Starting phenix.real_space_refine on Fri Mar 15 18:44:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jxl_8179/03_2024/5jxl_8179_neut.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 143 5.16 5 C 43010 2.51 5 N 12320 2.21 5 O 14520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 2": "NH1" <-> "NH2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 740": "NH1" <-> "NH2" Residue "C ARG 2": "NH1" <-> "NH2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 740": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 740": "NH1" <-> "NH2" Residue "E ARG 2": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 740": "NH1" <-> "NH2" Residue "F ARG 2": "NH1" <-> "NH2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 740": "NH1" <-> "NH2" Residue "A ARG 2": "NH1" <-> "NH2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 740": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 740": "NH1" <-> "NH2" Residue "I ARG 2": "NH1" <-> "NH2" Residue "I TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 306": "NH1" <-> "NH2" Residue "I PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 740": "NH1" <-> "NH2" Residue "J ARG 2": "NH1" <-> "NH2" Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 740": "NH1" <-> "NH2" Residue "K ARG 2": "NH1" <-> "NH2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 306": "NH1" <-> "NH2" Residue "K PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 740": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69993 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "C" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "D" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "E" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "F" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "A" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "G" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "H" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "I" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "J" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Chain: "K" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6363 Classifications: {'peptide': 851} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 812} Time building chain proxies: 26.47, per 1000 atoms: 0.38 Number of scatterers: 69993 At special positions: 0 Unit cell: (274.32, 276.48, 258.12, 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 143 16.00 O 14520 8.00 N 12320 7.00 C 43010 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: 20.88 Conformation dependent library (CDL) restraints added in 9.7 seconds 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16808 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 242 sheets defined 15.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 27 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 474 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP A 589 " --> pdb=" O LYS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 589' Processing helix chain 'A' and resid 742 through 744 No H-bonds generated for 'chain 'A' and resid 742 through 744' Processing helix chain 'A' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 27 Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU B 377 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU B 472 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 474 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 27 Processing helix chain 'C' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 removed outlier: 5.035A pdb=" N LEU C 472 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 474 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP C 589 " --> pdb=" O LYS C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 586 through 589' Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 815 through 851 removed outlier: 3.592A pdb=" N GLN C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 851 " --> pdb=" O ILE C 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 27 Processing helix chain 'D' and resid 314 through 324 removed outlier: 3.519A pdb=" N ALA D 318 " --> pdb=" O SER D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU D 472 " --> pdb=" O GLN D 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D 474 " --> pdb=" O SER D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.704A pdb=" N ILE D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP D 589 " --> pdb=" O LYS D 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 586 through 589' Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 843 " --> pdb=" O SER D 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS D 850 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN D 851 " --> pdb=" O ILE D 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 27 Processing helix chain 'E' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU E 377 " --> pdb=" O SER E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR E 464 " --> pdb=" O ALA E 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 468 " --> pdb=" O TYR E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU E 472 " --> pdb=" O GLN E 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN E 474 " --> pdb=" O SER E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU E 486 " --> pdb=" O THR E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 585 removed outlier: 3.704A pdb=" N ILE E 584 " --> pdb=" O ALA E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP E 589 " --> pdb=" O LYS E 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 586 through 589' Processing helix chain 'E' and resid 742 through 744 No H-bonds generated for 'chain 'E' and resid 742 through 744' Processing helix chain 'E' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS E 850 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN E 851 " --> pdb=" O ILE E 847 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 27 Processing helix chain 'F' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA F 318 " --> pdb=" O SER F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU F 377 " --> pdb=" O SER F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR F 464 " --> pdb=" O ALA F 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 468 " --> pdb=" O TYR F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU F 472 " --> pdb=" O GLN F 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN F 474 " --> pdb=" O SER F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 497 removed outlier: 3.516A pdb=" N LEU F 486 " --> pdb=" O THR F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE F 584 " --> pdb=" O ALA F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 589 removed outlier: 3.563A pdb=" N ASP F 589 " --> pdb=" O LYS F 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 586 through 589' Processing helix chain 'F' and resid 742 through 744 No H-bonds generated for 'chain 'F' and resid 742 through 744' Processing helix chain 'F' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 843 " --> pdb=" O SER F 839 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS F 850 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN F 851 " --> pdb=" O ILE F 847 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 27 Processing helix chain 'G' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA G 318 " --> pdb=" O SER G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 363 Processing helix chain 'G' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU G 377 " --> pdb=" O SER G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR G 464 " --> pdb=" O ALA G 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE G 468 " --> pdb=" O TYR G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU G 472 " --> pdb=" O GLN G 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN G 474 " --> pdb=" O SER G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 497 removed outlier: 3.516A pdb=" N LEU G 486 " --> pdb=" O THR G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 585 removed outlier: 3.704A pdb=" N ILE G 584 " --> pdb=" O ALA G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP G 589 " --> pdb=" O LYS G 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 586 through 589' Processing helix chain 'G' and resid 742 through 744 No H-bonds generated for 'chain 'G' and resid 742 through 744' Processing helix chain 'G' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN G 826 " --> pdb=" O LEU G 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 843 " --> pdb=" O SER G 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS G 850 " --> pdb=" O LEU G 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN G 851 " --> pdb=" O ILE G 847 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 27 Processing helix chain 'H' and resid 314 through 324 removed outlier: 3.519A pdb=" N ALA H 318 " --> pdb=" O SER H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 373 through 377 removed outlier: 3.620A pdb=" N GLU H 377 " --> pdb=" O SER H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR H 464 " --> pdb=" O ALA H 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 468 " --> pdb=" O TYR H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU H 472 " --> pdb=" O GLN H 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 474 " --> pdb=" O SER H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU H 486 " --> pdb=" O THR H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE H 584 " --> pdb=" O ALA H 580 " (cutoff:3.500A) Processing helix chain 'H' and resid 586 through 589 removed outlier: 3.563A pdb=" N ASP H 589 " --> pdb=" O LYS H 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 586 through 589' Processing helix chain 'H' and resid 742 through 744 No H-bonds generated for 'chain 'H' and resid 742 through 744' Processing helix chain 'H' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN H 826 " --> pdb=" O LEU H 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU H 843 " --> pdb=" O SER H 839 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 850 " --> pdb=" O LEU H 846 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN H 851 " --> pdb=" O ILE H 847 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 27 Processing helix chain 'I' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA I 318 " --> pdb=" O SER I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 363 Processing helix chain 'I' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU I 377 " --> pdb=" O SER I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR I 464 " --> pdb=" O ALA I 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE I 468 " --> pdb=" O TYR I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU I 472 " --> pdb=" O GLN I 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN I 474 " --> pdb=" O SER I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU I 486 " --> pdb=" O THR I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 585 removed outlier: 3.704A pdb=" N ILE I 584 " --> pdb=" O ALA I 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP I 589 " --> pdb=" O LYS I 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 586 through 589' Processing helix chain 'I' and resid 742 through 744 No H-bonds generated for 'chain 'I' and resid 742 through 744' Processing helix chain 'I' and resid 815 through 851 removed outlier: 3.592A pdb=" N GLN I 826 " --> pdb=" O LEU I 822 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU I 843 " --> pdb=" O SER I 839 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS I 850 " --> pdb=" O LEU I 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN I 851 " --> pdb=" O ILE I 847 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 27 Processing helix chain 'J' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA J 318 " --> pdb=" O SER J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 363 Processing helix chain 'J' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU J 377 " --> pdb=" O SER J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR J 464 " --> pdb=" O ALA J 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 468 " --> pdb=" O TYR J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU J 472 " --> pdb=" O GLN J 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN