_final: 0.6773 (t0) REVERT: L 216 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6309 (tp) REVERT: L 224 LYS cc_start: 0.6472 (mttm) cc_final: 0.6133 (mttp) REVERT: L 269 GLU cc_start: 0.5651 (tp30) cc_final: 0.4945 (tp30) REVERT: L 321 ARG cc_start: 0.6436 (ttt90) cc_final: 0.5910 (ttt90) REVERT: L 370 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.4737 (pt0) REVERT: L 419 ASN cc_start: 0.6089 (m-40) cc_final: 0.4838 (t0) REVERT: L 429 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6573 (ptm-80) REVERT: L 438 ASP cc_start: 0.6498 (m-30) cc_final: 0.6075 (m-30) outliers start: 173 outliers final: 57 residues processed: 857 average time/residue: 1.7266 time to fit residues: 1750.8034 Evaluate side-chains 758 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 664 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 GLU 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 37 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 37 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 328 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 67 ASP 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 370 GLN Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain F residue 37 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 216 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 37 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 216 LEU 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 39 VAL Chi-restraints excluded: chain I residue 120 GLU 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 254 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 39 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 J residue 370 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 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 K residue 370 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.0040 chunk 138 optimal weight: 8.9990 chunk 371 optimal weight: 0.3980 chunk 304 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 447 optimal weight: 5.9990 chunk 483 optimal weight: 1.9990 chunk 398 optimal weight: 8.9990 chunk 443 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 overall best weight: 1.8798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 111 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 443 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40900 Z= 0.203 Angle : 0.555 8.627 55360 Z= 0.298 Chirality : 0.042 0.154 5964 Planarity : 0.005 0.048 7260 Dihedral : 6.108 56.892 5406 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.27 % Allowed : 12.00 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.12), residues: 4884 helix: 1.92 (0.11), residues: 2028 sheet: -0.04 (0.17), residues: 912 loop : 0.20 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 425 HIS 0.006 0.002 HIS I 195 PHE 0.022 0.002 PHE H 285 TYR 0.026 0.002 TYR B 296 ARG 0.008 0.001 ARG K 19 *********************** 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 811 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 669 time to evaluate : 4.610 Fit side-chains REVERT: A 8 ASP cc_start: 0.5713 (m-30) cc_final: 0.5262 (m-30) REVERT: A 16 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6258 (mm-30) REVERT: A 19 ARG cc_start: 0.6253 (mmm160) cc_final: 0.4872 (mmm-85) REVERT: A 47 ASP cc_start: 0.6403 (m-30) cc_final: 0.5502 (t70) REVERT: A 51 MET cc_start: 0.7273 (mtp) cc_final: 0.6926 (ttm) REVERT: A 149 GLU cc_start: 0.6513 (pt0) cc_final: 0.6034 (tt0) REVERT: A 269 GLU cc_start: 0.5642 (tp30) cc_final: 0.4848 (tp30) REVERT: A 321 ARG cc_start: 0.6477 (ttt90) cc_final: 0.5975 (ttt90) REVERT: A 370 GLN cc_start: 0.5274 (OUTLIER) cc_final: 0.5058 (pt0) REVERT: A 403 GLU cc_start: 0.5990 (mm-30) cc_final: 0.5339 (mm-30) REVERT: A 407 LYS cc_start: 0.6547 (tttp) cc_final: 0.6241 (ttpp) REVERT: A 416 GLN cc_start: 0.6196 (mm110) cc_final: 0.5973 (mm110) REVERT: A 419 ASN cc_start: 0.6037 (m-40) cc_final: 0.4779 (t0) REVERT: A 429 ARG cc_start: 0.6936 (ttp80) cc_final: 0.6617 (ptm-80) REVERT: A 434 GLU cc_start: 0.6579 (tp30) cc_final: 0.5370 (pm20) REVERT: A 438 ASP cc_start: 0.6490 (m-30) cc_final: 0.6091 (m-30) REVERT: B 8 ASP cc_start: 0.5829 (m-30) cc_final: 0.5359 (m-30) REVERT: B 17 ASN cc_start: 0.6226 (t0) cc_final: 0.5794 (t0) REVERT: B 22 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7224 (tpp80) REVERT: B 39 VAL cc_start: 0.6408 (OUTLIER) cc_final: 0.6112 (m) REVERT: B 58 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4775 (mt-10) REVERT: B 269 GLU cc_start: 0.5788 (tp30) cc_final: 0.5244 (tp30) REVERT: B 321 ARG cc_start: 0.6370 (tmt-80) cc_final: 0.5711 (ttt90) REVERT: B 363 LYS cc_start: 0.6409 (tppt) cc_final: 0.5736 (mmmm) REVERT: B 370 GLN cc_start: 0.4836 (OUTLIER) cc_final: 0.4518 (pt0) REVERT: B 407 LYS cc_start: 0.6514 (ttpp) cc_final: 0.6201 (ttpp) REVERT: B 419 ASN cc_start: 0.5956 (m-40) cc_final: 0.4583 (t0) REVERT: B 427 TYR cc_start: 0.6882 (m-80) cc_final: 0.5385 (t80) REVERT: C 11 LYS cc_start: 0.5955 (ttmm) cc_final: 0.4913 (tptt) REVERT: C 17 ASN cc_start: 0.6362 (t0) cc_final: 0.5962 (t0) REVERT: C 142 GLU cc_start: 0.5357 (pm20) cc_final: 0.5056 (mp0) REVERT: C 149 GLU cc_start: 0.6325 (pt0) cc_final: 0.5828 (tt0) REVERT: C 153 ASP cc_start: 0.6672 (t0) cc_final: 0.6340 (t0) REVERT: C 184 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6950 (mm-30) REVERT: C 216 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6335 (tp) REVERT: C 224 LYS cc_start: 0.6785 (mttt) cc_final: 0.6513 (mttp) REVERT: C 254 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6177 (mppt) REVERT: C 269 GLU cc_start: 0.5326 (tp30) cc_final: 0.4958 (tp30) REVERT: C 321 ARG cc_start: 0.6497 (ttt90) cc_final: 0.6240 (ttt90) REVERT: C 363 LYS cc_start: 0.6757 (mmmt) cc_final: 0.6145 (mmmm) REVERT: C 407 LYS cc_start: 0.6584 (tttp) cc_final: 0.6155 (ttpp) REVERT: C 419 ASN cc_start: 0.5781 (m-40) cc_final: 0.4594 (t0) REVERT: C 434 GLU cc_start: 0.6453 (tp30) cc_final: 0.5551 (pm20) REVERT: D 8 ASP cc_start: 0.5824 (m-30) cc_final: 0.5339 (m-30) REVERT: D 22 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7051 (tpp80) REVERT: D 37 VAL cc_start: 0.6888 (OUTLIER) cc_final: 0.6653 (m) REVERT: D 120 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: D 223 ARG cc_start: 0.6660 (tpp-160) cc_final: 0.6057 (ttt180) REVERT: D 255 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5735 (pp20) REVERT: D 269 GLU cc_start: 0.5672 (tp30) cc_final: 0.5163 (tp30) REVERT: D 321 ARG cc_start: 0.6466 (tmt-80) cc_final: 0.5942 (ttp80) REVERT: D 419 ASN cc_start: 0.5989 (m-40) cc_final: 0.4599 (t0) REVERT: D 427 TYR cc_start: 0.6861 (m-80) cc_final: 0.5381 (t80) REVERT: D 434 GLU cc_start: 0.6438 (tp30) cc_final: 0.5301 (pm20) REVERT: D 441 MET cc_start: 0.6334 (ttt) cc_final: 0.5915 (tpt) REVERT: E 8 ASP cc_start: 0.5826 (m-30) cc_final: 0.5373 (m-30) REVERT: E 11 LYS cc_start: 0.5682 (ttmm) cc_final: 0.5190 (ttpp) REVERT: E 17 ASN cc_start: 0.6171 (t0) cc_final: 0.5709 (t0) REVERT: E 22 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7140 (tpp80) REVERT: E 39 VAL cc_start: 0.6385 (OUTLIER) cc_final: 0.6083 (m) REVERT: E 50 MET cc_start: 0.6729 (mmm) cc_final: 0.6481 (tpt) REVERT: E 58 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4822 (mt-10) REVERT: E 67 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4964 (t0) REVERT: E 69 TYR cc_start: 0.7324 (m-80) cc_final: 0.6922 (m-80) REVERT: E 149 GLU cc_start: 0.6528 (pt0) cc_final: 0.6308 (pt0) REVERT: E 269 GLU cc_start: 0.5418 (tp30) cc_final: 0.4997 (tp30) REVERT: E 370 GLN cc_start: 0.5048 (OUTLIER) cc_final: 0.4788 (pt0) REVERT: E 407 LYS cc_start: 0.6515 (ttpp) cc_final: 0.6257 (ttmm) REVERT: E 419 ASN cc_start: 0.5933 (m-40) cc_final: 0.4562 (t0) REVERT: E 427 TYR cc_start: 0.6875 (m-80) cc_final: 0.5370 (t80) REVERT: E 434 GLU cc_start: 0.6508 (tp30) cc_final: 0.5344 (pm20) REVERT: E 441 MET cc_start: 0.6307 (ttt) cc_final: 0.5868 (tpt) REVERT: F 8 ASP cc_start: 0.5703 (m-30) cc_final: 0.5294 (m-30) REVERT: F 16 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6209 (mm-30) REVERT: F 17 ASN cc_start: 0.6169 (t0) cc_final: 0.5767 (t0) REVERT: F 19 ARG cc_start: 0.6269 (mmm160) cc_final: 0.4822 (mmm-85) REVERT: F 22 ARG cc_start: 0.7475 (mtt90) cc_final: 0.7213 (mmm-85) REVERT: F 37 VAL cc_start: 0.6894 (OUTLIER) cc_final: 0.6679 (m) REVERT: F 47 ASP cc_start: 0.6376 (m-30) cc_final: 0.5494 (t70) REVERT: F 149 GLU cc_start: 0.6532 (pt0) cc_final: 0.5931 (pt0) REVERT: F 153 ASP cc_start: 0.6945 (t0) cc_final: 0.6692 (t0) REVERT: F 170 ARG cc_start: 0.5986 (tpp80) cc_final: 0.5654 (tpp80) REVERT: F 184 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: F 223 ARG cc_start: 0.6727 (mtp85) cc_final: 0.6511 (ttt90) REVERT: F 269 GLU cc_start: 0.5560 (tp30) cc_final: 0.4819 (tp30) REVERT: F 321 ARG cc_start: 0.6446 (ttt90) cc_final: 0.5858 (ttt90) REVERT: F 335 ARG cc_start: 0.6892 (mtp-110) cc_final: 0.6668 (mtp85) REVERT: F 403 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5356 (mm-30) REVERT: F 419 ASN cc_start: 0.6006 (m-40) cc_final: 0.4780 (t0) REVERT: F 429 ARG cc_start: 0.6914 (ttp80) cc_final: 0.6507 (ptm-80) REVERT: F 434 GLU cc_start: 0.6578 (tp30) cc_final: 0.6208 (tp30) REVERT: F 438 ASP cc_start: 0.6496 (m-30) cc_final: 0.6095 (m-30) REVERT: G 8 ASP cc_start: 0.5844 (m-30) cc_final: 0.5349 (m-30) REVERT: G 17 ASN cc_start: 0.6219 (t0) cc_final: 0.5796 (t0) REVERT: G 22 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7116 (tpp80) REVERT: G 37 VAL cc_start: 0.6895 (OUTLIER) cc_final: 0.6684 (m) REVERT: G 67 ASP cc_start: 0.5341 (t70) cc_final: 0.5064 (t0) REVERT: G 69 TYR cc_start: 0.7323 (m-80) cc_final: 0.6936 (m-80) REVERT: G 120 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5945 (mt-10) REVERT: G 223 ARG cc_start: 0.6654 (tpp-160) cc_final: 0.6052 (ttt180) REVERT: G 252 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6266 (mtpt) REVERT: G 254 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6202 (mppt) REVERT: G 255 GLU cc_start: 0.6459 (tt0) cc_final: 0.5511 (pp20) REVERT: G 269 GLU cc_start: 0.5494 (tp30) cc_final: 0.5244 (tp30) REVERT: G 321 ARG cc_start: 0.6399 (tmt-80) cc_final: 0.5948 (ttp80) REVERT: G 370 GLN cc_start: 0.4986 (OUTLIER) cc_final: 0.4645 (pt0) REVERT: G 419 ASN cc_start: 0.5974 (m-40) cc_final: 0.4591 (t0) REVERT: G 434 GLU cc_start: 0.6475 (tp30) cc_final: 0.5357 (pm20) REVERT: G 441 MET cc_start: 0.6281 (ttt) cc_final: 0.5878 (tpt) REVERT: H 8 ASP cc_start: 0.5711 (m-30) cc_final: 0.5272 (m-30) REVERT: H 16 GLU cc_start: 0.6502 (mm-30) cc_final: 0.6204 (mm-30) REVERT: H 19 ARG cc_start: 0.6259 (mmm160) cc_final: 0.4781 (mmm-85) REVERT: H 22 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6688 (mtt-85) REVERT: H 37 VAL cc_start: 0.6897 (OUTLIER) cc_final: 0.6625 (m) REVERT: H 47 ASP cc_start: 0.6421 (m-30) cc_final: 0.5519 (t70) REVERT: H 67 ASP cc_start: 0.5400 (t70) cc_final: 0.5148 (t0) REVERT: H 142 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5838 (mp0) REVERT: H 149 GLU cc_start: 0.6491 (pt0) cc_final: 0.6013 (tt0) REVERT: H 216 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6314 (tp) REVERT: H 224 LYS cc_start: 0.6580 (mttm) cc_final: 0.6326 (mttp) REVERT: H 269 GLU cc_start: 0.5647 (tp30) cc_final: 0.4883 (tp30) REVERT: H 321 ARG cc_start: 0.6495 (ttt90) cc_final: 0.5907 (ttt90) REVERT: H 419 ASN cc_start: 0.6021 (m-40) cc_final: 0.4777 (t0) REVERT: H 429 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6540 (ptm-80) REVERT: H 438 ASP cc_start: 0.6486 (m-30) cc_final: 0.6070 (m-30) REVERT: I 11 LYS cc_start: 0.5940 (ttmm) cc_final: 0.4908 (tptt) REVERT: I 17 ASN cc_start: 0.6400 (t0) cc_final: 0.5986 (t0) REVERT: I 51 MET cc_start: 0.7200 (mtp) cc_final: 0.6915 (ttm) REVERT: I 67 ASP cc_start: 0.5473 (t70) cc_final: 0.5229 (t70) REVERT: I 117 LYS cc_start: 0.5811 (tptp) cc_final: 0.5449 (tptp) REVERT: I 120 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: I 142 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5623 (mp0) REVERT: I 149 GLU cc_start: 0.6529 (pt0) cc_final: 0.6032 (tt0) REVERT: I 153 ASP cc_start: 0.6661 (t0) cc_final: 0.6352 (t0) REVERT: I 216 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6347 (tp) REVERT: I 224 LYS cc_start: 0.6789 (mttt) cc_final: 0.6517 (mttp) REVERT: I 254 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6183 (mppt) REVERT: I 269 GLU cc_start: 0.5284 (tp30) cc_final: 0.4961 (tp30) REVERT: I 321 ARG cc_start: 0.6446 (ttt90) cc_final: 0.6216 (ttt90) REVERT: I 363 LYS cc_start: 0.6655 (mmmt) cc_final: 0.6107 (mmmm) REVERT: I 370 GLN cc_start: 0.5088 (OUTLIER) cc_final: 0.4868 (pt0) REVERT: I 407 LYS cc_start: 0.6487 (tttm) cc_final: 0.6084 (ttpp) REVERT: I 419 ASN cc_start: 0.5742 (m-40) cc_final: 0.4543 (t0) REVERT: I 434 GLU cc_start: 0.6568 (tp30) cc_final: 0.5628 (pm20) REVERT: J 11 LYS cc_start: 0.5958 (ttmm) cc_final: 0.4923 (tptt) REVERT: J 17 ASN cc_start: 0.6333 (t0) cc_final: 0.5916 (t0) REVERT: J 37 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6765 (m) REVERT: J 39 VAL cc_start: 0.6246 (OUTLIER) cc_final: 0.6040 (m) REVERT: J 149 GLU cc_start: 0.6345 (pt0) cc_final: 0.5833 (tt0) REVERT: J 153 ASP cc_start: 0.6683 (t0) cc_final: 0.6381 (t0) REVERT: J 216 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6350 (tp) REVERT: J 269 GLU cc_start: 0.5398 (tp30) cc_final: 0.5069 (tp30) REVERT: J 370 GLN cc_start: 0.5219 (OUTLIER) cc_final: 0.4935 (pt0) REVERT: J 419 ASN cc_start: 0.5771 (m-40) cc_final: 0.4554 (t0) REVERT: J 429 ARG cc_start: 0.6930 (ttp80) cc_final: 0.6679 (ptm160) REVERT: J 441 MET cc_start: 0.6393 (ttt) cc_final: 0.6017 (tpt) REVERT: K 11 LYS cc_start: 0.5942 (ttmm) cc_final: 0.4913 (tptt) REVERT: K 17 ASN cc_start: 0.6386 (t0) cc_final: 0.5965 (t0) REVERT: K 37 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6749 (m) REVERT: K 39 VAL cc_start: 0.6229 (OUTLIER) cc_final: 0.6015 (m) REVERT: K 149 GLU cc_start: 0.6317 (pt0) cc_final: 0.5817 (tt0) REVERT: K 153 ASP cc_start: 0.6686 (t0) cc_final: 0.6381 (t0) REVERT: K 216 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6336 (tp) REVERT: K 265 MET cc_start: 0.5812 (tpp) cc_final: 0.5584 (tpp) REVERT: K 269 GLU cc_start: 0.5435 (tp30) cc_final: 0.5090 (tp30) REVERT: K 370 GLN cc_start: 0.5247 (OUTLIER) cc_final: 0.4937 (pt0) REVERT: K 419 ASN cc_start: 0.5787 (m-40) cc_final: 0.4569 (t0) REVERT: K 429 ARG cc_start: 0.6944 (ttp80) cc_final: 0.6695 (ptm160) REVERT: K 441 MET cc_start: 0.6424 (ttt) cc_final: 0.6041 (tpt) REVERT: L 8 ASP cc_start: 0.5698 (m-30) cc_final: 0.5267 (m-30) REVERT: L 16 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6211 (mm-30) REVERT: L 19 ARG cc_start: 0.6262 (mmm160) cc_final: 0.4899 (mmm-85) REVERT: L 37 VAL cc_start: 0.6893 (OUTLIER) cc_final: 0.6649 (m) REVERT: L 47 ASP cc_start: 0.6394 (m-30) cc_final: 0.5493 (t70) REVERT: L 50 MET cc_start: 0.6967 (tpp) cc_final: 0.6671 (tpt) REVERT: L 51 MET cc_start: 0.7316 (mtp) cc_final: 0.7066 (ttm) REVERT: L 142 GLU cc_start: 0.6690 (mm-30) cc_final: 0.5811 (mp0) REVERT: L 149 GLU cc_start: 0.6389 (pt0) cc_final: 0.5928 (tt0) REVERT: L 153 ASP cc_start: 0.7009 (t0) cc_final: 0.6766 (t0) REVERT: L 224 LYS cc_start: 0.6509 (mttm) cc_final: 0.6177 (mttp) REVERT: L 269 GLU cc_start: 0.5657 (tp30) cc_final: 0.4898 (tp30) REVERT: L 321 ARG cc_start: 0.6507 (ttt90) cc_final: 0.5960 (ttt90) REVERT: L 370 GLN cc_start: 0.5058 (OUTLIER) cc_final: 0.4837 (pt0) REVERT: L 403 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5370 (mm-30) REVERT: L 419 ASN cc_start: 0.6038 (m-40) cc_final: 0.4793 (t0) REVERT: L 429 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6534 (ptm-80) REVERT: L 438 ASP cc_start: 0.6515 (m-30) cc_final: 0.6116 (m-30) outliers start: 142 outliers final: 61 residues processed: 796 average time/residue: 1.7021 time to fit residues: 1607.9454 Evaluate side-chains 755 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 656 time to evaluate : 4.512 ------------------------------------------------------------------------------- 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 A residue 370 GLN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 GLU 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 C residue 37 VAL Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 120 GLU 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 58 GLU Chi-restraints excluded: chain E residue 67 ASP 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 370 GLN Chi-restraints excluded: chain F residue 37 VAL 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 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 120 GLU 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 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 39 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 319 LEU Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 370 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 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 319 LEU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 325 SER Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 300 optimal weight: 0.8980 chunk 449 optimal weight: 4.9990 chunk 475 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 425 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 128 ASN A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 225 HIS B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 226 ASN E 443 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 HIS F 443 GLN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN G 443 GLN H 24 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN L 24 GLN L 443 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40900 Z= 0.350 Angle : 0.673 9.821 55360 Z= 0.368 Chirality : 0.048 0.198 5964 Planarity : 0.007 0.063 7260 Dihedral : 6.504 59.639 5399 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.55 % Allowed : 11.72 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4884 helix: 1.60 (0.11), residues: 2028 sheet: -0.15 (0.17), residues: 912 loop : 0.06 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 425 HIS 0.006 0.002 HIS I 228 PHE 0.030 0.002 PHE H 285 TYR 0.034 0.003 TYR G 296 ARG 0.009 0.001 ARG C 114 *********************** 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 809 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 655 time to evaluate : 5.110 Fit side-chains REVERT: A 8 ASP cc_start: 0.5850 (m-30) cc_final: 0.5467 (m-30) REVERT: A 16 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6301 (mm-30) REVERT: A 17 ASN cc_start: 0.6253 (t0) cc_final: 0.5848 (t0) REVERT: A 19 ARG cc_start: 0.6253 (mmm160) cc_final: 0.4876 (mmm-85) REVERT: A 47 ASP cc_start: 0.6370 (m-30) cc_final: 0.5515 (t70) REVERT: A 50 MET cc_start: 0.6798 (mmm) cc_final: 0.6483 (tpt) REVERT: A 142 GLU cc_start: 0.6563 (mm-30) cc_final: 0.5708 (mp0) REVERT: A 149 GLU cc_start: 0.6524 (pt0) cc_final: 0.6008 (tt0) REVERT: A 254 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6472 (mptt) REVERT: A 269 GLU cc_start: 0.5612 (tp30) cc_final: 0.4812 (tp30) REVERT: A 321 ARG cc_start: 0.6449 (ttt90) cc_final: 0.5889 (ttt90) REVERT: A 403 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5403 (mm-30) REVERT: A 407 LYS cc_start: 0.6561 (tttp) cc_final: 0.6222 (ttpp) REVERT: A 416 GLN cc_start: 0.6332 (mm110) cc_final: 0.6096 (mm110) REVERT: A 419 ASN cc_start: 0.5980 (m-40) cc_final: 0.4745 (t0) REVERT: A 434 GLU cc_start: 0.6608 (tp30) cc_final: 0.5444 (pm20) REVERT: A 438 ASP cc_start: 0.6511 (m-30) cc_final: 0.6093 (m-30) REVERT: B 8 ASP cc_start: 0.5773 (m-30) cc_final: 0.5353 (m-30) REVERT: B 17 ASN cc_start: 0.6232 (t0) cc_final: 0.5783 (t0) REVERT: B 22 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7255 (tpp80) REVERT: B 58 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4700 (mt-10) REVERT: B 254 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6550 (mttp) REVERT: B 269 GLU cc_start: 0.5704 (tp30) cc_final: 0.5158 (tp30) REVERT: B 321 ARG cc_start: 0.6386 (tmt-80) cc_final: 0.5857 (ttp80) REVERT: B 370 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4845 (pt0) REVERT: B 386 GLN cc_start: 0.6689 (mt0) cc_final: 0.5939 (mt0) REVERT: B 407 LYS cc_start: 0.6548 (ttpp) cc_final: 0.6259 (ttmm) REVERT: B 419 ASN cc_start: 0.5965 (m-40) cc_final: 0.4577 (t0) REVERT: B 427 TYR cc_start: 0.6897 (m-80) cc_final: 0.5363 (t80) REVERT: C 11 LYS cc_start: 0.5844 (ttmm) cc_final: 0.5629 (ttpp) REVERT: C 142 GLU cc_start: 0.5359 (pm20) cc_final: 0.5127 (mp0) REVERT: C 149 GLU cc_start: 0.6437 (pt0) cc_final: 0.5864 (tt0) REVERT: C 184 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: C 216 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6298 (tp) REVERT: C 254 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6130 (mppt) REVERT: C 269 GLU cc_start: 0.5402 (tp30) cc_final: 0.4844 (tp30) REVERT: C 321 ARG cc_start: 0.6499 (ttt90) cc_final: 0.6151 (ttt90) REVERT: C 329 SER cc_start: 0.7310 (p) cc_final: 0.7049 (p) REVERT: C 363 LYS cc_start: 0.6783 (mmmt) cc_final: 0.6203 (mmmm) REVERT: C 407 LYS cc_start: 0.6880 (tttp) cc_final: 0.6480 (ttpp) REVERT: C 419 ASN cc_start: 0.5787 (m-40) cc_final: 0.4580 (t0) REVERT: C 434 GLU cc_start: 0.6517 (tp30) cc_final: 0.5494 (pm20) REVERT: D 8 ASP cc_start: 0.5705 (m-30) cc_final: 0.5269 (m-30) REVERT: D 22 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7094 (tpp80) REVERT: D 37 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6524 (m) REVERT: D 223 ARG cc_start: 0.6626 (tpp-160) cc_final: 0.6036 (ttt180) REVERT: D 269 GLU cc_start: 0.5694 (tp30) cc_final: 0.5138 (tp30) REVERT: D 321 ARG cc_start: 0.6437 (tmt-80) cc_final: 0.5920 (ttp80) REVERT: D 386 GLN cc_start: 0.6653 (mt0) cc_final: 0.5918 (mt0) REVERT: D 419 ASN cc_start: 0.5975 (m-40) cc_final: 0.4588 (t0) REVERT: D 427 TYR cc_start: 0.6910 (m-80) cc_final: 0.5392 (t80) REVERT: D 434 GLU cc_start: 0.6445 (tp30) cc_final: 0.5350 (pm20) REVERT: D 441 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.5967 (tpt) REVERT: E 8 ASP cc_start: 0.5764 (m-30) cc_final: 0.5343 (m-30) REVERT: E 17 ASN cc_start: 0.6175 (t0) cc_final: 0.5738 (t0) REVERT: E 22 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7207 (tpp80) REVERT: E 58 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4706 (mt-10) REVERT: E 67 ASP cc_start: 0.5401 (OUTLIER) cc_final: 0.5113 (t0) REVERT: E 269 GLU cc_start: 0.5640 (tp30) cc_final: 0.5159 (tp30) REVERT: E 321 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5784 (ttt90) REVERT: E 370 GLN cc_start: 0.5169 (OUTLIER) cc_final: 0.4905 (pt0) REVERT: E 386 GLN cc_start: 0.6613 (mt0) cc_final: 0.5897 (mt0) REVERT: E 407 LYS cc_start: 0.6509 (ttpp) cc_final: 0.6259 (ttmm) REVERT: E 419 ASN cc_start: 0.5941 (m-40) cc_final: 0.4555 (t0) REVERT: E 427 TYR cc_start: 0.6892 (m-80) cc_final: 0.5376 (t80) REVERT: E 434 GLU cc_start: 0.6477 (tp30) cc_final: 0.5366 (pm20) REVERT: E 441 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5933 (tpt) REVERT: F 8 ASP cc_start: 0.5809 (m-30) cc_final: 0.5441 (m-30) REVERT: F 16 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6279 (mm-30) REVERT: F 19 ARG cc_start: 0.6238 (mmm160) cc_final: 0.4842 (mmm-85) REVERT: F 47 ASP cc_start: 0.6417 (m-30) cc_final: 0.5507 (t70) REVERT: F 142 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5618 (mp0) REVERT: F 149 GLU cc_start: 0.6471 (pt0) cc_final: 0.6010 (tt0) REVERT: F 184 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: F 223 ARG cc_start: 0.6749 (mtp85) cc_final: 0.6441 (ttt90) REVERT: F 252 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6247 (mtpt) REVERT: F 269 GLU cc_start: 0.5612 (tp30) cc_final: 0.4785 (tp30) REVERT: F 321 ARG cc_start: 0.6425 (ttt90) cc_final: 0.5826 (ttt90) REVERT: F 335 ARG cc_start: 0.6891 (mtp-110) cc_final: 0.6676 (mtp85) REVERT: F 403 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5452 (mm-30) REVERT: F 419 ASN cc_start: 0.6000 (m-40) cc_final: 0.4769 (t0) REVERT: F 429 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6817 (ttp80) REVERT: F 438 ASP cc_start: 0.6518 (m-30) cc_final: 0.6098 (m-30) REVERT: G 8 ASP cc_start: 0.5721 (m-30) cc_final: 0.5272 (m-30) REVERT: G 17 ASN cc_start: 0.6266 (t0) cc_final: 0.5826 (t0) REVERT: G 22 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7132 (tpp80) REVERT: G 37 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6585 (m) REVERT: G 69 TYR cc_start: 0.7317 (m-80) cc_final: 0.6980 (m-80) REVERT: G 223 ARG cc_start: 0.6620 (tpp-160) cc_final: 0.6029 (ttt180) REVERT: G 254 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6642 (mttm) REVERT: G 269 GLU cc_start: 0.5526 (tp30) cc_final: 0.5222 (tp30) REVERT: G 321 ARG cc_start: 0.6446 (tmt-80) cc_final: 0.5933 (ttp80) REVERT: G 370 GLN cc_start: 0.5239 (OUTLIER) cc_final: 0.4909 (pt0) REVERT: G 386 GLN cc_start: 0.6675 (mt0) cc_final: 0.5931 (mt0) REVERT: G 419 ASN cc_start: 0.5981 (m-40) cc_final: 0.4596 (t0) REVERT: G 434 GLU cc_start: 0.6491 (tp30) cc_final: 0.5408 (pm20) REVERT: G 441 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5977 (tpt) REVERT: H 8 ASP cc_start: 0.5864 (m-30) cc_final: 0.5499 (m-30) REVERT: H 16 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6275 (mm-30) REVERT: H 19 ARG cc_start: 0.6243 (mmm160) cc_final: 0.4805 (mmm-85) REVERT: H 22 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6818 (mtt-85) REVERT: H 47 ASP cc_start: 0.6383 (m-30) cc_final: 0.5536 (t70) REVERT: H 142 GLU cc_start: 0.6538 (mm-30) cc_final: 0.5711 (mp0) REVERT: H 149 GLU cc_start: 0.6507 (pt0) cc_final: 0.5985 (tt0) REVERT: H 216 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6221 (tp) REVERT: H 269 GLU cc_start: 0.5631 (tp30) cc_final: 0.4897 (tp30) REVERT: H 321 ARG cc_start: 0.6430 (ttt90) cc_final: 0.5833 (ttt90) REVERT: H 403 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5480 (mm-30) REVERT: H 419 ASN cc_start: 0.5978 (m-40) cc_final: 0.4724 (t0) REVERT: H 438 ASP cc_start: 0.6495 (m-30) cc_final: 0.6068 (m-30) REVERT: I 51 MET cc_start: 0.7102 (mtp) cc_final: 0.6816 (ttm) REVERT: I 117 LYS cc_start: 0.5715 (tptp) cc_final: 0.5374 (tptp) REVERT: I 120 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: I 142 