J 474 " --> pdb=" O SER J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 497 removed outlier: 3.515A pdb=" N LEU J 486 " --> pdb=" O THR J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 585 removed outlier: 3.704A pdb=" N ILE J 584 " --> pdb=" O ALA J 580 " (cutoff:3.500A) Processing helix chain 'J' and resid 586 through 589 removed outlier: 3.564A pdb=" N ASP J 589 " --> pdb=" O LYS J 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 586 through 589' Processing helix chain 'J' and resid 742 through 744 No H-bonds generated for 'chain 'J' and resid 742 through 744' Processing helix chain 'J' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN J 826 " --> pdb=" O LEU J 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 843 " --> pdb=" O SER J 839 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS J 850 " --> pdb=" O LEU J 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN J 851 " --> pdb=" O ILE J 847 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 27 Processing helix chain 'K' and resid 314 through 324 removed outlier: 3.518A pdb=" N ALA K 318 " --> pdb=" O SER K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 373 through 377 removed outlier: 3.621A pdb=" N GLU K 377 " --> pdb=" O SER K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 458 through 468 removed outlier: 3.705A pdb=" N TYR K 464 " --> pdb=" O ALA K 460 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE K 468 " --> pdb=" O TYR K 464 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 474 removed outlier: 5.034A pdb=" N LEU K 472 " --> pdb=" O GLN K 469 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN K 474 " --> pdb=" O SER K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 497 removed outlier: 3.516A pdb=" N LEU K 486 " --> pdb=" O THR K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 585 removed outlier: 3.703A pdb=" N ILE K 584 " --> pdb=" O ALA K 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 586 through 589 removed outlier: 3.563A pdb=" N ASP K 589 " --> pdb=" O LYS K 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 586 through 589' Processing helix chain 'K' and resid 742 through 744 No H-bonds generated for 'chain 'K' and resid 742 through 744' Processing helix chain 'K' and resid 815 through 851 removed outlier: 3.593A pdb=" N GLN K 826 " --> pdb=" O LEU K 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 843 " --> pdb=" O SER K 839 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS K 850 " --> pdb=" O LEU K 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN K 851 " --> pdb=" O ILE K 847 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG A 37 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR A 75 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP A 39 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU A 64 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 84 through 86 Processing sheet with id= 4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id= 5, first strand: chain 'A' and resid 112 through 114 Processing sheet with id= 6, first strand: chain 'A' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE A 100 " --> pdb=" O TRP A 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP A 138 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET A 102 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 104 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 140 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 759 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 747 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE A 100 " --> pdb=" O TRP A 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP A 138 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET A 102 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 104 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE A 747 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 759 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 140 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 120 through 121 Processing sheet with id= 10, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY A 732 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL A 172 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 713 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA A 176 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 715 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 178 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL A 172 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU A 171 " --> pdb=" O THR A 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR A 726 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 173 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 724 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 177 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN A 217 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 478 through 480 Processing sheet with id= 15, first strand: chain 'A' and resid 261 through 264 Processing sheet with id= 16, first strand: chain 'A' and resid 282 through 283 Processing sheet with id= 17, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU A 302 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 301 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 365 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 419 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 522 through 526 Processing sheet with id= 19, first strand: chain 'A' and resid 541 through 543 Processing sheet with id= 20, first strand: chain 'A' and resid 561 through 562 Processing sheet with id= 21, first strand: chain 'A' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU A 641 " --> pdb=" O GLN A 632 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 774 through 775 Processing sheet with id= 23, first strand: chain 'B' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG B 37 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 75 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP B 39 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU B 64 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 84 through 86 Processing sheet with id= 26, first strand: chain 'B' and resid 94 through 95 Processing sheet with id= 27, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= 28, first strand: chain 'B' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE B 100 " --> pdb=" O TRP B 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP B 138 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET B 102 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 104 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 140 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL B 759 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 747 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE B 100 " --> pdb=" O TRP B 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP B 138 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET B 102 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 104 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 746 through 748 removed outlier: 6.641A pdb=" N ILE B 747 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL B 759 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 140 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 120 through 121 Processing sheet with id= 32, first strand: chain 'B' and resid 163 through 164 removed outlier: 3.566A pdb=" N GLY B 732 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL B 172 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL B 713 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA B 176 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER B 715 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 178 " --> pdb=" O SER B 715 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL B 172 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 171 " --> pdb=" O THR B 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 726 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA B 173 " --> pdb=" O GLN B 724 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 724 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 177 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN B 217 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 478 through 480 Processing sheet with id= 37, first strand: chain 'B' and resid 261 through 264 Processing sheet with id= 38, first strand: chain 'B' and resid 282 through 283 Processing sheet with id= 39, first strand: chain 'B' and resid 305 through 307 removed outlier: 3.828A pdb=" N LEU B 302 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 301 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 365 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 419 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 522 through 526 Processing sheet with id= 41, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= 42, first strand: chain 'B' and resid 561 through 562 Processing sheet with id= 43, first strand: chain 'B' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU B 641 " --> pdb=" O GLN B 632 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 774 through 775 Processing sheet with id= 45, first strand: chain 'C' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG C 37 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR C 75 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 39 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU C 64 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 84 through 86 Processing sheet with id= 48, first strand: chain 'C' and resid 94 through 95 Processing sheet with id= 49, first strand: chain 'C' and resid 112 through 114 Processing sheet with id= 50, first strand: chain 'C' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE C 100 " --> pdb=" O TRP C 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP C 138 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET C 102 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 104 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 140 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL C 759 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 747 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE C 100 " --> pdb=" O TRP C 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP C 138 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET C 102 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 104 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE C 747 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL C 759 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 140 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 120 through 121 Processing sheet with id= 54, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.564A pdb=" N GLY C 732 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 685 through 687 removed outlier: 6.012A pdb=" N VAL C 172 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL C 713 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA C 176 " --> pdb=" O VAL C 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER C 715 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU C 178 " --> pdb=" O SER C 715 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 685 through 687 removed outlier: 6.012A pdb=" N VAL C 172 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU C 171 " --> pdb=" O THR C 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR C 726 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA C 173 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN C 724 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 177 " --> pdb=" O THR C 720 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN C 217 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 478 through 480 Processing sheet with id= 59, first strand: chain 'C' and resid 261 through 264 Processing sheet with id= 60, first strand: chain 'C' and resid 282 through 283 Processing sheet with id= 61, first strand: chain 'C' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU C 302 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 301 " --> pdb=" O THR C 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 