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5620 (mp0) REVERT: I 149 GLU cc_start: 0.6323 (pt0) cc_final: 0.5853 (tt0) REVERT: I 216 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6318 (tp) REVERT: I 254 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6120 (mppt) REVERT: I 269 GLU cc_start: 0.5219 (tp30) cc_final: 0.4959 (mm-30) REVERT: I 321 ARG cc_start: 0.6482 (ttt90) cc_final: 0.6130 (ttt90) REVERT: I 363 LYS cc_start: 0.6742 (mmmt) cc_final: 0.6172 (mmmm) REVERT: I 407 LYS cc_start: 0.6729 (tttm) cc_final: 0.6342 (ttpp) REVERT: I 419 ASN cc_start: 0.5785 (m-40) cc_final: 0.4579 (t0) REVERT: I 434 GLU cc_start: 0.6587 (tp30) cc_final: 0.5574 (pm20) REVERT: J 11 LYS cc_start: 0.5831 (ttmm) cc_final: 0.5628 (ttpp) REVERT: J 149 GLU cc_start: 0.6446 (pt0) cc_final: 0.5858 (tt0) REVERT: J 216 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6310 (tp) REVERT: J 269 GLU cc_start: 0.5194 (tp30) cc_final: 0.4957 (mm-30) REVERT: J 370 GLN cc_start: 0.5144 (OUTLIER) cc_final: 0.4901 (pt0) REVERT: J 419 ASN cc_start: 0.5775 (m-40) cc_final: 0.4526 (t0) REVERT: J 429 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6920 (ttp80) REVERT: J 441 MET cc_start: 0.6418 (ttt) cc_final: 0.5998 (tpt) REVERT: K 11 LYS cc_start: 0.5810 (ttmm) cc_final: 0.5609 (ttpp) REVERT: K 22 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6501 (mmt-90) REVERT: K 51 MET cc_start: 0.7086 (mtt) cc_final: 0.6815 (mtt) REVERT: K 149 GLU cc_start: 0.6451 (pt0) cc_final: 0.5901 (tt0) REVERT: K 216 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6299 (tp) REVERT: K 254 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6174 (mppt) REVERT: K 265 MET cc_start: 0.5909 (tpp) cc_final: 0.5617 (tpp) REVERT: K 269 GLU cc_start: 0.5186 (tp30) cc_final: 0.4954 (mm-30) REVERT: K 370 GLN cc_start: 0.5172 (OUTLIER) cc_final: 0.4955 (pt0) REVERT: K 419 ASN cc_start: 0.5791 (m-40) cc_final: 0.4540 (t0) REVERT: K 441 MET cc_start: 0.6416 (ttt) cc_final: 0.6000 (tpt) REVERT: L 8 ASP cc_start: 0.5842 (m-30) cc_final: 0.5482 (m-30) REVERT: L 16 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6292 (mm-30) REVERT: L 19 ARG cc_start: 0.6238 (mmm160) cc_final: 0.4886 (mmm-85) REVERT: L 47 ASP cc_start: 0.6361 (m-30) cc_final: 0.5505 (t70) REVERT: L 142 GLU cc_start: 0.6655 (mm-30) cc_final: 0.5768 (mp0) REVERT: L 149 GLU cc_start: 0.6482 (pt0) cc_final: 0.5978 (tt0) REVERT: L 224 LYS cc_start: 0.6740 (mttm) cc_final: 0.6415 (mttp) REVERT: L 254 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6304 (mptt) REVERT: L 269 GLU cc_start: 0.5641 (tp30) cc_final: 0.4932 (tp30) REVERT: L 321 ARG cc_start: 0.6451 (ttt90) cc_final: 0.5886 (ttt90) REVERT: L 370 GLN cc_start: 0.5425 (OUTLIER) cc_final: 0.5220 (pt0) REVERT: L 403 GLU cc_start: 0.6046 (mm-30) cc_final: 0.5438 (mm-30) REVERT: L 419 ASN cc_start: 0.5995 (m-40) cc_final: 0.4740 (t0) REVERT: L 434 GLU cc_start: 0.6558 (tp30) cc_final: 0.6236 (tp30) REVERT: L 438 ASP cc_start: 0.6517 (m-30) cc_final: 0.6112 (m-30) outliers start: 154 outliers final: 84 residues processed: 789 average time/residue: 1.7233 time to fit residues: 1617.5504 Evaluate side-chains 755 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 638 time to evaluate : 4.422 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 441 MET Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 67 ASP 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 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain F residue 37 VAL 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 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 252 LYS Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 120 GLU 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 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 39 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 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 370 GLN Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 39 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR 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 325 SER Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 405 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 426 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** 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 D 402 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40900 Z= 0.271 Angle : 0.601 8.962 55360 Z= 0.329 Chirality : 0.045 0.163 5964 Planarity : 0.006 0.049 7260 Dihedral : 6.386 59.299 5399 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.29 % Allowed : 12.25 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 4884 helix: 1.70 (0.11), residues: 2028 sheet: -0.20 (0.17), residues: 912 loop : 0.08 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 425 HIS 0.005 0.002 HIS J 195 PHE 0.025 0.002 PHE H 285 TYR 0.030 0.003 TYR D 296 ARG 0.007 0.001 ARG C 335 *********************** 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 787 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 644 time to evaluate : 4.551 Fit side-chains REVERT: A 8 ASP cc_start: 0.5817 (m-30) cc_final: 0.5375 (m-30) REVERT: A 16 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6279 (mm-30) REVERT: A 19 ARG cc_start: 0.6253 (mmm160) cc_final: 0.4890 (mmm-85) REVERT: A 47 ASP cc_start: 0.6396 (m-30) cc_final: 0.5526 (t70) REVERT: A 149 GLU cc_start: 0.6485 (pt0) cc_final: 0.5939 (tt0) REVERT: A 254 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6381 (mppt) REVERT: A 269 GLU cc_start: 0.5611 (tp30) cc_final: 0.4841 (tp30) REVERT: A 321 ARG cc_start: 0.6532 (ttt90) cc_final: 0.5849 (ttt90) REVERT: A 403 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5368 (mm-30) REVERT: A 407 LYS cc_start: 0.6534 (tttp) cc_final: 0.6173 (ttpp) REVERT: A 416 GLN cc_start: 0.6318 (mm110) cc_final: 0.6084 (mm110) REVERT: A 419 ASN cc_start: 0.5978 (m-40) cc_final: 0.4741 (t0) REVERT: A 434 GLU cc_start: 0.6563 (tp30) cc_final: 0.5366 (pm20) REVERT: A 438 ASP cc_start: 0.6499 (m-30) cc_final: 0.6073 (m-30) REVERT: B 8 ASP cc_start: 0.5738 (m-30) cc_final: 0.5313 (m-30) REVERT: B 17 ASN cc_start: 0.6211 (t0) cc_final: 0.5760 (t0) REVERT: B 22 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7324 (tpp80) REVERT: B 58 GLU cc_start: 0.5008 (OUTLIER) cc_final: 0.4747 (mt-10) REVERT: B 254 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6560 (mttt) REVERT: B 269 GLU cc_start: 0.5722 (tp30) cc_final: 0.5146 (tp30) REVERT: B 321 ARG cc_start: 0.6396 (tmt-80) cc_final: 0.5870 (ttp80) REVERT: B 370 GLN cc_start: 0.5128 (OUTLIER) cc_final: 0.4822 (pt0) REVERT: B 386 GLN cc_start: 0.6704 (mt0) cc_final: 0.5966 (mt0) REVERT: B 419 ASN cc_start: 0.5963 (m-40) cc_final: 0.4573 (t0) REVERT: B 427 TYR cc_start: 0.6937 (m-80) cc_final: 0.5413 (t80) REVERT: C 11 LYS cc_start: 0.5759 (ttmm) cc_final: 0.5501 (ttpp) REVERT: C 142 GLU cc_start: 0.5284 (pm20) cc_final: 0.5022 (mp0) REVERT: C 149 GLU cc_start: 0.6448 (pt0) cc_final: 0.5914 (tt0) REVERT: C 153 ASP cc_start: 0.6846 (t0) cc_final: 0.6606 (t0) REVERT: C 184 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: C 216 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6295 (tp) REVERT: C 254 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6057 (mppt) REVERT: C 269 GLU cc_start: 0.5379 (tp30) cc_final: 0.4889 (tp30) REVERT: C 321 ARG cc_start: 0.6499 (ttt90) cc_final: 0.6210 (ttt90) REVERT: C 329 SER cc_start: 0.7322 (p) cc_final: 0.7073 (p) REVERT: C 363 LYS cc_start: 0.6879 (mmmt) cc_final: 0.6285 (mmmm) REVERT: C 407 LYS cc_start: 0.6822 (tttp) cc_final: 0.6427 (ttpp) REVERT: C 419 ASN cc_start: 0.5804 (m-40) cc_final: 0.4572 (t0) REVERT: C 434 GLU cc_start: 0.6498 (tp30) cc_final: 0.5454 (pm20) REVERT: D 8 ASP cc_start: 0.5738 (m-30) cc_final: 0.5287 (m-30) REVERT: D 22 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7116 (tpp80) REVERT: D 37 VAL cc_start: 0.6885 (OUTLIER) cc_final: 0.6587 (m) REVERT: D 223 ARG cc_start: 0.6657 (tpp-160) cc_final: 0.6074 (ttt180) REVERT: D 269 GLU cc_start: 0.5679 (tp30) cc_final: 0.5093 (tp30) REVERT: D 321 ARG cc_start: 0.6459 (tmt-80) cc_final: 0.5925 (ttp80) REVERT: D 386 GLN cc_start: 0.6672 (mt0) cc_final: 0.5932 (mt0) REVERT: D 419 ASN cc_start: 0.5977 (m-40) cc_final: 0.4585 (t0) REVERT: D 427 TYR cc_start: 0.6912 (m-80) cc_final: 0.5435 (t80) REVERT: D 434 GLU cc_start: 0.6450 (tp30) cc_final: 0.5337 (pm20) REVERT: D 441 MET cc_start: 0.6354 (ttt) cc_final: 0.5922 (tpt) REVERT: E 8 ASP cc_start: 0.5719 (m-30) cc_final: 0.5311 (m-30) REVERT: E 17 ASN cc_start: 0.6135 (t0) cc_final: 0.5690 (t0) REVERT: E 22 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7049 (tpp80) REVERT: E 58 GLU cc_start: 0.5010 (OUTLIER) cc_final: 0.4751 (mt-10) REVERT: E 67 ASP cc_start: 0.5301 (OUTLIER) cc_final: 0.5009 (t0) REVERT: E 269 GLU cc_start: 0.5587 (tp30) cc_final: 0.5112 (tp30) REVERT: E 321 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5807 (ttt90) REVERT: E 370 GLN cc_start: 0.5319 (OUTLIER) cc_final: 0.5084 (pt0) REVERT: E 386 GLN cc_start: 0.6601 (mt0) cc_final: 0.5869 (mt0) REVERT: E 419 ASN cc_start: 0.5939 (m-40) cc_final: 0.4556 (t0) REVERT: E 427 TYR cc_start: 0.6925 (m-80) cc_final: 0.5419 (t80) REVERT: E 434 GLU cc_start: 0.6465 (tp30) cc_final: 0.5342 (pm20) REVERT: E 441 MET cc_start: 0.6402 (ttt) cc_final: 0.5993 (tpt) REVERT: F 8 ASP cc_start: 0.5828 (m-30) cc_final: 0.5386 (m-30) REVERT: F 16 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6321 (mm-30) REVERT: F 19 ARG cc_start: 0.6246 (mmm160) cc_final: 0.4877 (mmm-85) REVERT: F 37 VAL cc_start: 0.6915 (OUTLIER) cc_final: 0.6656 (m) REVERT: F 47 ASP cc_start: 0.6422 (m-30) cc_final: 0.5524 (t70) REVERT: F 149 GLU cc_start: 0.6362 (pt0) cc_final: 0.5928 (tt0) REVERT: F 159 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6684 (pp) REVERT: F 184 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: F 223 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6475 (ttt90) REVERT: F 252 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6262 (mtpt) REVERT: F 269 GLU cc_start: 0.5600 (tp30) cc_final: 0.4798 (tp30) REVERT: F 321 ARG cc_start: 0.6441 (ttt90) cc_final: 0.5802 (ttt90) REVERT: F 335 ARG cc_start: 0.6939 (mtp-110) cc_final: 0.6718 (mtp85) REVERT: F 403 GLU cc_start: 0.6041 (mm-30) cc_final: 0.5423 (mm-30) REVERT: F 419 ASN cc_start: 0.5982 (m-40) cc_final: 0.4745 (t0) REVERT: F 429 ARG cc_start: 0.6993 (ttp80) cc_final: 0.6528 (ptm-80) REVERT: F 438 ASP cc_start: 0.6506 (m-30) cc_final: 0.6077 (m-30) REVERT: G 8 ASP cc_start: 0.5752 (m-30) cc_final: 0.5305 (m-30) REVERT: G 22 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7106 (tpp80) REVERT: G 37 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6633 (m) REVERT: G 39 VAL cc_start: 0.6513 (OUTLIER) cc_final: 0.6239 (m) REVERT: G 69 TYR cc_start: 0.7311 (m-80) cc_final: 0.6960 (m-80) REVERT: G 223 ARG cc_start: 0.6653 (tpp-160) cc_final: 0.6066 (ttt180) REVERT: G 254 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6658 (mttm) REVERT: G 269 GLU cc_start: 0.5455 (tp30) cc_final: 0.5242 (tp30) REVERT: G 321 ARG cc_start: 0.6468 (tmt-80) cc_final: 0.5937 (ttp80) REVERT: G 370 GLN cc_start: 0.5373 (OUTLIER) cc_final: 0.5073 (pt0) REVERT: G 386 GLN cc_start: 0.6676 (mt0) cc_final: 0.5929 (mt0) REVERT: G 419 ASN cc_start: 0.5983 (m-40) cc_final: 0.4591 (t0) REVERT: G 434 GLU cc_start: 0.6491 (tp30) cc_final: 0.5404 (pm20) REVERT: G 441 MET cc_start: 0.6420 (ttt) cc_final: 0.6026 (tpt) REVERT: H 8 ASP cc_start: 0.5823 (m-30) cc_final: 0.5396 (m-30) REVERT: H 16 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6285 (mm-30) REVERT: H 19 ARG cc_start: 0.6245 (mmm160) cc_final: 0.4802 (mmm-85) REVERT: H 22 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6721 (mtt-85) REVERT: H 47 ASP cc_start: 0.6378 (m-30) cc_final: 0.5528 (t70) REVERT: H 142 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5737 (mp0) REVERT: H 149 GLU cc_start: 0.6463 (pt0) cc_final: 0.5912 (tt0) REVERT: H 216 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6268 (tp) REVERT: H 269 GLU cc_start: 0.5508 (tp30) cc_final: 0.4778 (tp30) REVERT: H 321 ARG cc_start: 0.6451 (ttt90) cc_final: 0.5828 (ttt90) REVERT: H 403 GLU cc_start: 0.6054 (mm-30) cc_final: 0.5447 (mm-30) REVERT: H 419 ASN cc_start: 0.5951 (m-40) cc_final: 0.4704 (t0) REVERT: H 438 ASP cc_start: 0.6495 (m-30) cc_final: 0.6064 (m-30) REVERT: I 11 LYS cc_start: 0.5622 (ttpp) cc_final: 0.4662 (tptt) REVERT: I 22 ARG cc_start: 0.7727 (mtt90) cc_final: 0.7282 (tpp80) REVERT: I 51 MET cc_start: 0.7085 (mtp) cc_final: 0.6796 (ttm) REVERT: I 117 LYS cc_start: 0.5724 (tptp) cc_final: 0.5391 (tptp) REVERT: I 120 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: I 142 GLU cc_start: 0.6334 (mm-30) cc_final: 0.5623 (mp0) REVERT: I 149 GLU cc_start: 0.6448 (pt0) cc_final: 0.5863 (tt0) REVERT: I 153 ASP cc_start: 0.6845 (t0) cc_final: 0.6606 (t0) REVERT: I 216 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6309 (tp) REVERT: I 254 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5998 (mppt) REVERT: I 269 GLU cc_start: 0.5113 (tp30) cc_final: 0.4720 (tp30) REVERT: I 321 ARG cc_start: 0.6476 (ttt90) cc_final: 0.6190 (ttt90) REVERT: I 363 LYS cc_start: 0.6818 (mmmt) cc_final: 0.6251 (mmmm) REVERT: I 407 LYS cc_start: 0.6705 (tttm) cc_final: 0.6310 (ttpp) REVERT: I 419 ASN cc_start: 0.5800 (m-40) cc_final: 0.4568 (t0) REVERT: I 434 GLU cc_start: 0.6574 (tp30) cc_final: 0.5520 (pm20) REVERT: J 11 LYS cc_start: 0.5769 (ttmm) cc_final: 0.5508 (ttpp) REVERT: J 37 VAL cc_start: 0.6965 (OUTLIER) cc_final: 0.6686 (m) REVERT: J 153 ASP cc_start: 0.6848 (t0) cc_final: 0.6608 (t0) REVERT: J 216 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6307 (tp) REVERT: J 419 ASN cc_start: 0.5788 (m-40) cc_final: 0.4526 (t0) REVERT: J 429 ARG cc_start: 0.7043 (ttp80) cc_final: 0.6801 (ttp80) REVERT: J 441 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5950 (tpt) REVERT: K 11 LYS cc_start: 0.5751 (ttmm) cc_final: 0.5493 (ttpp) REVERT: K 22 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6527 (mmt-90) REVERT: K 37 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6667 (m) REVERT: K 51 MET cc_start: 0.7077 (mtt) cc_final: 0.6814 (mtt) REVERT: K 153 ASP cc_start: 0.6855 (t0) cc_final: 0.6614 (t0) REVERT: K 216 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6296 (tp) REVERT: K 254 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6149 (mppt) REVERT: K 265 MET cc_start: 0.5913 (tpp) cc_final: 0.5614 (tpp) REVERT: K 370 GLN cc_start: 0.5186 (OUTLIER) cc_final: 0.4951 (pt0) REVERT: K 419 ASN cc_start: 0.5806 (m-40) cc_final: 0.4542 (t0) REVERT: K 441 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5947 (tpt) REVERT: L 8 ASP cc_start: 0.5801 (m-30) cc_final: 0.5382 (m-30) REVERT: L 16 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6318 (mm-30) REVERT: L 19 ARG cc_start: 0.6246 (mmm160) cc_final: 0.4889 (mmm-85) REVERT: L 47 ASP cc_start: 0.6380 (m-30) cc_final: 0.5507 (t70) REVERT: L 50 MET cc_start: 0.6774 (mmm) cc_final: 0.6528 (tpt) REVERT: L 142 GLU cc_start: 0.6670 (mm-30) cc_final: 0.5808 (mp0) REVERT: L 149 GLU cc_start: 0.6472 (pt0) cc_final: 0.5934 (tt0) REVERT: L 159 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6689 (pp) REVERT: L 224 LYS cc_start: 0.6720 (mttm) cc_final: 0.6375 (mttp) REVERT: L 269 GLU cc_start: 0.5626 (tp30) cc_final: 0.4916 (tp30) REVERT: L 321 ARG cc_start: 0.6460 (ttt90) cc_final: 0.5876 (ttt90) REVERT: L 370 GLN cc_start: 0.5461 (OUTLIER) cc_final: 0.5246 (pt0) REVERT: L 403 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5400 (mm-30) REVERT: L 419 ASN cc_start: 0.5967 (m-40) cc_final: 0.4720 (t0) REVERT: L 438 ASP cc_start: 0.6516 (m-30) cc_final: 0.6087 (m-30) outliers start: 143 outliers final: 74 residues processed: 771 average time/residue: 1.6964 time to fit residues: 1551.3866 Evaluate side-chains 746 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 635 time to evaluate : 4.477 ------------------------------------------------------------------------------- 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 99 THR 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 58 GLU Chi-restraints excluded: chain E residue 67 ASP 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 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain F residue 37 VAL 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 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU 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 120 GLU 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 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 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 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 441 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 370 GLN Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain L residue 37 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 Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 1.9990 chunk 428 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 476 optimal weight: 6.9990 chunk 395 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** 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** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 443 GLN F 17 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 128 ASN L 443 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40900 Z= 0.351 Angle : 0.673 9.794 55360 Z= 0.369 Chirality : 0.048 0.214 5964 Planarity : 0.007 0.062 7260 Dihedral : 6.602 59.617 5399 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.22 % Allowed : 12.34 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.12), residues: 4884 helix: 1.52 (0.11), residues: 2028 sheet: -0.24 (0.17), residues: 912 loop : -0.06 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 425 HIS 0.007 0.002 HIS H 228 PHE 0.031 0.002 PHE C 285 TYR 0.034 0.003 TYR G 296 ARG 0.008 0.001 ARG I 114 *********************** 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 781 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 641 time to evaluate : 4.590 Fit side-chains REVERT: A 8 ASP cc_start: 0.5773 (m-30) cc_final: 0.5442 (m-30) REVERT: A 16 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6411 (mm-30) REVERT: A 17 ASN cc_start: 0.6222 (t0) cc_final: 0.5822 (t0) REVERT: A 19 ARG cc_start: 0.6236 (mmm160) cc_final: 0.4876 (mmm-85) REVERT: A 47 ASP cc_start: 0.6352 (m-30) cc_final: 0.5511 (t70) REVERT: A 142 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5704 (mp0) REVERT: A 254 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6497 (mptt) REVERT: A 269 GLU cc_start: 0.5623 (tp30) cc_final: 0.4820 (tp30) REVERT: A 321 ARG cc_start: 0.6509 (ttt90) cc_final: 0.5813 (ttt90) REVERT: A 403 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5398 (mm-30) REVERT: A 407 LYS cc_start: 0.6555 (tttp) cc_final: 0.6207 (ttpp) REVERT: A 419 ASN cc_start: 0.5861 (m-40) cc_final: 0.4614 (t0) REVERT: A 434 GLU cc_start: 0.6614 (tp30) cc_final: 0.5456 (pm20) REVERT: A 438 ASP cc_start: 0.6500 (m-30) cc_final: 0.6069 (m-30) REVERT: B 8 ASP cc_start: 0.5753 (m-30) cc_final: 0.5303 (m-30) REVERT: B 17 ASN cc_start: 0.6187 (t0) cc_final: 0.5745 (t0) REVERT: B 22 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7172 (tpp80) REVERT: B 58 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4702 (mt-10) REVERT: B 254 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6582 (mttt) REVERT: B 269 GLU cc_start: 0.5647 (tp30) cc_final: 0.5406 (tp30) REVERT: B 321 ARG cc_start: 0.6375 (tmt-80) cc_final: 0.5875 (ttp80) REVERT: B 370 GLN cc_start: 0.5502 (OUTLIER) cc_final: 0.5191 (pt0) REVERT: B 386 GLN cc_start: 0.6629 (mt0) cc_final: 0.5905 (mt0) REVERT: B 419 ASN cc_start: 0.5981 (m-40) cc_final: 0.4587 (t0) REVERT: B 427 TYR cc_start: 0.6885 (m-80) cc_final: 0.5320 (t80) REVERT: C 153 ASP cc_start: 0.6836 (t0) cc_final: 0.6587 (t0) REVERT: C 184 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: C 216 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6291 (tp) REVERT: C 254 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6059 (mppt) REVERT: C 269 GLU cc_start: 0.5396 (tp30) cc_final: 0.4910 (tp30) REVERT: C 321 ARG cc_start: 0.6449 (ttt90) cc_final: 0.6165 (ttt90) REVERT: C 329 SER cc_start: 0.7310 (p) cc_final: 0.7054 (p) REVERT: C 363 LYS cc_start: 0.6910 (mmmt) cc_final: 0.6329 (mmmm) REVERT: C 407 LYS cc_start: 0.6825 (tttp) cc_final: 0.6411 (ttpp) REVERT: C 419 ASN cc_start: 0.5821 (m-40) cc_final: 0.4556 (t0) REVERT: C 434 GLU cc_start: 0.6523 (tp30) cc_final: 0.5491 (pm20) REVERT: D 8 ASP cc_start: 0.5744 (m-30) cc_final: 0.5309 (m-30) REVERT: D 22 ARG cc_start: 0.7614 (ttm170) cc_final: 0.6922 (tpp80) REVERT: D 37 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6541 (m) REVERT: D 223 ARG cc_start: 0.6664 (tpp-160) cc_final: 0.6063 (ttt180) REVERT: D 254 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6340 (mttp) REVERT: D 269 GLU cc_start: 0.5663 (tp30) cc_final: 0.5444 (tp30) REVERT: D 321 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5844 (ttp80) REVERT: D 386 GLN cc_start: 0.6622 (mt0) cc_final: 0.5901 (mt0) REVERT: D 419 ASN cc_start: 0.6000 (m-40) cc_final: 0.4600 (t0) REVERT: D 427 TYR cc_start: 0.6949 (m-80) cc_final: 0.5385 (t80) REVERT: D 434 GLU cc_start: 0.6457 (tp30) cc_final: 0.5365 (pm20) REVERT: D 441 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6001 (tpt) REVERT: E 8 ASP cc_start: 0.5741 (m-30) cc_final: 0.5301 (m-30) REVERT: E 17 ASN cc_start: 0.6148 (t0) cc_final: 0.5744 (t0) REVERT: E 22 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7139 (tpp80) REVERT: E 67 ASP cc_start: 0.5386 (OUTLIER) cc_final: 0.5083 (t0) REVERT: E 269 GLU cc_start: 0.5634 (tp30) cc_final: 0.5154 (tp30) REVERT: E 321 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5917 (ttt90) REVERT: E 370 GLN cc_start: 0.5563 (OUTLIER) cc_final: 0.5333 (pt0) REVERT: E 386 GLN cc_start: 0.6610 (mt0) cc_final: 0.5905 (mt0) REVERT: E 419 ASN cc_start: 0.5958 (m-40) cc_final: 0.4564 (t0) REVERT: E 427 TYR cc_start: 0.6930 (m-80) cc_final: 0.5331 (t80) REVERT: E 434 GLU cc_start: 0.6468 (tp30) cc_final: 0.5403 (pm20) REVERT: E 441 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5984 (tpt) REVERT: F 8 ASP cc_start: 0.5737 (m-30) cc_final: 0.5421 (m-30) REVERT: F 16 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6393 (mm-30) REVERT: F 19 ARG cc_start: 0.6247 (mmm160) cc_final: 0.4899 (mmm-85) REVERT: F 37 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6567 (m) REVERT: F 47 ASP cc_start: 0.6384 (m-30) cc_final: 0.5521 (t70) REVERT: F 142 GLU cc_start: 0.6460 (mm-30) cc_final: 0.5609 (mp0) REVERT: F 149 GLU cc_start: 0.6392 (pt0) cc_final: 0.5961 (tt0) REVERT: F 159 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6771 (pp) REVERT: F 184 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: F 223 ARG cc_start: 0.6797 (mtp85) cc_final: 0.6487 (ttt90) REVERT: F 252 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6247 (mtpt) REVERT: F 269 GLU cc_start: 0.5620 (tp30) cc_final: 0.4799 (tp30) REVERT: F 321 ARG cc_start: 0.6418 (ttt90) cc_final: 0.5757 (ttt90) REVERT: F 370 GLN cc_start: 0.5553 (OUTLIER) cc_final: 0.5344 (pt0) REVERT: F 403 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5416 (mm-30) REVERT: F 419 ASN cc_start: 0.5987 (m-40) cc_final: 0.4763 (t0) REVERT: F 429 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6798 (ttp80) REVERT: F 438 ASP cc_start: 0.6507 (m-30) cc_final: 0.6074 (m-30) REVERT: G 8 ASP cc_start: 0.5765 (m-30) cc_final: 0.5336 (m-30) REVERT: G 17 ASN cc_start: 0.6281 (t0) cc_final: 0.5884 (t0) REVERT: G 22 ARG cc_start: 0.7615 (ttm170) cc_final: 0.7105 (tpp80) REVERT: G 37 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6558 (m) REVERT: G 69 TYR cc_start: 0.7317 (m-80) cc_final: 0.6952 (m-80) REVERT: G 223 ARG cc_start: 0.6658 (tpp-160) cc_final: 0.6054 (ttt180) REVERT: G 254 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6645 (mttm) REVERT: G 321 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5855 (ttp80) REVERT: G 370 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.5342 (pt0) REVERT: G 386 GLN cc_start: 0.6631 (mt0) cc_final: 0.5903 (mt0) REVERT: G 419 ASN cc_start: 0.6006 (m-40) cc_final: 0.4608 (t0) REVERT: G 434 GLU cc_start: 0.6462 (tp30) cc_final: 0.5390 (pm20) REVERT: G 441 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6020 (tpt) REVERT: H 8 ASP cc_start: 0.5835 (m-30) cc_final: 0.5483 (m-30) REVERT: H 16 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6325 (mm-30) REVERT: H 19 ARG cc_start: 0.6228 (mmm160) cc_final: 0.4815 (mmm-85) REVERT: H 22 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6847 (mtt-85) REVERT: H 47 ASP cc_start: 0.6407 (m-30) cc_final: 0.5567 (t70) REVERT: H 142 GLU cc_start: 0.6513 (mm-30) cc_final: 0.5663 (mp0) REVERT: H 216 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6220 (tp) REVERT: H 269 GLU cc_start: 0.5585 (tp30) cc_final: 0.4800 (tp30) REVERT: H 321 ARG cc_start: 0.6496 (ttt90) cc_final: 0.5778 (ttt90) REVERT: H 403 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5479 (mm-30) REVERT: H 419 ASN cc_start: 0.5842 (m-40) cc_final: 0.4595 (t0) REVERT: H 438 ASP cc_start: 0.6486 (m-30) cc_final: 0.6052 (m-30) REVERT: I 11 LYS cc_start: 0.5640 (ttpp) cc_final: 0.4740 (tptt) REVERT: I 51 MET cc_start: 0.6976 (mtp) cc_final: 0.6752 (ttm) REVERT: I 120 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: I 149 GLU cc_start: 0.6416 (pt0) cc_final: 0.5945 (tt0) REVERT: I 153 ASP cc_start: 0.6850 (t0) cc_final: 0.6622 (t0) REVERT: I 216 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6304 (tp) REVERT: I 254 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6002 (mppt) REVERT: I 269 GLU cc_start: 0.5181 (tp30) cc_final: 0.4768 (tp30) REVERT: I 321 ARG cc_start: 0.6457 (ttt90) cc_final: 0.6179 (ttt90) REVERT: I 329 SER cc_start: 0.7322 (p) cc_final: 0.7065 (p) REVERT: I 363 LYS cc_start: 0.6867 (mmmt) cc_final: 0.6280 (mmmm) REVERT: I 407 LYS cc_start: 0.6715 (tttm) cc_final: 0.6311 (ttpp) REVERT: I 419 ASN cc_start: 0.5818 (m-40) cc_final: 0.4554 (t0) REVERT: I 434 GLU cc_start: 0.6569 (tp30) cc_final: 0.5533 (pm20) REVERT: J 153 ASP cc_start: 