365 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 419 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 522 through 526 Processing sheet with id= 63, first strand: chain 'C' and resid 541 through 543 Processing sheet with id= 64, first strand: chain 'C' and resid 561 through 562 Processing sheet with id= 65, first strand: chain 'C' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU C 641 " --> pdb=" O GLN C 632 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'C' and resid 774 through 775 Processing sheet with id= 67, first strand: chain 'D' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG D 37 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR D 75 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP D 39 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU D 64 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= 70, first strand: chain 'D' and resid 94 through 95 Processing sheet with id= 71, first strand: chain 'D' and resid 112 through 114 Processing sheet with id= 72, first strand: chain 'D' and resid 792 through 793 removed outlier: 17.008A pdb=" N PHE D 100 " --> pdb=" O TRP D 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP D 138 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET D 102 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 104 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 140 " --> pdb=" O VAL D 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL D 759 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 747 " --> pdb=" O VAL D 759 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 112 through 114 removed outlier: 17.008A pdb=" N PHE D 100 " --> pdb=" O TRP D 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP D 138 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET D 102 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 104 " --> pdb=" O VAL D 134 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE D 747 " --> pdb=" O VAL D 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL D 759 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 140 " --> pdb=" O VAL D 759 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 120 through 121 Processing sheet with id= 76, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY D 732 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL D 172 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 713 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA D 176 " --> pdb=" O VAL D 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER D 715 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU D 178 " --> pdb=" O SER D 715 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL D 172 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU D 171 " --> pdb=" O THR D 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR D 726 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA D 173 " --> pdb=" O GLN D 724 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN D 724 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 177 " --> pdb=" O THR D 720 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN D 217 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 478 through 480 Processing sheet with id= 81, first strand: chain 'D' and resid 261 through 264 Processing sheet with id= 82, first strand: chain 'D' and resid 282 through 283 Processing sheet with id= 83, first strand: chain 'D' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU D 302 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 301 " --> pdb=" O THR D 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 365 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 419 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 522 through 526 Processing sheet with id= 85, first strand: chain 'D' and resid 541 through 543 Processing sheet with id= 86, first strand: chain 'D' and resid 561 through 562 Processing sheet with id= 87, first strand: chain 'D' and resid 608 through 613 removed outlier: 7.153A pdb=" N GLU D 641 " --> pdb=" O GLN D 632 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'D' and resid 774 through 775 Processing sheet with id= 89, first strand: chain 'E' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG E 37 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR E 75 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP E 39 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'E' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU E 64 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= 92, first strand: chain 'E' and resid 94 through 95 Processing sheet with id= 93, first strand: chain 'E' and resid 112 through 114 Processing sheet with id= 94, first strand: chain 'E' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE E 100 " --> pdb=" O TRP E 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP E 138 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET E 102 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER E 104 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 140 " --> pdb=" O VAL E 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL E 759 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 747 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'E' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE E 100 " --> pdb=" O TRP E 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP E 138 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET E 102 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER E 104 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'E' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE E 747 " --> pdb=" O VAL E 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL E 759 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 140 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'E' and resid 120 through 121 Processing sheet with id= 98, first strand: chain 'E' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY E 732 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL E 172 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL E 713 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA E 176 " --> pdb=" O VAL E 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER E 715 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU E 178 " --> pdb=" O SER E 715 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL E 172 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU E 171 " --> pdb=" O THR E 726 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR E 726 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA E 173 " --> pdb=" O GLN E 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN E 724 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 177 " --> pdb=" O THR E 720 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'E' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN E 217 " --> pdb=" O THR E 229 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'E' and resid 478 through 480 Processing sheet with id=103, first strand: chain 'E' and resid 261 through 264 Processing sheet with id=104, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=105, first strand: chain 'E' and resid 305 through 307 removed outlier: 3.830A pdb=" N LEU E 302 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 301 " --> pdb=" O THR E 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 365 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 419 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'E' and resid 522 through 526 Processing sheet with id=107, first strand: chain 'E' and resid 541 through 543 Processing sheet with id=108, first strand: chain 'E' and resid 561 through 562 Processing sheet with id=109, first strand: chain 'E' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU E 641 " --> pdb=" O GLN E 632 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'E' and resid 774 through 775 Processing sheet with id=111, first strand: chain 'F' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG F 37 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR F 75 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 39 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU F 64 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=114, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=115, first strand: chain 'F' and resid 112 through 114 Processing sheet with id=116, first strand: chain 'F' and resid 792 through 793 removed outlier: 17.008A pdb=" N PHE F 100 " --> pdb=" O TRP F 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP F 138 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET F 102 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 104 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 140 " --> pdb=" O VAL F 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL F 759 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE F 747 " --> pdb=" O VAL F 759 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'F' and resid 112 through 114 removed outlier: 17.008A pdb=" N PHE F 100 " --> pdb=" O TRP F 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP F 138 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET F 102 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 104 " --> pdb=" O VAL F 134 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'F' and resid 746 through 748 removed outlier: 6.643A pdb=" N ILE F 747 " --> pdb=" O VAL F 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL F 759 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 140 " --> pdb=" O VAL F 759 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'F' and resid 120 through 121 Processing sheet with id=120, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY F 732 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'F' and resid 685 through 687 removed outlier: 6.012A pdb=" N VAL F 172 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL F 713 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA F 176 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER F 715 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 178 " --> pdb=" O SER F 715 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'F' and resid 685 through 687 removed outlier: 6.012A pdb=" N VAL F 172 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU F 171 " --> pdb=" O THR F 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR F 726 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA F 173 " --> pdb=" O GLN F 724 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN F 724 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN F 177 " --> pdb=" O THR F 720 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'F' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN F 217 " --> pdb=" O THR F 229 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'F' and resid 478 through 480 Processing sheet with id=125, first strand: chain 'F' and resid 261 through 264 Processing sheet with id=126, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=127, first strand: chain 'F' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU F 302 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN F 301 " --> pdb=" O THR F 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 365 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 419 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'F' and resid 522 through 526 Processing sheet with id=129, first strand: chain 'F' and resid 541 through 543 Processing sheet with id=130, first strand: chain 'F' and resid 561 through 562 Processing sheet with id=131, first strand: chain 'F' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU F 641 " --> pdb=" O GLN F 632 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'F' and resid 774 through 775 Processing sheet with id=133, first strand: chain 'G' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG G 37 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR G 75 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP G 39 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'G' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU G 64 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=136, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=137, first strand: chain 