0.6852 (t0) cc_final: 0.6625 (t0) REVERT: J 216 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6305 (tp) REVERT: J 269 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4814 (tp30) REVERT: J 419 ASN cc_start: 0.5831 (m-40) cc_final: 0.4548 (t0) REVERT: J 429 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6977 (ttp80) REVERT: J 441 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6006 (tpt) REVERT: K 22 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6547 (mmt-90) REVERT: K 51 MET cc_start: 0.7059 (mtt) cc_final: 0.6829 (mtt) REVERT: K 153 ASP cc_start: 0.6845 (t0) cc_final: 0.6598 (t0) REVERT: K 216 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6292 (tp) REVERT: K 254 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6185 (mppt) REVERT: K 265 MET cc_start: 0.5940 (tpp) cc_final: 0.5631 (tpt) REVERT: K 269 GLU cc_start: 0.5269 (mm-30) cc_final: 0.4818 (tp30) REVERT: K 419 ASN cc_start: 0.5847 (m-40) cc_final: 0.4565 (t0) REVERT: K 441 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6004 (tpt) REVERT: L 8 ASP cc_start: 0.5842 (m-30) cc_final: 0.5492 (m-30) REVERT: L 16 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6334 (mm-30) REVERT: L 19 ARG cc_start: 0.6225 (mmm160) cc_final: 0.4889 (mmm-85) REVERT: L 47 ASP cc_start: 0.6342 (m-30) cc_final: 0.5501 (t70) REVERT: L 142 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5627 (mp0) REVERT: L 159 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6737 (pp) REVERT: L 254 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6277 (mptt) REVERT: L 269 GLU cc_start: 0.5589 (tp30) cc_final: 0.4843 (tp30) REVERT: L 321 ARG cc_start: 0.6513 (ttt90) cc_final: 0.5833 (ttt90) REVERT: L 370 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.5294 (pt0) REVERT: L 403 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5391 (mm-30) REVERT: L 419 ASN cc_start: 0.5874 (m-40) cc_final: 0.4629 (t0) REVERT: L 438 ASP cc_start: 0.6507 (m-30) cc_final: 0.6074 (m-30) outliers start: 140 outliers final: 82 residues processed: 761 average time/residue: 1.6356 time to fit residues: 1481.9606 Evaluate side-chains 757 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 636 time to evaluate : 5.010 ------------------------------------------------------------------------------- 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 99 THR 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 254 LYS Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain E residue 67 ASP 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 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU 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 252 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 321 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain I residue 132 GLU 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 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 132 GLU 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 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 441 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain L residue 37 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 325 SER Chi-restraints excluded: chain L residue 364 VAL Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 474 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** 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** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN ** 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** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 443 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 40900 Z= 0.333 Angle : 0.655 9.513 55360 Z= 0.359 Chirality : 0.047 0.199 5964 Planarity : 0.006 0.056 7260 Dihedral : 6.590 59.957 5399 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 3.34 % Allowed : 12.07 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4884 helix: 1.53 (0.11), residues: 2028 sheet: -0.27 (0.17), residues: 912 loop : -0.08 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 425 HIS 0.006 0.002 HIS L 228 PHE 0.028 0.002 PHE H 285 TYR 0.033 0.003 TYR G 296 ARG 0.007 0.001 ARG C 114 *********************** 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 789 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 644 time to evaluate : 4.610 Fit side-chains REVERT: A 8 ASP cc_start: 0.5783 (m-30) cc_final: 0.5418 (m-30) REVERT: A 16 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6362 (mm-30) REVERT: A 17 ASN cc_start: 0.6211 (t0) cc_final: 0.5818 (t0) REVERT: A 19 ARG cc_start: 0.6233 (mmm160) cc_final: 0.4870 (mmm-85) REVERT: A 47 ASP cc_start: 0.6357 (m-30) cc_final: 0.5510 (t70) REVERT: A 142 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5658 (mp0) REVERT: A 143 LYS cc_start: 0.6313 (OUTLIER) cc_final: 0.5878 (mmmt) REVERT: A 254 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6466 (mptt) REVERT: A 269 GLU cc_start: 0.5587 (tp30) cc_final: 0.4781 (tp30) REVERT: A 321 ARG cc_start: 0.6538 (ttt90) cc_final: 0.5797 (ttt90) REVERT: A 403 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5385 (mm-30) REVERT: A 407 LYS cc_start: 0.6589 (tttp) cc_final: 0.6233 (ttpp) REVERT: A 416 GLN cc_start: 0.6426 (mm110) cc_final: 0.6218 (mm110) REVERT: A 419 ASN cc_start: 0.5964 (m-40) cc_final: 0.4721 (t0) REVERT: A 434 GLU cc_start: 0.6614 (tp30) cc_final: 0.5453 (pm20) REVERT: A 438 ASP cc_start: 0.6502 (m-30) cc_final: 0.6069 (m-30) REVERT: B 8 ASP cc_start: 0.5762 (m-30) cc_final: 0.5325 (m-30) REVERT: B 17 ASN cc_start: 0.6162 (t0) cc_final: 0.5735 (t0) REVERT: B 22 ARG cc_start: 0.7693 (ttm170) cc_final: 0.7167 (tpp80) REVERT: B 58 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.4692 (mt-10) REVERT: B 254 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6587 (mttt) REVERT: B 269 GLU cc_start: 0.5619 (tp30) cc_final: 0.4991 (tp30) REVERT: B 321 ARG cc_start: 0.6412 (tmt-80) cc_final: 0.5889 (ttp80) REVERT: B 370 GLN cc_start: 0.5537 (OUTLIER) cc_final: 0.5243 (pt0) REVERT: B 386 GLN cc_start: 0.6630 (mt0) cc_final: 0.5925 (mt0) REVERT: B 419 ASN cc_start: 0.5994 (m-40) cc_final: 0.4591 (t0) REVERT: B 427 TYR cc_start: 0.6936 (m-80) cc_final: 0.5366 (t80) REVERT: C 153 ASP cc_start: 0.6844 (t0) cc_final: 0.6596 (t0) REVERT: C 184 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: C 216 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6277 (tp) REVERT: C 254 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6024 (mppt) REVERT: C 269 GLU cc_start: 0.5399 (tp30) cc_final: 0.4943 (tp30) REVERT: C 321 ARG cc_start: 0.6513 (ttt90) cc_final: 0.6177 (ttt90) REVERT: C 329 SER cc_start: 0.7320 (p) cc_final: 0.7066 (p) REVERT: C 363 LYS cc_start: 0.6894 (mmmt) cc_final: 0.6320 (mmmm) REVERT: C 407 LYS cc_start: 0.6837 (tttp) cc_final: 0.6412 (ttpp) REVERT: C 419 ASN cc_start: 0.5840 (m-40) cc_final: 0.4559 (t0) REVERT: C 434 GLU cc_start: 0.6501 (tp30) cc_final: 0.5472 (pm20) REVERT: D 8 ASP cc_start: 0.5755 (m-30) cc_final: 0.5301 (m-30) REVERT: D 22 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7079 (tpp80) REVERT: D 37 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6537 (m) REVERT: D 223 ARG cc_start: 0.6651 (tpp-160) cc_final: 0.6040 (ttt180) REVERT: D 254 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6339 (mttp) REVERT: D 269 GLU cc_start: 0.5591 (tp30) cc_final: 0.4969 (tp30) REVERT: D 321 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5868 (ttp80) REVERT: D 386 GLN cc_start: 0.6621 (mt0) cc_final: 0.5901 (mt0) REVERT: D 419 ASN cc_start: 0.6004 (m-40) cc_final: 0.4601 (t0) REVERT: D 427 TYR cc_start: 0.6932 (m-80) cc_final: 0.5371 (t80) REVERT: D 434 GLU cc_start: 0.6454 (tp30) cc_final: 0.5355 (pm20) REVERT: D 441 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5960 (tpt) REVERT: E 8 ASP cc_start: 0.5745 (m-30) cc_final: 0.5317 (m-30) REVERT: E 17 ASN cc_start: 0.6140 (t0) cc_final: 0.5723 (t0) REVERT: E 22 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7187 (tpp80) REVERT: E 67 ASP cc_start: 0.5387 (OUTLIER) cc_final: 0.5082 (t0) REVERT: E 269 GLU cc_start: 0.5688 (tp30) cc_final: 0.5195 (tp30) REVERT: E 321 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5886 (ttt90) REVERT: E 370 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.5323 (pt0) REVERT: E 386 GLN cc_start: 0.6638 (mt0) cc_final: 0.5921 (mt0) REVERT: E 419 ASN cc_start: 0.5972 (m-40) cc_final: 0.4568 (t0) REVERT: E 427 TYR cc_start: 0.6931 (m-80) cc_final: 0.5354 (t80) REVERT: E 434 GLU cc_start: 0.6452 (tp30) cc_final: 0.5357 (pm20) REVERT: E 441 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6005 (tpt) REVERT: F 8 ASP cc_start: 0.5783 (m-30) cc_final: 0.5425 (m-30) REVERT: F 16 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6391 (mm-30) REVERT: F 19 ARG cc_start: 0.6249 (mmm160) cc_final: 0.4901 (mmm-85) REVERT: F 37 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6587 (m) REVERT: F 47 ASP cc_start: 0.6410 (m-30) cc_final: 0.5534 (t70) REVERT: F 142 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5625 (mp0) REVERT: F 149 GLU cc_start: 0.6485 (pt0) cc_final: 0.5969 (tt0) REVERT: F 159 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6699 (pp) REVERT: F 184 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: F 223 ARG cc_start: 0.6782 (mtp85) cc_final: 0.6488 (ttt90) REVERT: F 252 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6255 (mtpt) REVERT: F 269 GLU cc_start: 0.5606 (tp30) cc_final: 0.4856 (tp30) REVERT: F 321 ARG cc_start: 0.6510 (ttt90) cc_final: 0.5740 (ttt90) REVERT: F 403 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5415 (mm-30) REVERT: F 419 ASN cc_start: 0.5988 (m-40) cc_final: 0.4764 (t0) REVERT: F 438 ASP cc_start: 0.6508 (m-30) cc_final: 0.6072 (m-30) REVERT: G 8 ASP cc_start: 0.5766 (m-30) cc_final: 0.5315 (m-30) REVERT: G 17 ASN cc_start: 0.6257 (t0) cc_final: 0.5872 (t0) REVERT: G 22 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7075 (tpp80) REVERT: G 37 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6575 (m) REVERT: G 39 VAL cc_start: 0.6530 (OUTLIER) cc_final: 0.6323 (m) REVERT: G 69 TYR cc_start: 0.7311 (m-80) cc_final: 0.6971 (m-80) REVERT: G 223 ARG cc_start: 0.6646 (tpp-160) cc_final: 0.6055 (ttt180) REVERT: G 254 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6657 (mttm) REVERT: G 269 GLU cc_start: 0.5406 (tp30) cc_final: 0.5138 (tp30) REVERT: G 321 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5880 (ttp80) REVERT: G 370 GLN cc_start: 0.5609 (OUTLIER) cc_final: 0.5357 (pt0) REVERT: G 386 GLN cc_start: 0.6615 (mt0) cc_final: 0.5891 (mt0) REVERT: G 419 ASN cc_start: 0.6012 (m-40) cc_final: 0.4611 (t0) REVERT: G 434 GLU cc_start: 0.6458 (tp30) cc_final: 0.5373 (pm20) REVERT: G 441 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6016 (tpt) REVERT: H 8 ASP cc_start: 0.5846 (m-30) cc_final: 0.5497 (m-30) REVERT: H 16 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6323 (mm-30) REVERT: H 19 ARG cc_start: 0.6225 (mmm160) cc_final: 0.4823 (mmm-85) REVERT: H 22 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6807 (mtt-85) REVERT: H 47 ASP cc_start: 0.6409 (m-30) cc_final: 0.5566 (t70) REVERT: H 142 GLU cc_start: 0.6512 (mm-30) cc_final: 0.5669 (mp0) REVERT: H 216 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6221 (tp) REVERT: H 269 GLU cc_start: 0.5621 (tp30) cc_final: 0.4846 (tp30) REVERT: H 321 ARG cc_start: 0.6549 (ttt90) cc_final: 0.5778 (ttt90) REVERT: H 403 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5465 (mm-30) REVERT: H 419 ASN cc_start: 0.5946 (m-40) cc_final: 0.4703 (t0) REVERT: H 438 ASP cc_start: 0.6489 (m-30) cc_final: 0.6051 (m-30) REVERT: I 51 MET cc_start: 0.7070 (mtp) cc_final: 0.6845 (ttm) REVERT: I 153 ASP cc_start: 0.6857 (t0) cc_final: 0.6629 (t0) REVERT: I 216 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6291 (tp) REVERT: I 254 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5995 (mppt) REVERT: I 269 GLU cc_start: 0.5194 (tp30) cc_final: 0.4785 (tp30) REVERT: I 321 ARG cc_start: 0.6514 (ttt90) cc_final: 0.6189 (ttt90) REVERT: I 329 SER cc_start: 0.7327 (p) cc_final: 0.7072 (p) REVERT: I 363 LYS cc_start: 0.6934 (mmmt) cc_final: 0.6360 (mmmm) REVERT: I 407 LYS cc_start: 0.6714 (tttm) cc_final: 0.6306 (ttpp) REVERT: I 419 ASN cc_start: 0.5836 (m-40) cc_final: 0.4556 (t0) REVERT: I 434 GLU cc_start: 0.6504 (tp30) cc_final: 0.5518 (pm20) REVERT: J 153 ASP cc_start: 0.6859 (t0) cc_final: 0.6621 (t0) REVERT: J 269 GLU cc_start: 0.5277 (mm-30) cc_final: 0.4849 (tp30) REVERT: J 419 ASN cc_start: 0.5833 (m-40) cc_final: 0.4548 (t0) REVERT: J 441 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: K 22 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6548 (mmt-90) REVERT: K 51 MET cc_start: 0.7066 (mtt) cc_final: 0.6861 (mtt) REVERT: K 153 ASP cc_start: 0.6852 (t0) cc_final: 0.6606 (t0) REVERT: K 254 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6107 (mppt) REVERT: K 265 MET cc_start: 0.5901 (tpp) cc_final: 0.5580 (tpt) REVERT: K 269 GLU cc_start: 0.5279 (mm-30) cc_final: 0.4854 (tp30) REVERT: K 419 ASN cc_start: 0.5847 (m-40) cc_final: 0.4562 (t0) REVERT: K 441 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5977 (tpt) REVERT: L 8 ASP cc_start: 0.5827 (m-30) cc_final: 0.5482 (m-30) REVERT: L 16 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6320 (mm-30) REVERT: L 19 ARG cc_start: 0.6225 (mmm160) cc_final: 0.4886 (mmm-85) REVERT: L 47 ASP cc_start: 0.6342 (m-30) cc_final: 0.5500 (t70) REVERT: L 142 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5643 (mp0) REVERT: L 159 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6730 (pp) REVERT: L 254 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6272 (mptt) REVERT: L 269 GLU cc_start: 0.5567 (tp30) cc_final: 0.4847 (tp30) REVERT: L 321 ARG cc_start: 0.6504 (ttt90) cc_final: 0.5808 (ttt90) REVERT: L 370 GLN cc_start: 0.5491 (OUTLIER) cc_final: 0.5289 (pt0) REVERT: L 403 GLU cc_start: 0.6057 (mm-30) cc_final: 0.5415 (mm-30) REVERT: L 419 ASN cc_start: 0.5964 (m-40) cc_final: 0.4721 (t0) REVERT: L 438 ASP cc_start: 0.6533 (m-30) cc_final: 0.6101 (m-30) outliers start: 145 outliers final: 87 residues processed: 765 average time/residue: 1.7137 time to fit residues: 1555.5597 Evaluate side-chains 761 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 637 time to evaluate : 4.752 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 143 LYS 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 184 GLU 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 254 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 254 LYS Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 67 ASP 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 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 LEU 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 252 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 321 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 119 MET Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 216 LEU 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 132 GLU 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 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 441 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 132 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 119 MET 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 Chi-restraints excluded: chain L residue 370 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 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 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** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 245 HIS L 443 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 40900 Z= 0.255 Angle : 0.586 8.939 55360 Z= 0.321 Chirality : 0.044 0.167 5964 Planarity : 0.005 0.050 7260 Dihedral : 6.360 59.861 5395 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.90 % Allowed : 12.55 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 4884 helix: 1.71 (0.11), residues: 2028 sheet: -0.26 (0.17), residues: 912 loop : 0.01 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 425 HIS 0.005 0.002 HIS K 195 PHE 0.023 0.002 PHE B 285 TYR 0.029 0.003 TYR B 296 ARG 0.006 0.001 ARG C 335 *********************** 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 779 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 653 time to evaluate : 4.688 Fit side-chains REVERT: A 8 ASP cc_start: 0.5769 (m-30) cc_final: 0.5332 (m-30) REVERT: A 16 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6325 (mm-30) REVERT: A 19 ARG cc_start: 0.6241 (mmm160) cc_final: 0.4891 (mmm-85) REVERT: A 47 ASP cc_start: 0.6342 (m-30) cc_final: 0.5503 (t70) REVERT: A 143 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5894 (mmmt) REVERT: A 254 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6543 (mptt) REVERT: A 269 GLU cc_start: 0.5499 (tp30) cc_final: 0.4727 (tp30) REVERT: A 321 ARG cc_start: 0.6522 (ttt90) cc_final: 0.5764 (ttt90) REVERT: A 403 GLU cc_start: 0.6004 (mm-30) cc_final: 0.5356 (mm-30) REVERT: A 407 LYS cc_start: 0.6600 (tttp) cc_final: 0.6244 (ttpp) REVERT: A 419 ASN cc_start: 0.5956 (m-40) cc_final: 0.4726 (t0) REVERT: A 434 GLU cc_start: 0.6568 (tp30) cc_final: 0.5347 (pm20) REVERT: A 438 ASP cc_start: 0.6510 (m-30) cc_final: 0.6074 (m-30) REVERT: B 8 ASP cc_start: 0.5730 (m-30) cc_final: 0.5251 (m-30) REVERT: B 17 ASN cc_start: 0.6184 (t0) cc_final: 0.5761 (t0) REVERT: B 22 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7183 (tpp80) REVERT: B 58 GLU cc_start: 0.4999 (OUTLIER) cc_final: 0.4720 (mt-10) REVERT: B 254 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6548 (mttp) REVERT: B 269 GLU cc_start: 0.5602 (tp30) cc_final: 0.4976 (tp30) REVERT: B 321 ARG cc_start: 0.6435 (tmt-80) cc_final: 0.5800 (ttp80) REVERT: B 370 GLN cc_start: 0.5514 (OUTLIER) cc_final: 0.5234 (pt0) REVERT: B 386 GLN cc_start: 0.6647 (mt0) cc_final: 0.5927 (mt0) REVERT: B 419 ASN cc_start: 0.5986 (m-40) cc_final: 0.4579 (t0) REVERT: B 427 TYR cc_start: 0.6938 (m-80) cc_final: 0.5406 (t80) REVERT: C 153 ASP cc_start: 0.6850 (t0) cc_final: 0.6616 (t0) REVERT: C 184 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: C 254 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6022 (mppt) REVERT: C 269 GLU cc_start: 0.5362 (tp30) cc_final: 0.4957 (tp30) REVERT: C 321 ARG cc_start: 0.6499 (ttt90) cc_final: 0.6138 (ttt90) REVERT: C 329 SER cc_start: 0.7372 (p) cc_final: 0.7125 (p) REVERT: C 363 LYS cc_start: 0.6881 (mmmt) cc_final: 0.6316 (mmmm) REVERT: C 407 LYS cc_start: 0.6768 (tttp) cc_final: 0.6346 (ttpp) REVERT: C 419 ASN cc_start: 0.5830 (m-40) cc_final: 0.4539 (t0) REVERT: C 434 GLU cc_start: 0.6509 (tp30) cc_final: 0.5422 (pm20) REVERT: D 8 ASP cc_start: 0.5715 (m-30) cc_final: 0.5255 (m-30) REVERT: D 22 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7096 (tpp80) REVERT: D 37 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6617 (m) REVERT: D 39 VAL cc_start: 0.6476 (OUTLIER) cc_final: 0.6207 (m) REVERT: D 223 ARG cc_start: 0.6659 (tpp-160) cc_final: 0.6081 (ttt180) REVERT: D 254 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6402 (mttp) REVERT: D 269 GLU cc_start: 0.5606 (tp30) cc_final: 0.4981 (tp30) REVERT: D 321 ARG cc_start: 0.6526 (tmt-80) cc_final: 0.5865 (ttp80) REVERT: D 386 GLN cc_start: 0.6632 (mt0) cc_final: 0.5907 (mt0) REVERT: D 419 ASN cc_start: 0.6041 (m-40) cc_final: 0.4614 (t0) REVERT: D 427 TYR cc_start: 0.6925 (m-80) cc_final: 0.5411 (t80) REVERT: D 434 GLU cc_start: 0.6480 (tp30) cc_final: 0.5351 (pm20) REVERT: D 441 MET cc_start: 0.6370 (ttt) cc_final: 0.5958 (tpt) REVERT: E 8 ASP cc_start: 0.5719 (m-30) cc_final: 0.5245 (m-30) REVERT: E 17 ASN cc_start: 0.6090 (t0) cc_final: 0.5673 (t0) REVERT: E 22 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7037 (tpp80) REVERT: E 67 ASP cc_start: 0.5287 (OUTLIER) cc_final: 0.5011 (t0) REVERT: E 69 TYR cc_start: 0.7312 (m-80) cc_final: 0.7020 (m-80) REVERT: E 269 GLU cc_start: 0.5644 (tp30) cc_final: 0.5152 (tp30) REVERT: E 321 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5774 (ttt90) REVERT: E 370 GLN cc_start: 0.5545 (OUTLIER) cc_final: 0.5330 (pt0) REVERT: E 386 GLN cc_start: 0.6650 (mt0) cc_final: 0.5934 (mt0) REVERT: E 419 ASN cc_start: 0.5960 (m-40) cc_final: 0.4561 (t0) REVERT: E 427 TYR cc_start: 0.6945 (m-80) cc_final: 0.5407 (t80) REVERT: E 434 GLU cc_start: 0.6468 (tp30) cc_final: 0.5341 (pm20) REVERT: E 441 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6009 (tpt) REVERT: F 8 ASP cc_start: 0.5788 (m-30) cc_final: 0.5335 (m-30) REVERT: F 16 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6326 (mm-30) REVERT: F 19 ARG cc_start: 0.6254 (mmm160) cc_final: 0.4897 (mmm-85) REVERT: F 37 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6660 (m) REVERT: F 47 ASP cc_start: 0.6398 (m-30) cc_final: 0.5519 (t70) REVERT: F 149 GLU cc_start: 0.6469 (pt0) cc_final: 0.5919 (tt0) REVERT: F 159 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6655 (pp) REVERT: F 184 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: F 223 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6506 (ttt90) REVERT: F 252 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6360 (mtpt) REVERT: F 269 GLU cc_start: 0.5588 (tp30) cc_final: 0.4844 (tp30) REVERT: F 321 ARG cc_start: 0.6524 (ttt90) cc_final: 0.5739 (ttt90) REVERT: F 403 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5383 (mm-30) REVERT: F 419 ASN cc_start: 0.5972 (m-40) cc_final: 0.4728 (t0) REVERT: F 438 ASP cc_start: 0.6518 (m-30) cc_final: 0.6080 (m-30) REVERT: G 8 ASP cc_start: 0.5740 (m-30) cc_final: 0.5283 (m-30) REVERT: G 22 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7129 (tpp80) REVERT: G 37 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6617 (m) REVERT: G 39 VAL cc_start: 0.6511 (OUTLIER) cc_final: 0.6302 (m) REVERT: G 69 TYR cc_start: 0.7310 (m-80) cc_final: 0.6901 (m-80) REVERT: G 223 ARG cc_start: 0.6655 (tpp-160) cc_final: 0.6072 (ttt180) REVERT: G 254 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6657 (mttm) REVERT: G 321 ARG cc_start: 0.6535 (tmt-80) cc_final: 0.5878 (ttp80) REVERT: G 370 GLN cc_start: 0.5630 (OUTLIER) cc_final: 0.5372 (pt0) REVERT: G 386 GLN cc_start: 0.6642 (mt0) cc_final: 0.5909 (mt0) REVERT: G 419 ASN cc_start: 0.6049 (m-40) cc_final: 0.4624 (t0) REVERT: G 434 GLU cc_start: 0.6493 (tp30) cc_final: 0.5399 (pm20) REVERT: G 441 MET cc_start: 0.6412 (ttt) cc_final: 0.6016 (tpt) REVERT: H 8 ASP cc_start: 0.5862 (m-30) cc_final: 0.5440 (m-30) REVERT: H 16 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6308 (mm-30) REVERT: H 19 ARG cc_start: 0.6229 (mmm160) cc_final: 0.4809 (mmm-85) REVERT: H 22 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6719 (mtt-85) REVERT: H 47 ASP cc_start: 0.6424 (m-30) cc_final: 0.5570 (t70) REVERT: H 216 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6253 (tp) REVERT: H 224 LYS cc_start: 0.6655 (mttm) cc_final: 0.6337 (mttp) REVERT: H 269 GLU cc_start: 0.5660 (tp30) cc_final: 0.4887 (tp30) REVERT: H 321 ARG cc_start: 0.6553 (ttt90) cc_final: 0.5763 (ttt90) REVERT: H 403 GLU cc_start: 0.6097 (mm-30) cc_final: 0.5462 (mm-30) REVERT: H 419 ASN cc_start: 0.5952 (m-40) cc_final: 0.4724 (t0) REVERT: H 438 ASP cc_start: 0.6497 (m-30) cc_final: 0.6057 (m-30) REVERT: I 11 LYS cc_start: 0.5643 (ttpp) cc_final: 0.4695 (tptt) REVERT: I 51 MET cc_start: 0.6935 (mtp) cc_final: 0.6716 (ttm) REVERT: I 153 ASP cc_start: 0.6852 (t0) cc_final: 0.6628 (t0) REVERT: I 184 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: I 254 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.5992 (mppt) REVERT: I 269 GLU cc_start: 0.5203 (tp30) cc_final: 0.4855 (tp30) REVERT: I 321 ARG cc_start: 0.6462 (ttt90) cc_final: 0.6115 (ttt90) REVERT: I 329 SER cc_start: 0.7331 (p) cc_final: 0.7083 (p) REVERT: I 363 LYS cc_start: 0.6892 (mmmt) cc_final: 0.6328 (mmmm) REVERT: I 407 LYS cc_start: 0.6693 (tttm) cc_final: 0.6291 (ttpp) REVERT: I 419 ASN cc_start: 0.5826 (m-40) cc_final: 0.4536 (t0) REVERT: I 434 GLU cc_start: 0.6552 (tp30) cc_final: 0.5550 (pm20) REVERT: J 37 VAL cc_start: 0.6915 (OUTLIER) cc_final: 0.6674 (m) REVERT: J 153 ASP cc_start: 0.6855 (t0) cc_final: 0.6631 (t0) REVERT: J 269 GLU cc_start: 0.5520 (mm-30) cc_final: 0.5056 (tp30) REVERT: J 419 ASN cc_start: 0.5825 (m-40) cc_final: 0.4529 (t0) REVERT: J 441 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: K 22 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6472 (mmt-90) REVERT: K 37 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6645 (m) REVERT: K 51 MET cc_start: 0.7097 (mtt) cc_final: 0.6875 (mtt) REVERT: K 153 ASP cc_start: 0.6850 (t0) cc_final: 0.6620 (t0) REVERT: K 254 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6207 (mppt) REVERT: K 265 MET cc_start: 0.6065 (tpp) cc_final: 0.5731 (tpt) REVERT: K 269 GLU cc_start: 0.5524 (mm-30) cc_final: 0.5062 (tp30) REVERT: K 419 ASN cc_start: 0.5836 (m-40) cc_final: 0.4542 (t0) REVERT: K 441 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5979 (tpt) REVERT: L 8 ASP cc_start: 0.5843 (m-30) cc_final: 0.5427 (m-30) REVERT: L 16 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6318 (mm-30) REVERT: L 19 ARG cc_start: 0.6232 (mmm160) cc_final: 0.4890 (mmm-85) REVERT: L 47 ASP cc_start: 0.6327 (m-30) cc_final: 0.5484 (t70) REVERT: L 159 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6659 (pp) REVERT: L 224 LYS cc_start: 0.6753 (mttm) cc_final: 0.6420 (mttp) REVERT: L 269 GLU cc_start: 0.5523 (tp30) cc_final: 0.4832 (tp30) REVERT: L 321 ARG cc_start: 0.6545 (ttt90) cc_final: 0.5786 (ttt90) REVERT: L 403 GLU cc_start: 0.6022 (mm-30) cc_final: 0.5387 (mm-30) REVERT: L 419 ASN cc_start: 0.5970 (m-40) cc_final: 0.4741 (t0) REVERT: L 438 ASP cc_start: 0.6541 (m-30) cc_final: 0.6108 (m-30) outliers start: 126 outliers final: 78 residues processed: 766 average time/residue: 1.6958 time to fit residues: 1546.0128 Evaluate side-chains 759 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 647 time to evaluate : 4.503 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 143 LYS 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 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 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 254 