'G' and resid 112 through 114 Processing sheet with id=138, first strand: chain 'G' and resid 792 through 793 removed outlier: 17.008A pdb=" N PHE G 100 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP G 138 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET G 102 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 104 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 140 " --> pdb=" O VAL G 759 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL G 759 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE G 747 " --> pdb=" O VAL G 759 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'G' and resid 112 through 114 removed outlier: 17.008A pdb=" N PHE G 100 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP G 138 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET G 102 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 104 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'G' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE G 747 " --> pdb=" O VAL G 759 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL G 759 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 140 " --> pdb=" O VAL G 759 " (cutoff:3.500A) Processing sheet with id=141, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=142, first strand: chain 'G' and resid 163 through 164 removed outlier: 3.566A pdb=" N GLY G 732 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'G' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL G 172 " --> pdb=" O SER G 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL G 713 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA G 176 " --> pdb=" O VAL G 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER G 715 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU G 178 " --> pdb=" O SER G 715 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'G' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL G 172 " --> pdb=" O SER G 702 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU G 171 " --> pdb=" O THR G 726 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR G 726 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 173 " --> pdb=" O GLN G 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN G 724 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN G 177 " --> pdb=" O THR G 720 " (cutoff:3.500A) Processing sheet with id=145, first strand: chain 'G' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN G 217 " --> pdb=" O THR G 229 " (cutoff:3.500A) Processing sheet with id=146, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=147, first strand: chain 'G' and resid 261 through 264 Processing sheet with id=148, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=149, first strand: chain 'G' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU G 302 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN G 301 " --> pdb=" O THR G 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 365 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 419 " --> pdb=" O LEU G 367 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'G' and resid 522 through 526 Processing sheet with id=151, first strand: chain 'G' and resid 541 through 543 Processing sheet with id=152, first strand: chain 'G' and resid 561 through 562 Processing sheet with id=153, first strand: chain 'G' and resid 608 through 613 removed outlier: 7.153A pdb=" N GLU G 641 " --> pdb=" O GLN G 632 " (cutoff:3.500A) Processing sheet with id=154, first strand: chain 'G' and resid 774 through 775 Processing sheet with id=155, first strand: chain 'H' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG H 37 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR H 75 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP H 39 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'H' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU H 64 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'H' and resid 84 through 86 Processing sheet with id=158, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=159, first strand: chain 'H' and resid 112 through 114 Processing sheet with id=160, first strand: chain 'H' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE H 100 " --> pdb=" O TRP H 138 " (cutoff:3.500A) removed outlier: 12.275A pdb=" N TRP H 138 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET H 102 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 104 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE H 140 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL H 759 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE H 747 " --> pdb=" O VAL H 759 " (cutoff:3.500A) Processing sheet with id=161, first strand: chain 'H' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE H 100 " --> pdb=" O TRP H 138 " (cutoff:3.500A) removed outlier: 12.275A pdb=" N TRP H 138 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET H 102 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER H 104 " --> pdb=" O VAL H 134 " (cutoff:3.500A) Processing sheet with id=162, first strand: chain 'H' and resid 746 through 748 removed outlier: 6.641A pdb=" N ILE H 747 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL H 759 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE H 140 " --> pdb=" O VAL H 759 " (cutoff:3.500A) Processing sheet with id=163, first strand: chain 'H' and resid 120 through 121 Processing sheet with id=164, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY H 732 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing sheet with id=165, first strand: chain 'H' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL H 172 " --> pdb=" O SER H 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL H 713 " --> pdb=" O ILE H 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA H 176 " --> pdb=" O VAL H 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER H 715 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU H 178 " --> pdb=" O SER H 715 " (cutoff:3.500A) Processing sheet with id=166, first strand: chain 'H' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL H 172 " --> pdb=" O SER H 702 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU H 171 " --> pdb=" O THR H 726 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR H 726 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA H 173 " --> pdb=" O GLN H 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN H 724 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN H 177 " --> pdb=" O THR H 720 " (cutoff:3.500A) Processing sheet with id=167, first strand: chain 'H' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN H 217 " --> pdb=" O THR H 229 " (cutoff:3.500A) Processing sheet with id=168, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=169, first strand: chain 'H' and resid 261 through 264 Processing sheet with id=170, first strand: chain 'H' and resid 282 through 283 Processing sheet with id=171, first strand: chain 'H' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU H 302 " --> pdb=" O VAL H 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN H 301 " --> pdb=" O THR H 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 365 " --> pdb=" O VAL H 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 419 " --> pdb=" O LEU H 367 " (cutoff:3.500A) Processing sheet with id=172, first strand: chain 'H' and resid 522 through 526 Processing sheet with id=173, first strand: chain 'H' and resid 541 through 543 Processing sheet with id=174, first strand: chain 'H' and resid 561 through 562 Processing sheet with id=175, first strand: chain 'H' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU H 641 " --> pdb=" O GLN H 632 " (cutoff:3.500A) Processing sheet with id=176, first strand: chain 'H' and resid 774 through 775 Processing sheet with id=177, first strand: chain 'I' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG I 37 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR I 75 " --> pdb=" O ARG I 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP I 39 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing sheet with id=178, first strand: chain 'I' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU I 64 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=179, first strand: chain 'I' and resid 84 through 86 Processing sheet with id=180, first strand: chain 'I' and resid 94 through 95 Processing sheet with id=181, first strand: chain 'I' and resid 112 through 114 Processing sheet with id=182, first strand: chain 'I' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE I 100 " --> pdb=" O TRP I 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP I 138 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET I 102 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 104 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE I 140 " --> pdb=" O VAL I 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL I 759 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE I 747 " --> pdb=" O VAL I 759 " (cutoff:3.500A) Processing sheet with id=183, first strand: chain 'I' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE I 100 " --> pdb=" O TRP I 138 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N TRP I 138 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET I 102 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 104 " --> pdb=" O VAL I 134 " (cutoff:3.500A) Processing sheet with id=184, first strand: chain 'I' and resid 746 through 748 removed outlier: 6.643A pdb=" N ILE I 747 " --> pdb=" O VAL I 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL I 759 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE I 140 " --> pdb=" O VAL I 759 " (cutoff:3.500A) Processing sheet with id=185, first strand: chain 'I' and resid 120 through 121 Processing sheet with id=186, first strand: chain 'I' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY I 732 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing sheet with id=187, first strand: chain 'I' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL I 172 " --> pdb=" O SER I 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL I 713 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA I 176 " --> pdb=" O VAL I 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER I 715 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU I 178 " --> pdb=" O SER I 715 " (cutoff:3.500A) Processing sheet with id=188, first strand: chain 'I' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL I 172 " --> pdb=" O SER I 702 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU I 171 " --> pdb=" O THR I 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR I 726 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA I 173 " --> pdb=" O GLN I 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN I 724 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN I 177 " --> pdb=" O THR I 720 " (cutoff:3.500A) Processing sheet with id=189, first strand: chain 'I' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN I 217 " --> pdb=" O THR I 229 " (cutoff:3.500A) Processing sheet with id=190, first strand: chain 'I' and resid 478 through 480 Processing sheet with id=191, first strand: chain 'I' and resid 261 through 264 Processing sheet with id=192, first strand: chain 'I' and resid 282 through 283 Processing sheet with id=193, first strand: chain 'I' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU I 302 " --> pdb=" O VAL I 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN I 301 " --> pdb=" O THR I 368 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE I 365 " --> pdb=" O VAL I 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 419 " --> pdb=" O LEU I 367 " (cutoff:3.500A) Processing sheet with id=194, first strand: chain 'I' and resid 522 through 526 Processing sheet with id=195, first strand: chain 'I' and resid 541 through 543 Processing sheet with id=196, first strand: chain 'I' and resid 561 through 562 Processing sheet with id=197, first strand: chain 'I' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU I 641 " --> pdb=" O GLN I 632 " (cutoff:3.500A) Processing sheet with id=198, first strand: chain 'I' and resid 774 through 775 Processing sheet with id=199, first strand: chain 'J' and resid 36 through 42 removed outlier: 6.306A pdb=" N ARG J 37 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP J 39 " --> pdb=" O SER J 73 " (cutoff:3.500A) Processing sheet with id=200, first strand: chain 'J' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU J 64 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=201, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=202, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=203, first strand: chain 'J' and resid 112 through 114 Processing sheet with id=204, first strand: chain 'J' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE J 100 " --> pdb=" O TRP J 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP J 138 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET J 102 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER J 104 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE J 140 " --> pdb=" O VAL J 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL J 759 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE J 747 " --> pdb=" O VAL J 759 " (cutoff:3.500A) Processing sheet with id=205, first strand: chain 'J' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE J 100 " --> pdb=" O TRP J 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP J 138 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET J 102 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER J 104 " --> pdb=" O VAL J 134 " (cutoff:3.500A) Processing sheet with id=206, first strand: chain 'J' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE J 747 " --> pdb=" O VAL J 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL J 759 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE J 140 " --> pdb=" O VAL J 759 " (cutoff:3.500A) Processing sheet with id=207, first strand: chain 'J' and resid 120 through 121 Processing sheet with id=208, first strand: chain 'J' and resid 163 through 164 removed outlier: 3.564A pdb=" N GLY J 732 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing sheet with id=209, first strand: chain 'J' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL J 172 " --> pdb=" O SER J 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL J 713 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA J 176 " --> pdb=" O VAL J 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER J 715 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU J 178 " --> pdb=" O SER J 715 " (cutoff:3.500A) Processing sheet with id=210, first strand: chain 'J' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL J 172 " --> pdb=" O SER J 702 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU J 171 " --> pdb=" O THR J 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR J 726 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA J 173 " --> pdb=" O GLN J 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN J 724 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN J 177 " --> pdb=" O THR J 720 " (cutoff:3.500A) Processing sheet with id=211, first strand: chain 'J' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN J 217 " --> pdb=" O THR J 229 " (cutoff:3.500A) Processing sheet with id=212, first strand: chain 'J' and resid 478 through 480 Processing sheet with id=213, first strand: chain 'J' and resid 261 through 264 Processing sheet with id=214, first strand: chain 'J' and resid 282 through 283 Processing sheet with id=215, first strand: chain 'J' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU J 302 " --> pdb=" O VAL J 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN J 301 " --> pdb=" O THR J 368 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE J 365 " --> pdb=" O VAL J 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 419 " --> pdb=" O LEU J 367 " (cutoff:3.500A) Processing sheet with id=216, first strand: chain 'J' and resid 522 through 526 Processing sheet with id=217, first strand: chain 'J' and resid 541 through 543 Processing sheet with id=218, first strand: chain 'J' and resid 561 through 562 Processing sheet with id=219, first strand: chain 'J' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU J 641 " --> pdb=" O GLN J 632 " (cutoff:3.500A) Processing sheet with id=220, first strand: chain 'J' and resid 774 through 775 Processing sheet with id=221, first strand: chain 'K' and resid 36 through 42 removed outlier: 6.305A pdb=" N ARG K 37 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR K 75 " --> pdb=" O ARG K 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP K 39 " --> pdb=" O SER K 73 " (cutoff:3.500A) Processing sheet with id=222, first strand: chain 'K' and resid 47 through 49 removed outlier: 6.795A pdb=" N LEU K 64 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=223, first strand: chain 'K' and resid 84 through 86 Processing sheet with id=224, first strand: chain 'K' and resid 94 through 95 Processing sheet with id=225, first strand: chain 'K' and resid 112 through 114 Processing sheet with id=226, first strand: chain 'K' and resid 792 through 793 removed outlier: 17.007A pdb=" N PHE K 100 " --> pdb=" O TRP K 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP K 138 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET K 102 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER K 104 " --> pdb=" O VAL K 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE K 140 " --> pdb=" O VAL K 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL K 759 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE K 747 " --> pdb=" O VAL K 759 " (cutoff:3.500A) Processing sheet with id=227, first strand: chain 'K' and resid 112 through 114 removed outlier: 17.007A pdb=" N PHE K 100 " --> pdb=" O TRP K 138 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N TRP K 138 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET K 102 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER K 104 " --> pdb=" O VAL K 134 " (cutoff:3.500A) Processing sheet with id=228, first strand: chain 'K' and resid 746 through 748 removed outlier: 6.642A pdb=" N ILE K 747 " --> pdb=" O VAL K 759 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL K 759 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE K 140 " --> pdb=" O VAL K 759 " (cutoff:3.500A) Processing sheet with id=229, first strand: chain 'K' and resid 120 through 121 Processing sheet with id=230, first strand: chain 'K' and resid 163 through 164 removed outlier: 3.565A pdb=" N GLY K 732 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing sheet with id=231, first strand: chain 'K' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL K 172 " --> pdb=" O SER K 702 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL K 713 " --> pdb=" O ILE K 174 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA K 176 " --> pdb=" O VAL K 713 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER K 715 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU K 178 " --> pdb=" O SER K 715 " (cutoff:3.500A) Processing sheet with id=232, first strand: chain 'K' and resid 685 through 687 removed outlier: 6.013A pdb=" N VAL K 172 " --> pdb=" O SER K 702 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU K 171 " --> pdb=" O THR K 726 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR K 726 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 173 " --> pdb=" O GLN K 724 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN K 724 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN K 177 " --> pdb=" O THR K 720 " (cutoff:3.500A) Processing sheet with id=233, first strand: chain 'K' and resid 217 through 220 removed outlier: 4.381A pdb=" N GLN K 217 " --> pdb=" O THR K 229 " (cutoff:3.500A) Processing sheet with id=234, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=235, first strand: chain 'K' and resid 261 through 264 Processing sheet with id=236, first strand: chain 'K' and resid 282 through 283 Processing sheet with id=237, first strand: chain 'K' and resid 305 through 307 removed outlier: 3.829A pdb=" N LEU K 302 " --> pdb=" O VAL K 305 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN K 301 " --> pdb=" O THR K 368 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 365 " --> pdb=" O VAL K 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL K 419 " --> pdb=" O LEU K 367 " (cutoff:3.500A) Processing sheet with id=238, first strand: chain 'K' and resid 522 through 526 Processing sheet with id=239, first strand: chain 'K' and resid 541 through 543 Processing sheet with id=240, first strand: chain 'K' and resid 561 through 562 Processing sheet with id=241, first strand: chain 'K' and resid 608 through 613 removed outlier: 7.152A pdb=" N GLU K 641 " --> pdb=" O GLN K 632 " (cutoff:3.500A) Processing sheet with id=242, first strand: chain 'K' and resid 774 through 775 2200 hydrogen bonds defined for protein. 5412 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: 37.92 Time building geometry restraints manager: 23.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 23985 1.33 - 1.45: 9028 1.45 - 1.57: 37805 1.57 - 1.69: 11 1.69 - 1.81: 286 Bond restraints: 71115 Sorted by residual: bond pdb=" CA ASN B 384 " pdb=" C ASN B 384 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.22e+00 bond pdb=" CA ASN K 384 " pdb=" C ASN K 384 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.20e+00 bond pdb=" CA ASN E 384 " pdb=" C ASN E 384 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.15e+00 bond pdb=" CA ASN H 384 " pdb=" C ASN H 384 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.14e+00 bond pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 1.523 1.564 -0.040 1.34e-02 5.57e+03 9.09e+00 ... (remaining 71110 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.85: 1431 105.85 - 112.98: 37581 112.98 - 120.11: 24059 120.11 - 127.24: 33190 127.24 - 134.37: 462 Bond angle restraints: 96723 Sorted by residual: angle pdb=" C ASP E 250 " pdb=" CA ASP E 250 " pdb=" CB ASP E 250 " ideal model delta sigma weight residual 116.54 108.36 8.18 1.15e+00 7.56e-01 5.06e+01 angle pdb=" C ASP J 250 " pdb=" CA ASP J 250 " pdb=" CB ASP J 250 " ideal model delta sigma weight residual 116.54 108.37 8.17 1.15e+00 7.56e-01 5.05e+01 angle pdb=" C ASP H 250 " pdb=" CA ASP H 250 " pdb=" CB ASP H 250 " ideal model delta sigma weight residual 116.54 108.37 8.17 1.15e+00 7.56e-01 5.05e+01 angle pdb=" C ASP A 250 " pdb=" CA ASP A 250 " pdb=" CB ASP A 250 " ideal model delta sigma weight residual 116.54 108.37 8.17 1.15e+00 7.56e-01 5.05e+01 angle pdb=" C ASP C 250 " pdb=" CA ASP C 250 " pdb=" CB ASP C 250 " ideal model delta sigma weight residual 116.54 108.37 8.17 1.15e+00 7.56e-01 5.05e+01 ... (remaining 96718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 40829 16.58 - 33.16: 1023 33.16 - 49.73: 245 49.73 - 66.31: 33 66.31 - 82.89: 55 Dihedral angle restraints: 42185 sinusoidal: 15829 harmonic: 26356 Sorted by residual: dihedral pdb=" CA ARG J 455 " pdb=" C ARG J 455 " pdb=" N PRO J 456 " pdb=" CA PRO J 456 " ideal model delta harmonic sigma weight residual -180.00 -146.16 -33.84 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA ARG C 455 " pdb=" C ARG C 455 " pdb=" N PRO C 456 " pdb=" CA PRO C 456 " ideal model delta harmonic sigma weight residual -180.00 -146.16 -33.84 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA ARG D 455 " pdb=" C ARG D 455 " pdb=" N PRO D 456 " pdb=" CA PRO D 456 " ideal model delta harmonic sigma weight residual -180.00 -146.17 -33.83 0 5.00e+00 4.00e-02 4.58e+01 ... (remaining 42182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5536 0.040 - 0.079: 3841 0.079 - 0.119: 1287 0.119 - 0.158: 248 0.158 - 0.198: 110 Chirality restraints: 11022 Sorted by residual: chirality pdb=" CA VAL G 28 " pdb=" N VAL G 28 " pdb=" C VAL G 28 " pdb=" CB VAL G 28 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA VAL C 28 " pdb=" N VAL C 28 " pdb=" C VAL C 28 " pdb=" CB VAL C 28 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA VAL J 28 " pdb=" N VAL J 28 " pdb=" C VAL J 28 " pdb=" CB VAL J 28 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.70e-01 ... (remaining 11019 not shown) Planarity restraints: 13068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 406 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.98e+00 pdb=" CG TRP I 406 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP I 406 