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 67 ASP 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 321 ARG Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain F residue 37 VAL 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 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 252 LYS Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU 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 132 GLU Chi-restraints excluded: chain I residue 184 GLU 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 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain J residue 441 MET Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 132 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain L residue 37 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 0.9990 chunk 454 optimal weight: 7.9990 chunk 414 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 417 optimal weight: 9.9990 chunk 440 optimal weight: 0.0070 overall best weight: 2.1404 ------------------------------------------------------------------------------- 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 ** 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** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 443 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 40900 Z= 0.217 Angle : 0.552 8.574 55360 Z= 0.303 Chirality : 0.043 0.154 5964 Planarity : 0.005 0.048 7260 Dihedral : 6.158 59.937 5391 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.56 % Allowed : 13.06 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 4884 helix: 1.85 (0.11), residues: 2028 sheet: -0.26 (0.17), residues: 912 loop : 0.08 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 425 HIS 0.005 0.001 HIS J 195 PHE 0.021 0.002 PHE B 285 TYR 0.027 0.002 TYR J 296 ARG 0.005 0.001 ARG C 335 *********************** 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 767 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 656 time to evaluate : 4.579 Fit side-chains REVERT: A 8 ASP cc_start: 0.5692 (m-30) cc_final: 0.5257 (m-30) REVERT: A 16 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 19 ARG cc_start: 0.6289 (mmm160) cc_final: 0.4914 (mmm-85) REVERT: A 47 ASP cc_start: 0.6348 (m-30) cc_final: 0.5518 (t70) REVERT: A 143 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5897 (mmmt) REVERT: A 170 ARG cc_start: 0.6019 (tpp80) cc_final: 0.5785 (tpp80) REVERT: A 254 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6387 (mppt) REVERT: A 269 GLU cc_start: 0.5527 (tp30) cc_final: 0.4753 (tp30) REVERT: A 321 ARG cc_start: 0.6545 (ttt90) cc_final: 0.5755 (ttt90) REVERT: A 403 GLU cc_start: 0.5932 (mm-30) cc_final: 0.5276 (mm-30) REVERT: A 407 LYS cc_start: 0.6581 (tttp) cc_final: 0.6226 (ttpp) REVERT: A 419 ASN cc_start: 0.5963 (m-40) cc_final: 0.4725 (t0) REVERT: A 434 GLU cc_start: 0.6563 (tp30) cc_final: 0.5386 (pm20) REVERT: A 438 ASP cc_start: 0.6505 (m-30) cc_final: 0.6064 (m-30) REVERT: B 8 ASP cc_start: 0.5736 (m-30) cc_final: 0.5266 (m-30) REVERT: B 17 ASN cc_start: 0.6181 (t0) cc_final: 0.5758 (t0) REVERT: B 22 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7382 (tpp80) REVERT: B 58 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4724 (mt-10) REVERT: B 254 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6538 (mttp) REVERT: B 269 GLU cc_start: 0.5558 (tp30) cc_final: 0.4972 (tp30) REVERT: B 321 ARG cc_start: 0.6435 (tmt-80) cc_final: 0.5802 (ttp80) REVERT: B 370 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.5348 (pt0) REVERT: B 386 GLN cc_start: 0.6660 (mt0) cc_final: 0.5937 (mt0) REVERT: B 419 ASN cc_start: 0.6025 (m-40) cc_final: 0.4603 (t0) REVERT: B 427 TYR cc_start: 0.6950 (m-80) cc_final: 0.5401 (t80) REVERT: B 434 GLU cc_start: 0.6491 (tp30) cc_final: 0.6187 (mm-30) REVERT: C 11 LYS cc_start: 0.5549 (ttpp) cc_final: 0.4629 (tptt) REVERT: C 153 ASP cc_start: 0.6842 (t0) cc_final: 0.6615 (t0) REVERT: C 184 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: C 254 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6063 (mppt) REVERT: C 269 GLU cc_start: 0.5384 (tp30) cc_final: 0.4999 (tp30) REVERT: C 321 ARG cc_start: 0.6497 (ttt90) cc_final: 0.6126 (ttt90) REVERT: C 329 SER cc_start: 0.7367 (p) cc_final: 0.7126 (p) REVERT: C 363 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6295 (mmmm) REVERT: C 407 LYS cc_start: 0.6748 (tttp) cc_final: 0.6404 (ttpp) REVERT: C 419 ASN cc_start: 0.5817 (m-40) cc_final: 0.4527 (t0) REVERT: C 434 GLU cc_start: 0.6514 (tp30) cc_final: 0.5502 (pm20) REVERT: D 8 ASP cc_start: 0.5723 (m-30) cc_final: 0.5233 (m-30) REVERT: D 22 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7052 (tpp80) REVERT: D 37 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6657 (m) REVERT: D 39 VAL cc_start: 0.6411 (OUTLIER) cc_final: 0.6128 (m) REVERT: D 223 ARG cc_start: 0.6654 (tpp-160) cc_final: 0.6063 (ttt180) REVERT: D 254 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.6396 (mttp) REVERT: D 269 GLU cc_start: 0.5617 (tp30) cc_final: 0.4992 (tp30) REVERT: D 321 ARG cc_start: 0.6548 (tmt-80) cc_final: 0.5886 (ttp80) REVERT: D 386 GLN cc_start: 0.6658 (mt0) cc_final: 0.5927 (mt0) REVERT: D 419 ASN cc_start: 0.6033 (m-40) cc_final: 0.4613 (t0) REVERT: D 427 TYR cc_start: 0.6934 (m-80) cc_final: 0.5415 (t80) REVERT: D 434 GLU cc_start: 0.6475 (tp30) cc_final: 0.5337 (pm20) REVERT: D 441 MET cc_start: 0.6359 (ttt) cc_final: 0.5954 (tpt) REVERT: E 8 ASP cc_start: 0.5723 (m-30) cc_final: 0.5226 (m-30) REVERT: E 17 ASN cc_start: 0.6048 (t0) cc_final: 0.5633 (t0) REVERT: E 22 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7026 (tpp80) REVERT: E 67 ASP cc_start: 0.5198 (OUTLIER) cc_final: 0.4971 (t0) REVERT: E 69 TYR cc_start: 0.7344 (m-80) cc_final: 0.6998 (m-80) REVERT: E 269 GLU cc_start: 0.5614 (tp30) cc_final: 0.5119 (tp30) REVERT: E 370 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.5313 (pt0) REVERT: E 386 GLN cc_start: 0.6654 (mt0) cc_final: 0.5929 (mt0) REVERT: E 419 ASN cc_start: 0.6001 (m-40) cc_final: 0.4579 (t0) REVERT: E 427 TYR cc_start: 0.6939 (m-80) cc_final: 0.5413 (t80) REVERT: E 434 GLU cc_start: 0.6459 (tp30) cc_final: 0.5328 (pm20) REVERT: E 441 MET cc_start: 0.6353 (ttt) cc_final: 0.5946 (tpt) REVERT: F 8 ASP cc_start: 0.5809 (m-30) cc_final: 0.5397 (m-30) REVERT: F 16 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6293 (mm-30) REVERT: F 19 ARG cc_start: 0.6255 (mmm160) cc_final: 0.4897 (mmm-85) REVERT: F 37 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6712 (m) REVERT: F 47 ASP cc_start: 0.6393 (m-30) cc_final: 0.5511 (t70) REVERT: F 149 GLU cc_start: 0.6456 (pt0) cc_final: 0.5903 (tt0) REVERT: F 159 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6647 (pp) REVERT: F 184 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: F 223 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6454 (ttt90) REVERT: F 269 GLU cc_start: 0.5604 (tp30) cc_final: 0.4813 (tp30) REVERT: F 321 ARG cc_start: 0.6558 (ttt90) cc_final: 0.5744 (ttt90) REVERT: F 335 ARG cc_start: 0.6884 (mtp-110) cc_final: 0.6645 (mtp85) REVERT: F 403 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5384 (mm-30) REVERT: F 419 ASN cc_start: 0.5968 (m-40) cc_final: 0.4728 (t0) REVERT: F 438 ASP cc_start: 0.6513 (m-30) cc_final: 0.6070 (m-30) REVERT: G 8 ASP cc_start: 0.5744 (m-30) cc_final: 0.5258 (m-30) REVERT: G 22 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7205 (tpp80) REVERT: G 37 VAL cc_start: 0.6883 (OUTLIER) cc_final: 0.6640 (m) REVERT: G 39 VAL cc_start: 0.6438 (OUTLIER) cc_final: 0.6173 (m) REVERT: G 69 TYR cc_start: 0.7299 (m-80) cc_final: 0.6893 (m-80) REVERT: G 223 ARG cc_start: 0.6648 (tpp-160) cc_final: 0.6054 (ttt180) REVERT: G 254 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6672 (mttm) REVERT: G 321 ARG cc_start: 0.6555 (tmt-80) cc_final: 0.5896 (ttp80) REVERT: G 370 GLN cc_start: 0.5655 (OUTLIER) cc_final: 0.5426 (pt0) REVERT: G 386 GLN cc_start: 0.6648 (mt0) cc_final: 0.5922 (mt0) REVERT: G 419 ASN cc_start: 0.6041 (m-40) cc_final: 0.4614 (t0) REVERT: G 434 GLU cc_start: 0.6488 (tp30) cc_final: 0.5384 (pm20) REVERT: G 441 MET cc_start: 0.6362 (ttt) cc_final: 0.5962 (tpt) REVERT: H 8 ASP cc_start: 0.5766 (m-30) cc_final: 0.5360 (m-30) REVERT: H 16 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6305 (mm-30) REVERT: H 19 ARG cc_start: 0.6241 (mmm160) cc_final: 0.4806 (mmm-85) REVERT: H 22 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6636 (mtt-85) REVERT: H 47 ASP cc_start: 0.6415 (m-30) cc_final: 0.5560 (t70) REVERT: H 216 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6298 (tp) REVERT: H 224 LYS cc_start: 0.6644 (mttm) cc_final: 0.6319 (mttp) REVERT: H 269 GLU cc_start: 0.5574 (tp30) cc_final: 0.4811 (tp30) REVERT: H 321 ARG cc_start: 0.6562 (ttt90) cc_final: 0.5759 (ttt90) REVERT: H 403 GLU cc_start: 0.6057 (mm-30) cc_final: 0.5411 (mm-30) REVERT: H 419 ASN cc_start: 0.5950 (m-40) cc_final: 0.4717 (t0) REVERT: H 438 ASP cc_start: 0.6493 (m-30) cc_final: 0.6049 (m-30) REVERT: I 11 LYS cc_start: 0.5617 (ttpp) cc_final: 0.4694 (tptt) REVERT: I 51 MET cc_start: 0.6928 (mtp) cc_final: 0.6708 (ttm) REVERT: I 153 ASP cc_start: 0.6828 (t0) cc_final: 0.6604 (t0) REVERT: I 254 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6029 (mppt) REVERT: I 269 GLU cc_start: 0.5329 (tp30) cc_final: 0.4975 (tp30) REVERT: I 321 ARG cc_start: 0.6451 (ttt90) cc_final: 0.6088 (ttt90) REVERT: I 329 SER cc_start: 0.7370 (p) cc_final: 0.7126 (p) REVERT: I 363 LYS cc_start: 0.6867 (mmmt) cc_final: 0.6307 (mmmm) REVERT: I 407 LYS cc_start: 0.6682 (tttm) cc_final: 0.6284 (ttpp) REVERT: I 419 ASN cc_start: 0.5814 (m-40) cc_final: 0.4524 (t0) REVERT: I 434 GLU cc_start: 0.6547 (tp30) cc_final: 0.5510 (pm20) REVERT: J 11 LYS cc_start: 0.5542 (ttpp) cc_final: 0.4621 (tptt) REVERT: J 37 VAL cc_start: 0.6991 (OUTLIER) cc_final: 0.6746 (m) REVERT: J 153 ASP cc_start: 0.6830 (t0) cc_final: 0.6607 (t0) REVERT: J 170 ARG cc_start: 0.5928 (tpp80) cc_final: 0.5663 (ttm110) REVERT: J 269 GLU cc_start: 0.5449 (mm-30) cc_final: 0.5012 (tp30) REVERT: J 419 ASN cc_start: 0.5813 (m-40) cc_final: 0.4515 (t0) REVERT: J 441 MET cc_start: 0.6410 (ttt) cc_final: 0.6067 (tpt) REVERT: K 11 LYS cc_start: 0.5523 (ttpp) cc_final: 0.4604 (tptt) REVERT: K 17 ASN cc_start: 0.6368 (t0) cc_final: 0.5935 (t0) REVERT: K 22 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6443 (mmt-90) REVERT: K 37 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6676 (m) REVERT: K 51 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: K 153 ASP cc_start: 0.6835 (t0) cc_final: 0.6607 (t0) REVERT: K 254 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6198 (mppt) REVERT: K 265 MET cc_start: 0.6045 (tpp) cc_final: 0.5709 (tpt) REVERT: K 269 GLU cc_start: 0.5454 (mm-30) cc_final: 0.5017 (tp30) REVERT: K 419 ASN cc_start: 0.5826 (m-40) cc_final: 0.4525 (t0) REVERT: K 441 MET cc_start: 0.6409 (ttt) cc_final: 0.6019 (tpt) REVERT: L 8 ASP cc_start: 0.5733 (m-30) cc_final: 0.5322 (m-30) REVERT: L 16 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6325 (mm-30) REVERT: L 19 ARG cc_start: 0.6233 (mmm160) cc_final: 0.4890 (mmm-85) REVERT: L 47 ASP cc_start: 0.6323 (m-30) cc_final: 0.5494 (t70) REVERT: L 159 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6631 (pp) REVERT: L 224 LYS cc_start: 0.6653 (mttm) cc_final: 0.6325 (mttp) REVERT: L 269 GLU cc_start: 0.5460 (tp30) cc_final: 0.4779 (tp30) REVERT: L 321 ARG cc_start: 0.6543 (ttt90) cc_final: 0.5782 (ttt90) REVERT: L 403 GLU cc_start: 0.5947 (mm-30) cc_final: 0.5301 (mm-30) REVERT: L 419 ASN cc_start: 0.5967 (m-40) cc_final: 0.4734 (t0) REVERT: L 438 ASP cc_start: 0.6537 (m-30) cc_final: 0.6098 (m-30) outliers start: 111 outliers final: 73 residues processed: 759 average time/residue: 1.7308 time to fit residues: 1560.7647 Evaluate side-chains 755 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 653 time to evaluate : 4.327 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 143 LYS 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL 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 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 254 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 67 ASP 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 370 GLN Chi-restraints excluded: chain F residue 37 VAL 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 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ARG 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 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 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 216 LEU 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 239 VAL Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 MET 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 37 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 290 optimal weight: 5.9990 chunk 467 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 490 optimal weight: 5.9990 chunk 451 optimal weight: 10.0000 chunk 390 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** 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** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 