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP I 406 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP I 406 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 406 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 406 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 406 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 406 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 406 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 406 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.94e+00 pdb=" CG TRP H 406 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP H 406 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 406 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 406 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 406 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 406 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 406 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 406 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 406 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 406 " 0.017 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" CG TRP J 406 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP J 406 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP J 406 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 406 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 406 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 406 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 406 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 406 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 406 " 0.002 2.00e-02 2.50e+03 ... (remaining 13065 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 366 2.42 - 3.04: 47474 3.04 - 3.66: 101403 3.66 - 4.28: 149769 4.28 - 4.90: 245062 Nonbonded interactions: 544074 Sorted by model distance: nonbonded pdb=" OD1 ASP B 105 " pdb=" NE ARG K 58 " model vdw 1.795 2.520 nonbonded pdb=" ND2 ASN D 709 " pdb=" O GLY I 692 " model vdw 1.860 2.520 nonbonded pdb=" ND2 ASN B 709 " pdb=" O GLY G 692 " model vdw 1.860 2.520 nonbonded pdb=" ND2 ASN F 709 " pdb=" O GLY K 692 " model vdw 1.861 2.520 nonbonded pdb=" ND2 ASN E 709 " pdb=" O GLY J 692 " model vdw 1.861 2.520 ... (remaining 544069 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.790 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: 0.070 Extract box with map and model: 8.490 Check model and map are aligned: 0.820 Set scattering table: 0.500 Process input model: 154.010 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 71115 Z= 0.559 Angle : 1.386 10.047 96723 Z= 0.910 Chirality : 0.057 0.198 11022 Planarity : 0.005 0.042 13068 Dihedral : 9.647 82.889 25377 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 2.24 % Allowed : 8.72 % Favored : 89.05 % Rotamer: Outliers : 0.15 % Allowed : 1.89 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.08), residues: 9339 helix: -1.58 (0.10), residues: 1111 sheet: -2.73 (0.08), residues: 2255 loop : -0.68 (0.08), residues: 5973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP I 406 HIS 0.002 0.001 HIS H 623 PHE 0.024 0.003 PHE H 218 TYR 0.023 0.003 TYR C 427 ARG 0.008 0.001 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3074 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 3063 time to evaluate : 5.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7599 (tp40) REVERT: B 19 ASP cc_start: 0.7910 (m-30) cc_final: 0.7275 (m-30) REVERT: B 70 VAL cc_start: 0.8500 (t) cc_final: 0.8208 (p) REVERT: B 319 ILE cc_start: 0.8656 (mm) cc_final: 0.8065 (mm) REVERT: B 323 ASN cc_start: 0.8320 (m-40) cc_final: 0.7975 (m-40) REVERT: B 440 ILE cc_start: 0.7443 (mm) cc_final: 0.7087 (mm) REVERT: B 464 TYR cc_start: 0.8717 (t80) cc_final: 0.8289 (t80) REVERT: B 740 ARG cc_start: 0.8395 (ttt90) cc_final: 0.7012 (ttm110) REVERT: B 774 GLU cc_start: 0.8014 (tt0) cc_final: 0.7074 (tt0) REVERT: C 19 ASP cc_start: 0.7579 (m-30) cc_final: 0.7332 (m-30) REVERT: C 36 SER cc_start: 0.8880 (m) cc_final: 0.8553 (t) REVERT: C 70 VAL cc_start: 0.8444 (t) cc_final: 0.8214 (p) REVERT: C 323 ASN cc_start: 0.8360 (m-40) cc_final: 0.8114 (m-40) REVERT: C 440 ILE cc_start: 0.7800 (mm) cc_final: 0.7555 (mm) REVERT: C 584 ILE cc_start: 0.8008 (pt) cc_final: 0.6459 (pt) REVERT: C 662 THR cc_start: 0.8057 (p) cc_final: 0.7640 (p) REVERT: C 664 ILE cc_start: 0.9018 (mt) cc_final: 0.8603 (tp) REVERT: C 677 LEU cc_start: 0.8969 (tt) cc_final: 0.8742 (tp) REVERT: C 740 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7342 (ttm110) REVERT: C 764 MET cc_start: 0.8042 (ptp) cc_final: 0.7785 (ptm) REVERT: C 833 SER cc_start: 0.9391 (t) cc_final: 0.9189 (p) REVERT: C 840 ASP cc_start: 0.7603 (m-30) cc_final: 0.7378 (m-30) REVERT: D 15 GLN cc_start: 0.8793 (tp-100) cc_final: 0.7890 (tp-100) REVERT: D 19 ASP cc_start: 0.7308 (m-30) cc_final: 0.6983 (m-30) REVERT: D 49 LYS cc_start: 0.8551 (mttt) cc_final: 0.7870 (tttp) REVERT: D 70 VAL cc_start: 0.8209 (t) cc_final: 0.7908 (p) REVERT: D 206 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7487 (mmt180) REVERT: D 323 ASN cc_start: 0.8643 (m-40) cc_final: 0.8175 (m110) REVERT: D 367 LEU cc_start: 0.8067 (tt) cc_final: 0.7824 (tt) REVERT: D 464 TYR cc_start: 0.8270 (t80) cc_final: 0.8048 (t80) REVERT: D 630 VAL cc_start: 0.8772 (t) cc_final: 0.8394 (t) REVERT: D 662 THR cc_start: 0.7823 (p) cc_final: 0.6689 (p) REVERT: D 844 GLN cc_start: 0.8223 (pt0) cc_final: 0.7969 (mp-120) REVERT: E 36 SER cc_start: 0.8842 (m) cc_final: 0.8601 (t) REVERT: E 49 LYS cc_start: 0.8685 (mttt) cc_final: 0.8432 (mtpt) REVERT: E 133 PHE cc_start: 0.7706 (m-10) cc_final: 0.7471 (m-80) REVERT: E 326 THR cc_start: 0.8721 (t) cc_final: 0.8452 (p) REVERT: E 518 ILE cc_start: 0.7812 (mt) cc_final: 0.7534 (mt) REVERT: E 538 ASN cc_start: 0.8246 (t0) cc_final: 0.8006 (t0) REVERT: E 583 LYS cc_start: 0.7262 (ttpt) cc_final: 0.6906 (ttmm) REVERT: E 617 ASP cc_start: 0.7502 (m-30) cc_final: 0.7221 (m-30) REVERT: E 633 SER cc_start: 0.6816 (t) cc_final: 0.6599 (t) REVERT: E 740 ARG cc_start: 0.7901 (ttt90) cc_final: 0.6923 (ttp-170) REVERT: F 15 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8574 (tp40) REVERT: F 36 SER cc_start: 0.8915 (m) cc_final: 0.8671 (t) REVERT: F 49 LYS cc_start: 0.8367 (mttt) cc_final: 0.7961 (tmtt) REVERT: F 141 ASN cc_start: 0.8038 (t0) cc_final: 0.7742 (p0) REVERT: F 298 LEU cc_start: 0.7122 (pp) cc_final: 0.6794 (pp) REVERT: F 440 ILE cc_start: 0.8043 (mm) cc_final: 0.7637 (mm) REVERT: F 740 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7036 (ttm170) REVERT: A 49 LYS cc_start: 0.8407 (mttt) cc_final: 0.7808 (tmtt) REVERT: A 133 PHE cc_start: 0.8007 (m-10) cc_final: 0.7609 (m-80) REVERT: A 298 LEU cc_start: 0.7334 (pp) cc_final: 0.6892 (pp) REVERT: A 326 THR cc_start: 0.8956 (t) cc_final: 0.8514 (p) REVERT: A 716 ASN cc_start: 0.7933 (t0) cc_final: 0.7641 (t0) REVERT: A 740 ARG cc_start: 0.8089 (ttt90) cc_final: 0.6886 (ttm170) REVERT: A 843 LEU cc_start: 0.9517 (mt) cc_final: 0.9269 (mt) REVERT: G 49 LYS cc_start: 0.8970 (mttt) cc_final: 0.7874 (tmtt) REVERT: G 136 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8269 (mm-40) REVERT: G 426 LYS cc_start: 0.8370 (pttt) cc_final: 0.8113 (ptpt) REVERT: G 584 ILE cc_start: 0.8571 (pt) cc_final: 0.7439 (pt) REVERT: G 716 ASN cc_start: 0.7773 (t0) cc_final: 0.7270 (t0) REVERT: G 827 ARG cc_start: 0.9290 (mmt180) cc_final: 0.9070 (mmt-90) REVERT: G 843 LEU cc_start: 0.9475 (mt) cc_final: 0.9200 (mt) REVERT: H 298 LEU cc_start: 0.7431 (pp) cc_final: 0.7213 (pp) REVERT: I 92 ASP cc_start: 0.8583 (p0) cc_final: 0.8371 (p0) REVERT: I 122 ASP cc_start: 0.7262 (m-30) cc_final: 0.7049 (m-30) REVERT: I 133 PHE cc_start: 0.8336 (m-10) cc_final: 0.8021 (m-10) REVERT: I 440 ILE cc_start: 0.7983 (mm) cc_final: 0.7344 (mt) REVERT: I 583 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7486 (ttmm) REVERT: J 49 LYS cc_start: 0.8670 (mttt) cc_final: 0.7641 (tptp) REVERT: J 91 THR cc_start: 0.8973 (t) cc_final: 0.8541 (p) REVERT: J 122 ASP cc_start: 0.7324 (m-30) cc_final: 0.6996 (m-30) REVERT: J 314 SER cc_start: 0.6686 (p) cc_final: 0.5009 (t) REVERT: J 316 ASP cc_start: 0.8284 (p0) cc_final: 0.8039 (p0) REVERT: J 338 LYS cc_start: 0.8146 (tptp) cc_final: 0.7321 (mptt) REVERT: J 440 ILE cc_start: 0.8263 (mm) cc_final: 0.7424 (mt) REVERT: J 569 SER cc_start: 0.8148 (t) cc_final: 0.7766 (p) REVERT: J 740 ARG cc_start: 0.8075 (ttt90) cc_final: 0.6322 (ttm170) REVERT: K 95 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8597 (pp) REVERT: K 105 ASP cc_start: 0.6144 (t70) cc_final: 0.5909 (t70) REVERT: K 122 ASP cc_start: 0.7590 (m-30) cc_final: 0.7287 (m-30) REVERT: K 219 TYR cc_start: 0.7660 (p90) cc_final: 0.6887 (p90) REVERT: K 229 THR cc_start: 0.8596 (t) cc_final: 0.8348 (t) REVERT: K 319 ILE cc_start: 0.8919 (mm) cc_final: 0.8308 (mm) REVERT: K 323 ASN cc_start: 0.8079 (m-40) cc_final: 0.7764 (m-40) REVERT: K 362 MET cc_start: 0.8194 (mmt) cc_final: 0.7745 (mmp) REVERT: K 528 GLU cc_start: 0.8525 (pm20) cc_final: 0.8178 (pm20) REVERT: K 583 LYS cc_start: 0.8027 (ttpt) cc_final: 0.7734 (ttmm) REVERT: K 584 ILE cc_start: 0.8539 (pt) cc_final: 0.7407 (pt) REVERT: K 740 ARG cc_start: 0.7956 (ttt90) cc_final: 0.6435 (ttm170) REVERT: K 843 LEU cc_start: 0.9327 (mt) cc_final: 0.9106 (mt) outliers start: 11 outliers final: 0 residues processed: 3063 average time/residue: 0.6152 time to fit residues: 3267.5033 Evaluate side-chains 2006 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2005 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 95 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 789 optimal weight: 7.9990 chunk 708 optimal weight: 0.9990 chunk 393 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 478 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 732 optimal weight: 5.9990 chunk 283 optimal weight: 0.5980 chunk 445 optimal weight: 10.0000 chunk 545 optimal weight: 4.9990 chunk 849 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 139 ASN B 145 GLN B 201 ASN B 217 GLN B 283 GLN ** B 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN B 501 ASN B 538 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 830 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN C 283 GLN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 491 GLN C 501 ASN C 538 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 ASN C 724 GLN C 770 ASN D 46 GLN D 145 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 285 ASN D 474 ASN D 491 GLN D 501 ASN D 508 ASN D 538 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 643 GLN D 696 ASN D 716 ASN D 724 GLN D 830 GLN D 832 ASN E 14 HIS E 145 GLN E 211 ASN E 217 GLN E 242 ASN E 283 GLN E 309 ASN E 323 ASN E 491 GLN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 724 GLN E 789 ASN F 15 GLN F 136 GLN F 145 GLN ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN F 283 GLN F 491 GLN F 501 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 ASN F 724 GLN F 844 GLN A 14 HIS A 136 GLN A 145 GLN A 211 ASN A 242 ASN A 282 GLN A 283 GLN A 491 GLN A 501 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 724 GLN A 830 GLN G 136 GLN G 145 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN G 217 GLN G 283 GLN G 323 ASN ** G 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN G 501 ASN G 538 ASN ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 623 HIS G 643 GLN G 724 GLN G 841 GLN H 96 ASN H 145 GLN H 211 ASN H 217 GLN H 282 GLN H 283 GLN H 311 ASN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 GLN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 640 ASN H 724 GLN H 848 GLN I 96 ASN I 145 GLN I 217 GLN I 283 GLN I 323 ASN ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 GLN I 501 ASN I 538 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 560 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN I 724 GLN I 841 GLN J 136 GLN J 145 GLN ** J 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN J 242 ASN J 282 GLN J 283 GLN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 491 GLN J 501 ASN J 538 ASN ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 623 HIS ** J 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 724 GLN K 136 GLN K 145 GLN K 211 ASN ** K 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 GLN K 283 GLN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 GLN K 501 ASN ** K 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 560 ASN K 640 ASN K 643 GLN K 696 ASN K 716 ASN K 724 GLN Total number of N/Q/H flips: 130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 71115 Z= 0.234 Angle : 0.772 12.517 96723 Z= 0.412 Chirality : 0.048 0.215 11022 Planarity : 0.004 0.041 13068 Dihedral : 6.733 35.501 9847 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.75 % Favored : 93.75 % Rotamer: Outliers : 5.17 % Allowed : 12.90 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 3.57 % 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: -1.93 (0.08), residues: 9339 helix: 1.24 (0.13), residues: 1155 sheet: -2.19 (0.09), residues: 2332 loop : -1.43 (0.07), residues: 5852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 642 HIS 0.006 0.001 HIS E 623 PHE 0.032 0.002 PHE A 513 TYR 0.018 0.002 TYR E 383 ARG 0.007 0.001 ARG G 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2709 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 2317 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7073 (tp40) REVERT: B 19 ASP cc_start: 0.7836 (m-30) cc_final: 0.7006 (m-30) REVERT: B 37 ARG cc_start: 0.8349 (ptt90) cc_final: 0.8089 (ptt90) REVERT: B 95 ILE cc_start: 0.8598 (pp) cc_final: 0.8185 (mp) REVERT: B 162 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7667 (ttm) REVERT: B 189 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (ptm-80) REVERT: B 311 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7814 (t0) REVERT: B 315 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 319 ILE cc_start: 0.8857 (mm) cc_final: 0.8367 (mm) REVERT: B 323 ASN cc_start: 0.8343 (m-40) cc_final: 0.8048 (m110) REVERT: B 538 ASN cc_start: 0.8154 (t160) cc_final: 0.7825 (t0) REVERT: B 560 ASN cc_start: 0.7295 (m-40) cc_final: 0.6872 (m110) REVERT: B 584 ILE cc_start: 0.8933 (pt) cc_final: 0.8505 (mt) REVERT: B 682 PRO cc_start: 0.8977 (Cg_exo) cc_final: 0.8766 (Cg_endo) REVERT: B 740 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7119 (ttm110) REVERT: B 774 GLU cc_start: 0.7740 (tt0) cc_final: 0.7417 (tt0) REVERT: B 809 GLU cc_start: 0.8905 (tt0) cc_final: 0.8557 (tt0) REVERT: B 836 ILE cc_start: 0.8843 (mt) cc_final: 0.8539 (mt) REVERT: C 36 SER cc_start: 0.9084 (m) cc_final: 0.8678 (t) REVERT: C 102 MET cc_start: 0.8411 (mtp) cc_final: 0.8192 (mtp) REVERT: C 292 LYS cc_start: 0.5732 (tttt) cc_final: 0.4630 (tttm) REVERT: C 319 ILE cc_start: 0.9126 (mm) cc_final: 0.8902 (mm) REVERT: C 323 ASN cc_start: 0.8686 (m-40) cc_final: 0.8367 (m-40) REVERT: C 681 THR cc_start: 0.9016 (m) cc_final: 0.8602 (p) REVERT: C 740 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7126 (ttm110) REVERT: C 775 GLU cc_start: 0.7939 (tp30) cc_final: 0.7648 (tp30) REVERT: C 823 ILE cc_start: 0.9509 (mt) cc_final: 0.9195 (tt) REVERT: D 15 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7479 (tp-100) REVERT: D 19 ASP cc_start: 0.7584 (m-30) cc_final: 0.7127 (m-30) REVERT: D 49 LYS cc_start: 0.8746 (mttt) cc_final: 0.7988 (tmtt) REVERT: D 96 ASN cc_start: 0.8330 (t0) cc_final: 0.8103 (t0) REVERT: D 206 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7385 (mmt180) REVERT: D 338 LYS cc_start: 0.8095 (tptp) cc_final: 0.7469 (mptt) REVERT: D 464 TYR cc_start: 0.8117 (t80) cc_final: 0.7835 (t80) REVERT: D 488 GLU cc_start: 0.6836 (tp30) cc_final: 0.6339 (tp30) REVERT: D 643 GLN cc_start: 0.8552 (tt0) cc_final: 0.8336 (tt0) REVERT: D 740 ARG cc_start: 0.7757 (ttt90) cc_final: 0.7205 (ttm170) REVERT: E 49 LYS cc_start: 0.8897 (mttt) cc_final: 0.8348 (tptm) REVERT: E 315 LEU cc_start: 0.8533 (pp) cc_final: 0.8199 (pp) REVERT: E 326 THR cc_start: 0.8797 (t) cc_final: 0.8464 (p) REVERT: E 473 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8140 (mmmm) REVERT: E 569 SER cc_start: 0.8468 (t) cc_final: 0.7616 (p) REVERT: E 597 GLN cc_start: 0.7628 (pm20) cc_final: 0.7384 (pm20) REVERT: E 674 ASP cc_start: 0.7841 (p0) cc_final: 0.7626 (p0) REVERT: E 740 ARG cc_start: 0.7791 (ttt90) cc_final: 0.7188 (ttm110) REVERT: E 809 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7882 (tm-30) REVERT: E 836 ILE cc_start: 0.8996 (mt) cc_final: 0.8684 (mm) REVERT: F 36 SER cc_start: 0.9054 (m) cc_final: 0.8682 (t) REVERT: F 49 LYS cc_start: 0.8656 (mttt) cc_final: 0.8192 (tmtt) REVERT: F 95 ILE cc_start: 0.8684 (pp) cc_final: 0.8228 (mt) REVERT: F 338 LYS cc_start: 0.8000 (tptp) cc_final: 0.7716 (mptt) REVERT: F 740 ARG cc_start: 0.6993 (ttt90) cc_final: 0.6717 (ttm170) REVERT: A 49 LYS cc_start: 0.8503 (mttt) cc_final: 0.7835 (mtpp) REVERT: A 95 ILE cc_start: 0.8327 (pp) cc_final: 0.7929 (mt) REVERT: A 141 ASN cc_start: 0.7983 (t0) cc_final: 0.7723 (p0) REVERT: A 298 LEU cc_start: 0.7548 (pp) cc_final: 0.7108 (pp) REVERT: A 338 LYS cc_start: 0.8335 (tptp) cc_final: 0.7712 (mptt) REVERT: A 740 ARG cc_start: 0.7581 (ttt90) cc_final: 0.7017 (ttm170) REVERT: G 18 MET cc_start: 0.8833 (mmm) cc_final: 0.8281 (tpp) REVERT: G 49 LYS cc_start: 0.9045 (mttt) cc_final: 0.8051 (tptp) REVERT: G 90 ASN cc_start: 0.9067 (m-40) cc_final: 0.8796 (m110) REVERT: G 141 ASN cc_start: 0.8183 (t0) cc_final: 0.7500 (p0) REVERT: G 144 ASP cc_start: 0.7665 (m-30) cc_final: 0.7392 (m-30) REVERT: G 338 LYS cc_start: 0.8273 (tptp) cc_final: 0.7956 (mptt) REVERT: G 356 ASP cc_start: 0.7264 (p0) cc_final: 0.6995 (p0) REVERT: G 501 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7518 (p0) REVERT: G 565 ILE cc_start: 0.8798 (mt) cc_final: 0.8523 (mm) REVERT: G 714 SER cc_start: 0.8720 (p) cc_final: 0.8488 (t) REVERT: H 43 MET cc_start: 0.8054 (mmm) cc_final: 0.7840 (mmt) REVERT: H 210 GLU cc_start: 0.5338 (mp0) cc_final: 0.4519 (mp0) REVERT: H 292 LYS cc_start: 0.5940 (tptp) cc_final: 0.5737 (mmtm) REVERT: H 431 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7953 (t) REVERT: H 569 SER cc_start: 0.8255 (t) cc_final: 0.8016 (p) REVERT: H 662 THR cc_start: 0.7633 (p) cc_final: 0.7096 (p) REVERT: H 740 ARG cc_start: 0.7857 (ttt90) cc_final: 0.6883 (ttm110) REVERT: I 105 ASP cc_start: 0.5633 (t70) cc_final: 0.5164 (t70) REVERT: I 133 PHE cc_start: 0.8658 (m-10) cc_final: 0.8434 (m-10) REVERT: I 248 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9075 (tp) REVERT: I 298 LEU cc_start: 0.8204 (pt) cc_final: 0.7799 (pp) REVERT: I 440 ILE cc_start: 0.8201 (mm) cc_final: 0.7688 (mt) REVERT: I 740 ARG cc_start: 0.7521 (ttt90) cc_final: 0.6509 (ttm170) REVERT: J 49 LYS cc_start: 0.8889 (mttt) cc_final: 0.8206 (tmtt) REVERT: J 96 ASN cc_start: 0.7944 (t0) cc_final: 0.7592 (t0) REVERT: J 122 ASP cc_start: 0.7375 (m-30) cc_final: 0.6727 (m-30) REVERT: J 126 ASN cc_start: 0.7585 (p0) cc_final: 0.7272 (p0) REVERT: J 138 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.6687 (p90) REVERT: J 298 LEU cc_start: 0.8246 (pt) cc_final: 0.7926 (pp) REVERT: J 338 LYS cc_start: 0.8560 (tptp) cc_final: 0.7695 (mptt) REVERT: J 673 ASN cc_start: 0.8611 (t0) cc_final: 0.8341 (t0) REVERT: J 836 ILE cc_start: 0.8735 (mt) cc_final: 0.8316 (mt) REVERT: K 68 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8614 (pp) REVERT: K 122 ASP cc_start: 0.7488 (m-30) cc_final: 0.7079 (m-30) REVERT: K 130 ASN cc_start: 0.8303 (m-40) cc_final: 0.7890 (m-40) REVERT: K 219 TYR cc_start: 0.7481 (p90) cc_final: 0.6837 (p90) REVERT: K 248 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (tp) REVERT: K 311 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7674 (t0) REVERT: K 319 ILE cc_start: 0.9261 (mm) cc_final: 0.8985 (mm) REVERT: K 362 MET cc_start: 0.8492 (mmt) cc_final: 0.8205 (mmp) REVERT: K 528 GLU cc_start: 0.8403 (pm20) cc_final: 0.7860 (pm20) REVERT: K 563 PHE cc_start: 0.8689 (m-80) cc_final: 0.8474 (m-80) REVERT: K 670 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7250 (ttt180) REVERT: K 740 ARG cc_start: 0.7343 (ttt90) cc_final: 0.6154 (ttm170) REVERT: K 820 THR cc_start: 0.9077 (p) cc_final: 0.8849 (p) outliers start: 392 outliers final: 224 residues processed: 2515 average time/residue: 0.5993 time to fit residues: 2643.6666 Evaluate side-chains 2151 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1916 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 746 ASN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 593 VAL Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 706 SER Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 766 SER Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 624 THR Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 174 ILE Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 431 SER Chi-restraints excluded: chain H residue 555 THR Chi-restraints excluded: chain H residue 593 VAL Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 688 SER Chi-restraints excluded: chain H residue 705 THR Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 818 SER Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 555 THR Chi-restraints excluded: chain I residue 577 THR Chi-restraints excluded: chain I residue 593 VAL Chi-restraints excluded: chain I residue 637 ASP Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain I residue 688 SER Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 576 SER Chi-restraints excluded: chain J residue 577 THR Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 746 ASN Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 783 VAL Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 311 ASN Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 415 GLN Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 555 THR Chi-restraints excluded: chain K residue 576 SER Chi-restraints excluded: chain K residue 593 VAL Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 637 ASP Chi-restraints excluded: chain K residue 705 THR Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 756 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 471 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 706 optimal weight: 20.0000 chunk 578 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 850 optimal weight: 7.9990 chunk 918 optimal weight: 0.9990 chunk 757 optimal weight: 7.9990 chunk 843 optimal weight: 0.4980 chunk 289 optimal weight: 0.0570 chunk 682 optimal weight: 10.0000 overall best weight: 3.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 183 ASN B 198 HIS B 242 ASN B 252 GLN B 285 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN B 844 GLN C 27 ASN C 29 ASN C 96 ASN C 136 GLN C 139 ASN C 538 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 ASN C 578 ASN D 136 GLN D 501 ASN D 538 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN D 716 ASN D 830 GLN E 27 ASN E 96 ASN E 136 GLN E 183 ASN E 211 ASN E 242 ASN E 252 GLN E 309 ASN E 474 ASN E 578 ASN E 643 GLN E 696 ASN F 27 ASN F 136 GLN F 154 GLN F 183 ASN F 211 ASN F 217 GLN F 282 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 578 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 ASN F 697 GLN A 14 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 242 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 698 GLN A 716 ASN A 789 ASN A 826 GLN A 844 GLN G 29 ASN G 96 ASN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN G 179 ASN G 211 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 ASN G 516 ASN G 538 ASN ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN H 29 ASN H 96 ASN H 393 GLN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 596 ASN H 623 HIS H 643 GLN H 663 ASN H 733 ASN ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN I 29 ASN I 154 GLN I 205 GLN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 578 ASN I 596 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 623 HIS I 643 GLN I 830 GLN I 848 GLN J 27 ASN J 29 ASN ** J 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 698 GLN K 96 ASN K 282 GLN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN K 841 GLN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 71115 Z= 0.199 Angle : 0.688 13.654 96723 Z= 0.366 Chirality : 0.046 0.222 11022 Planarity : 0.004 0.039 13068 Dihedral : 5.831 31.740 9845 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.05 % Favored : 92.48 % Rotamer: Outliers : 5.67 % Allowed : 17.23 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 1.95 % 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: -1.78 (0.08), residues: 9339 helix: 2.14 (0.14), residues: 1155 sheet: -1.97 (0.09), residues: 2420 loop : -1.56 (0.07), residues: 5764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 200 HIS 0.003 0.001 HIS J 163 PHE 0.021 0.001 PHE I 588 TYR 0.018 0.001 TYR D 829 ARG 0.007 0.000 ARG E 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2479 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 430 poor density : 2049 time to evaluate : 6.