40900 Z= 0.259 Angle : 0.590 9.125 55360 Z= 0.325 Chirality : 0.045 0.166 5964 Planarity : 0.006 0.051 7260 Dihedral : 6.266 59.936 5391 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 13.04 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.12), residues: 4884 helix: 1.75 (0.11), residues: 2028 sheet: -0.27 (0.17), residues: 912 loop : 0.03 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 425 HIS 0.005 0.002 HIS H 228 PHE 0.024 0.002 PHE C 285 TYR 0.029 0.003 TYR G 296 ARG 0.006 0.001 ARG C 335 ********************** 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 764 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 651 time to evaluate : 4.282 Fit side-chains REVERT: A 8 ASP cc_start: 0.5754 (m-30) cc_final: 0.5312 (m-30) REVERT: A 16 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6318 (mm-30) REVERT: A 19 ARG cc_start: 0.6245 (mmm160) cc_final: 0.4883 (mmm-85) REVERT: A 47 ASP cc_start: 0.6339 (m-30) cc_final: 0.5501 (t70) REVERT: A 143 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5899 (mmmt) REVERT: A 254 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6393 (mppt) REVERT: A 269 GLU cc_start: 0.5522 (tp30) cc_final: 0.4695 (tp30) REVERT: A 321 ARG cc_start: 0.6496 (ttt90) cc_final: 0.5761 (ttt90) REVERT: A 403 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5352 (mm-30) REVERT: A 407 LYS cc_start: 0.6578 (tttp) cc_final: 0.6258 (ttpp) REVERT: A 419 ASN cc_start: 0.5955 (m-40) cc_final: 0.4718 (t0) REVERT: A 434 GLU cc_start: 0.6568 (tp30) cc_final: 0.5367 (pm20) REVERT: A 438 ASP cc_start: 0.6541 (m-30) cc_final: 0.6108 (m-30) REVERT: B 8 ASP cc_start: 0.5726 (m-30) cc_final: 0.5251 (m-30) REVERT: B 17 ASN cc_start: 0.6181 (t0) cc_final: 0.5752 (t0) REVERT: B 22 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7161 (tpp80) REVERT: B 58 GLU cc_start: 0.5005 (OUTLIER) cc_final: 0.4739 (mt-10) REVERT: B 254 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6526 (mttp) REVERT: B 269 GLU cc_start: 0.5457 (tp30) cc_final: 0.4868 (tp30) REVERT: B 321 ARG cc_start: 0.6494 (tmt-80) cc_final: 0.5955 (ttp80) REVERT: B 370 GLN cc_start: 0.5510 (OUTLIER) cc_final: 0.5285 (pt0) REVERT: B 386 GLN cc_start: 0.6651 (mt0) cc_final: 0.5906 (mt0) REVERT: B 419 ASN cc_start: 0.5989 (m-40) cc_final: 0.4579 (t0) REVERT: B 427 TYR cc_start: 0.6954 (m-80) cc_final: 0.5409 (t80) REVERT: C 11 LYS cc_start: 0.5645 (ttpp) cc_final: 0.4712 (tptt) REVERT: C 153 ASP cc_start: 0.6841 (t0) cc_final: 0.6606 (t0) REVERT: C 184 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: C 254 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6065 (mppt) REVERT: C 269 GLU cc_start: 0.5318 (tp30) cc_final: 0.4986 (tp30) REVERT: C 321 ARG cc_start: 0.6448 (ttt90) cc_final: 0.6076 (ttt90) REVERT: C 329 SER cc_start: 0.7361 (p) cc_final: 0.7115 (p) REVERT: C 363 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6396 (mmmm) REVERT: C 407 LYS cc_start: 0.6757 (tttp) cc_final: 0.6406 (ttpp) REVERT: C 419 ASN cc_start: 0.5829 (m-40) cc_final: 0.4559 (t0) REVERT: C 434 GLU cc_start: 0.6521 (tp30) cc_final: 0.5512 (pm20) REVERT: D 8 ASP cc_start: 0.5705 (m-30) cc_final: 0.5246 (m-30) REVERT: D 22 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7078 (tpp80) REVERT: D 37 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6621 (m) REVERT: D 39 VAL cc_start: 0.6474 (OUTLIER) cc_final: 0.6203 (m) REVERT: D 223 ARG cc_start: 0.6617 (tpp-160) cc_final: 0.6033 (ttt180) REVERT: D 254 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6377 (mttp) REVERT: D 269 GLU cc_start: 0.5586 (tp30) cc_final: 0.4954 (tp30) REVERT: D 321 ARG cc_start: 0.6549 (tmt-80) cc_final: 0.5973 (ttp80) REVERT: D 386 GLN cc_start: 0.6647 (mt0) cc_final: 0.5913 (mt0) REVERT: D 419 ASN cc_start: 0.6045 (m-40) cc_final: 0.4605 (t0) REVERT: D 427 TYR cc_start: 0.6947 (m-80) cc_final: 0.5424 (t80) REVERT: D 434 GLU cc_start: 0.6458 (tp30) cc_final: 0.5341 (pm20) REVERT: D 441 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5937 (tpt) REVERT: E 8 ASP cc_start: 0.5713 (m-30) cc_final: 0.5237 (m-30) REVERT: E 17 ASN cc_start: 0.6064 (t0) cc_final: 0.5677 (t0) REVERT: E 22 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7015 (tpp80) REVERT: E 67 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.4986 (t0) REVERT: E 69 TYR cc_start: 0.7343 (m-80) cc_final: 0.6970 (m-80) REVERT: E 269 GLU cc_start: 0.5639 (tp30) cc_final: 0.5139 (tp30) REVERT: E 370 GLN cc_start: 0.5537 (OUTLIER) cc_final: 0.5331 (pt0) REVERT: E 386 GLN cc_start: 0.6650 (mt0) cc_final: 0.5926 (mt0) REVERT: E 419 ASN cc_start: 0.5966 (m-40) cc_final: 0.4555 (t0) REVERT: E 427 TYR cc_start: 0.6905 (m-80) cc_final: 0.5372 (t80) REVERT: E 434 GLU cc_start: 0.6471 (tp30) cc_final: 0.5343 (pm20) REVERT: E 441 MET cc_start: 0.6409 (ttt) cc_final: 0.6000 (tpt) REVERT: F 8 ASP cc_start: 0.5739 (m-30) cc_final: 0.5311 (m-30) REVERT: F 16 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6321 (mm-30) REVERT: F 19 ARG cc_start: 0.6242 (mmm160) cc_final: 0.4885 (mmm-85) REVERT: F 37 VAL cc_start: 0.6919 (OUTLIER) cc_final: 0.6681 (m) REVERT: F 47 ASP cc_start: 0.6398 (m-30) cc_final: 0.5519 (t70) REVERT: F 149 GLU cc_start: 0.6455 (pt0) cc_final: 0.5921 (tt0) REVERT: F 159 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6686 (pp) REVERT: F 184 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: F 223 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6462 (ttt90) REVERT: F 269 GLU cc_start: 0.5605 (tp30) cc_final: 0.4871 (tp30) REVERT: F 321 ARG cc_start: 0.6553 (ttt90) cc_final: 0.5728 (ttt90) REVERT: F 335 ARG cc_start: 0.6891 (mtp-110) cc_final: 0.6648 (mtp85) REVERT: F 403 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5445 (mm-30) REVERT: F 419 ASN cc_start: 0.5977 (m-40) cc_final: 0.4730 (t0) REVERT: F 438 ASP cc_start: 0.6548 (m-30) cc_final: 0.6113 (m-30) REVERT: G 8 ASP cc_start: 0.5729 (m-30) cc_final: 0.5273 (m-30) REVERT: G 22 ARG cc_start: 0.7615 (ttm170) cc_final: 0.7055 (tpp80) REVERT: G 37 VAL cc_start: 0.6890 (OUTLIER) cc_final: 0.6620 (m) REVERT: G 39 VAL cc_start: 0.6491 (OUTLIER) cc_final: 0.6233 (m) REVERT: G 69 TYR cc_start: 0.7305 (m-80) cc_final: 0.6892 (m-80) REVERT: G 223 ARG cc_start: 0.6613 (tpp-160) cc_final: 0.6025 (ttt180) REVERT: G 254 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6627 (mttm) REVERT: G 321 ARG cc_start: 0.6556 (tmt-80) cc_final: 0.5980 (ttp80) REVERT: G 370 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.5660 (pt0) REVERT: G 386 GLN cc_start: 0.6636 (mt0) cc_final: 0.5912 (mt0) REVERT: G 419 ASN cc_start: 0.6052 (m-40) cc_final: 0.4613 (t0) REVERT: G 434 GLU cc_start: 0.6493 (tp30) cc_final: 0.5402 (pm20) REVERT: G 441 MET cc_start: 0.6405 (ttt) cc_final: 0.6010 (tpt) REVERT: H 8 ASP cc_start: 0.5823 (m-30) cc_final: 0.5393 (m-30) REVERT: H 16 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6319 (mm-30) REVERT: H 19 ARG cc_start: 0.6225 (mmm160) cc_final: 0.4786 (mmm-85) REVERT: H 22 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6708 (mtt-85) REVERT: H 47 ASP cc_start: 0.6424 (m-30) cc_final: 0.5571 (t70) REVERT: H 216 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6284 (tp) REVERT: H 224 LYS cc_start: 0.6780 (mttm) cc_final: 0.6458 (mttp) REVERT: H 269 GLU cc_start: 0.5661 (tp30) cc_final: 0.4899 (tp30) REVERT: H 321 ARG cc_start: 0.6549 (ttt90) cc_final: 0.5749 (ttt90) REVERT: H 403 GLU cc_start: 0.6108 (mm-30) cc_final: 0.5458 (mm-30) REVERT: H 419 ASN cc_start: 0.5940 (m-40) cc_final: 0.4708 (t0) REVERT: H 438 ASP cc_start: 0.6495 (m-30) cc_final: 0.6055 (m-30) REVERT: I 11 LYS cc_start: 0.5648 (ttpp) cc_final: 0.4706 (tptt) REVERT: I 51 MET cc_start: 0.6926 (mtp) cc_final: 0.6724 (ttm) REVERT: I 153 ASP cc_start: 0.6843 (t0) cc_final: 0.6618 (t0) REVERT: I 184 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: I 254 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6114 (mptt) REVERT: I 269 GLU cc_start: 0.5265 (tp30) cc_final: 0.4967 (tp30) REVERT: I 321 ARG cc_start: 0.6426 (ttt90) cc_final: 0.6066 (ttt90) REVERT: I 329 SER cc_start: 0.7365 (p) cc_final: 0.7120 (p) REVERT: I 363 LYS cc_start: 0.6885 (mmmt) cc_final: 0.6332 (mmmm) REVERT: I 407 LYS cc_start: 0.6687 (tttm) cc_final: 0.6287 (ttpp) REVERT: I 419 ASN cc_start: 0.5826 (m-40) cc_final: 0.4556 (t0) REVERT: I 434 GLU cc_start: 0.6555 (tp30) cc_final: 0.5518 (pm20) REVERT: J 11 LYS cc_start: 0.5653 (ttpp) cc_final: 0.4715 (tptt) REVERT: J 37 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6656 (m) REVERT: J 153 ASP cc_start: 0.6843 (t0) cc_final: 0.6618 (t0) REVERT: J 269 GLU cc_start: 0.5483 (mm-30) cc_final: 0.5052 (tp30) REVERT: J 419 ASN cc_start: 0.5818 (m-40) cc_final: 0.4536 (t0) REVERT: J 441 MET cc_start: 0.6388 (ttt) cc_final: 0.5948 (tpt) REVERT: K 11 LYS cc_start: 0.5635 (ttpp) cc_final: 0.4698 (tptt) REVERT: K 22 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6467 (mmt-90) REVERT: K 37 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6647 (m) REVERT: K 51 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6849 (mtt) REVERT: K 153 ASP cc_start: 0.6839 (t0) cc_final: 0.6606 (t0) REVERT: K 254 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6207 (mppt) REVERT: K 265 MET cc_start: 0.6129 (tpp) cc_final: 0.5873 (tpp) REVERT: K 269 GLU cc_start: 0.5488 (mm-30) cc_final: 0.5056 (tp30) REVERT: K 419 ASN cc_start: 0.5837 (m-40) cc_final: 0.4558 (t0) REVERT: K 441 MET cc_start: 0.6387 (ttt) cc_final: 0.5945 (tpt) REVERT: L 8 ASP cc_start: 0.5799 (m-30) cc_final: 0.5373 (m-30) REVERT: L 16 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6329 (mm-30) REVERT: L 19 ARG cc_start: 0.6216 (mmm160) cc_final: 0.4874 (mmm-85) REVERT: L 47 ASP cc_start: 0.6331 (m-30) cc_final: 0.5492 (t70) REVERT: L 142 GLU cc_start: 0.6572 (mm-30) cc_final: 0.5728 (mp0) REVERT: L 159 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6694 (pp) REVERT: L 224 LYS cc_start: 0.6784 (mttm) cc_final: 0.6445 (mttp) REVERT: L 269 GLU cc_start: 0.5559 (tp30) cc_final: 0.4825 (tp30) REVERT: L 321 ARG cc_start: 0.6537 (ttt90) cc_final: 0.5774 (ttt90) REVERT: L 403 GLU cc_start: 0.6021 (mm-30) cc_final: 0.5382 (mm-30) REVERT: L 419 ASN cc_start: 0.5958 (m-40) cc_final: 0.4725 (t0) REVERT: L 438 ASP cc_start: 0.6550 (m-30) cc_final: 0.6116 (m-30) outliers start: 113 outliers final: 78 residues processed: 756 average time/residue: 1.7397 time to fit residues: 1557.9249 Evaluate side-chains 758 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 649 time to evaluate : 4.585 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 143 LYS 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 248 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 132 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 325 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 39 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 254 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 67 ASP 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 370 GLN Chi-restraints excluded: chain F residue 37 VAL 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 184 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ARG 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 24 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 99 THR 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 254 LYS Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 370 GLN Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 37 VAL 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 216 LEU 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 132 GLU Chi-restraints excluded: chain I residue 184 GLU 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 325 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 132 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 325 SER Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain L residue 37 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 310 optimal weight: 7.9990 chunk 415 optimal weight: 0.0770 chunk 119 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 390 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- 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 ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133784 restraints weight = 33712.791| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.06 r_work: 0.3403 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: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 40900 Z= 0.177 Angle : 0.513 8.159 55360 Z= 0.280 Chirality : 0.042 0.149 5964 Planarity : 0.004 0.050 7260 Dihedral : 5.924 59.919 5391 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.44 % Allowed : 13.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 4884 helix: 2.01 (0.12), residues: 2028 sheet: -0.23 (0.17), residues: 912 loop : 0.18 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 425 HIS 0.006 0.001 HIS F 195 PHE 0.017 0.001 PHE B 285 TYR 0.025 0.002 TYR J 296 ARG 0.004 0.000 ARG K 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21226.94 seconds wall clock time: 376 minutes 15.37 seconds (22575.37 seconds total)