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8100 (tp-100) cc_final: 0.6971 (tp40) REVERT: B 19 ASP cc_start: 0.7942 (m-30) cc_final: 0.7120 (m-30) REVERT: B 37 ARG cc_start: 0.8482 (ptt90) cc_final: 0.8224 (ptt90) REVERT: B 338 LYS cc_start: 0.8207 (tptp) cc_final: 0.7831 (mptt) REVERT: B 341 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8227 (tppt) REVERT: B 560 ASN cc_start: 0.7394 (m-40) cc_final: 0.7139 (m-40) REVERT: B 740 ARG cc_start: 0.7704 (ttt90) cc_final: 0.7191 (ttm170) REVERT: B 782 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8089 (ttpt) REVERT: C 15 GLN cc_start: 0.8537 (tp40) cc_final: 0.8332 (tp-100) REVERT: C 36 SER cc_start: 0.9049 (m) cc_final: 0.8737 (t) REVERT: C 68 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8633 (pp) REVERT: C 95 ILE cc_start: 0.8571 (pp) cc_final: 0.8335 (mt) REVERT: C 128 VAL cc_start: 0.8641 (t) cc_final: 0.8245 (m) REVERT: C 292 LYS cc_start: 0.5760 (tttt) cc_final: 0.4411 (tttp) REVERT: C 319 ILE cc_start: 0.9192 (mm) cc_final: 0.8973 (mm) REVERT: C 323 ASN cc_start: 0.8794 (m-40) cc_final: 0.8558 (m-40) REVERT: C 338 LYS cc_start: 0.8381 (tptp) cc_final: 0.7844 (mptt) REVERT: C 426 LYS cc_start: 0.8824 (pttt) cc_final: 0.8538 (pttp) REVERT: C 488 GLU cc_start: 0.7660 (tp30) cc_final: 0.7423 (tp30) REVERT: C 614 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6309 (mt-10) REVERT: C 681 THR cc_start: 0.9115 (m) cc_final: 0.8718 (p) REVERT: C 709 ASN cc_start: 0.8402 (m110) cc_final: 0.8120 (m-40) REVERT: C 740 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7262 (ttm110) REVERT: D 15 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7706 (tp-100) REVERT: D 49 LYS cc_start: 0.8764 (mttt) cc_final: 0.7959 (tmtt) REVERT: D 206 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.7458 (mmt180) REVERT: D 309 ASN cc_start: 0.8124 (m-40) cc_final: 0.7810 (m-40) REVERT: D 464 TYR cc_start: 0.8317 (t80) cc_final: 0.7900 (t80) REVERT: D 488 GLU cc_start: 0.7152 (tp30) cc_final: 0.6601 (tp30) REVERT: D 560 ASN cc_start: 0.7672 (m-40) cc_final: 0.7135 (m110) REVERT: D 643 GLN cc_start: 0.8586 (tt0) cc_final: 0.8170 (tt0) REVERT: D 688 SER cc_start: 0.8911 (m) cc_final: 0.8588 (t) REVERT: D 740 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7237 (ttm170) REVERT: E 49 LYS cc_start: 0.8997 (mttt) cc_final: 0.8415 (tptm) REVERT: E 68 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8184 (pp) REVERT: E 89 LYS cc_start: 0.9251 (ttpp) cc_final: 0.8985 (ttpp) REVERT: E 212 ASP cc_start: 0.7809 (m-30) cc_final: 0.7564 (m-30) REVERT: E 326 THR cc_start: 0.8802 (t) cc_final: 0.8421 (p) REVERT: E 351 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (m) REVERT: E 484 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7637 (tp30) REVERT: E 569 SER cc_start: 0.8366 (t) cc_final: 0.7635 (p) REVERT: E 597 GLN cc_start: 0.7506 (pm20) cc_final: 0.7290 (pm20) REVERT: E 674 ASP cc_start: 0.7827 (p0) cc_final: 0.7623 (p0) REVERT: E 740 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6677 (ttm170) REVERT: F 18 MET cc_start: 0.8657 (tpp) cc_final: 0.8234 (tpp) REVERT: F 36 SER cc_start: 0.9097 (m) cc_final: 0.8789 (t) REVERT: F 49 LYS cc_start: 0.8670 (mttt) cc_final: 0.8091 (tptp) REVERT: F 95 ILE cc_start: 0.8605 (pp) cc_final: 0.8253 (mt) REVERT: F 338 LYS cc_start: 0.8296 (tptp) cc_final: 0.7909 (mptt) REVERT: F 484 GLU cc_start: 0.7838 (tp30) cc_final: 0.7504 (tp30) REVERT: F 681 THR cc_start: 0.9170 (m) cc_final: 0.8951 (p) REVERT: F 844 GLN cc_start: 0.8316 (pt0) cc_final: 0.8073 (mp10) REVERT: A 21 GLU cc_start: 0.8393 (tp30) cc_final: 0.8174 (tp30) REVERT: A 49 LYS cc_start: 0.8547 (mttt) cc_final: 0.7871 (mtpp) REVERT: A 95 ILE cc_start: 0.8355 (pp) cc_final: 0.8028 (mt) REVERT: A 210 GLU cc_start: 0.6067 (mp0) cc_final: 0.4293 (mp0) REVERT: A 338 LYS cc_start: 0.8314 (tptp) cc_final: 0.7681 (mptt) REVERT: A 740 ARG cc_start: 0.7373 (ttt90) cc_final: 0.6985 (ttp-170) REVERT: A 809 GLU cc_start: 0.8558 (tt0) cc_final: 0.8221 (tt0) REVERT: G 49 LYS cc_start: 0.9065 (mttt) cc_final: 0.8124 (tmtt) REVERT: G 338 LYS cc_start: 0.8521 (tptp) cc_final: 0.8104 (mptt) REVERT: G 421 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8996 (m) REVERT: G 740 ARG cc_start: 0.8448 (ttt90) cc_final: 0.6863 (ttm170) REVERT: G 773 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (pp) REVERT: G 839 SER cc_start: 0.9604 (m) cc_final: 0.9224 (t) REVERT: H 49 LYS cc_start: 0.9203 (mttt) cc_final: 0.8291 (tmtt) REVERT: H 74 SER cc_start: 0.9271 (p) cc_final: 0.8945 (p) REVERT: H 338 LYS cc_start: 0.8228 (tptp) cc_final: 0.7675 (mmtm) REVERT: H 431 SER cc_start: 0.8203 (p) cc_final: 0.7870 (t) REVERT: H 569 SER cc_start: 0.8318 (t) cc_final: 0.8075 (p) REVERT: H 653 GLU cc_start: 0.8085 (tp30) cc_final: 0.7637 (tp30) REVERT: H 740 ARG cc_start: 0.7270 (ttt90) cc_final: 0.6941 (ttm170) REVERT: H 746 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8148 (p0) REVERT: I 1 MET cc_start: 0.5496 (tpp) cc_final: 0.5185 (mmm) REVERT: I 21 GLU cc_start: 0.8271 (tp30) cc_final: 0.8005 (tp30) REVERT: I 65 GLN cc_start: 0.8397 (pt0) cc_final: 0.8117 (pt0) REVERT: I 68 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8787 (pp) REVERT: I 105 ASP cc_start: 0.6082 (t70) cc_final: 0.5836 (t70) REVERT: I 298 LEU cc_start: 0.8427 (pt) cc_final: 0.8042 (pp) REVERT: I 740 ARG cc_start: 0.7087 (ttt90) cc_final: 0.6595 (ttm170) REVERT: I 773 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8507 (pp) REVERT: J 49 LYS cc_start: 0.8919 (mttt) cc_final: 0.8394 (mtpp) REVERT: J 96 ASN cc_start: 0.8143 (t0) cc_final: 0.7689 (t0) REVERT: J 122 ASP cc_start: 0.7286 (m-30) cc_final: 0.6917 (m-30) REVERT: J 298 LEU cc_start: 0.8514 (pt) cc_final: 0.8187 (pp) REVERT: J 338 LYS cc_start: 0.8452 (tptp) cc_final: 0.7607 (mptt) REVERT: J 653 GLU cc_start: 0.7720 (tp30) cc_final: 0.7418 (tp30) REVERT: J 673 ASN cc_start: 0.8552 (t0) cc_final: 0.8299 (t0) REVERT: J 740 ARG cc_start: 0.7842 (ttt90) cc_final: 0.6926 (ttm170) REVERT: J 790 ILE cc_start: 0.8551 (mp) cc_final: 0.8216 (mm) REVERT: K 68 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8734 (pp) REVERT: K 219 TYR cc_start: 0.7463 (p90) cc_final: 0.6941 (p90) REVERT: K 224 ASN cc_start: 0.8010 (t0) cc_final: 0.7747 (t0) REVERT: K 319 ILE cc_start: 0.9202 (mm) cc_final: 0.8914 (mm) REVERT: K 362 MET cc_start: 0.8560 (mmt) cc_final: 0.8305 (mmp) REVERT: K 427 TYR cc_start: 0.8214 (m-80) cc_final: 0.7946 (m-80) REVERT: K 484 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7258 (tp30) REVERT: K 740 ARG cc_start: 0.7374 (ttt90) cc_final: 0.6623 (ttm170) REVERT: K 806 SER cc_start: 0.8900 (t) cc_final: 0.8640 (p) outliers start: 430 outliers final: 261 residues processed: 2249 average time/residue: 0.6486 time to fit residues: 2576.0938 Evaluate side-chains 2089 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1818 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 614 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain E residue 633 SER Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 746 ASN Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 617 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 790 ILE Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 512 THR Chi-restraints excluded: chain H residue 593 VAL Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 746 ASN Chi-restraints excluded: chain H residue 756 THR Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 SER Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 637 ASP Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 688 SER Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 720 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 637 ASP Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 741 VAL Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 576 SER Chi-restraints excluded: chain K residue 593 VAL Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 756 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 783 VAL Chi-restraints excluded: chain K residue 805 THR Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 840 optimal weight: 0.6980 chunk 639 optimal weight: 9.9990 chunk 441 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 405 optimal weight: 40.0000 chunk 571 optimal weight: 8.9990 chunk 853 optimal weight: 8.9990 chunk 903 optimal weight: 10.0000 chunk 446 optimal weight: 20.0000 chunk 809 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 303 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN C 139 ASN C 538 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 ASN C 643 GLN C 686 ASN C 696 ASN D 136 GLN D 211 ASN D 538 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D 716 ASN E 126 ASN E 211 ASN E 242 ASN E 309 ASN E 508 ASN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 ASN E 603 GLN ** E 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 832 ASN F 29 ASN F 384 ASN F 538 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 ASN ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 841 GLN A 14 HIS A 29 ASN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 242 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 698 GLN A 716 ASN ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 145 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN G 640 ASN H 29 ASN H 177 ASN H 217 GLN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 145 GLN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 596 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 848 GLN J 126 ASN J 353 ASN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN J 564 ASN J 640 ASN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 841 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 71115 Z= 0.257 Angle : 0.695 13.609 96723 Z= 0.368 Chirality : 0.046 0.212 11022 Planarity : 0.004 0.041 13068 Dihedral : 5.816 31.733 9845 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.42 % Favored : 93.19 % Rotamer: Outliers : 6.64 % Allowed : 17.71 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.08), residues: 9339 helix: 2.22 (0.15), residues: 1166 sheet: -1.80 (0.10), residues: 2068 loop : -1.64 (0.07), residues: 6105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 406 HIS 0.004 0.001 HIS F 623 PHE 0.024 0.002 PHE J 513 TYR 0.022 0.002 TYR H 729 ARG 0.007 0.001 ARG E 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2407 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 503 poor density : 1904 time to evaluate : 5.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8086 (tp-100) cc_final: 0.6928 (tp40) REVERT: B 19 ASP cc_start: 0.7984 (m-30) cc_final: 0.7203 (m-30) REVERT: B 37 ARG cc_start: 0.8712 (ptt90) cc_final: 0.8424 (ptt90) REVERT: B 311 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7839 (t0) REVERT: B 338 LYS cc_start: 0.8501 (tptp) cc_final: 0.8115 (mptt) REVERT: B 501 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8079 (p0) REVERT: B 560 ASN cc_start: 0.7907 (m-40) cc_final: 0.7465 (m-40) REVERT: B 740 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7330 (ttm110) REVERT: B 782 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8213 (ttpt) REVERT: B 830 GLN cc_start: 0.8635 (mm110) cc_final: 0.8408 (mt0) REVERT: C 15 GLN cc_start: 0.8534 (tp40) cc_final: 0.8333 (tp-100) REVERT: C 36 SER cc_start: 0.9116 (m) cc_final: 0.8731 (t) REVERT: C 68 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8616 (pp) REVERT: C 105 ASP cc_start: 0.6283 (t70) cc_final: 0.5978 (t70) REVERT: C 128 VAL cc_start: 0.8752 (t) cc_final: 0.8514 (m) REVERT: C 292 LYS cc_start: 0.5705 (tttt) cc_final: 0.4438 (tttp) REVERT: C 338 LYS cc_start: 0.8843 (tptp) cc_final: 0.8225 (mptt) REVERT: C 488 GLU cc_start: 0.8130 (tp30) cc_final: 0.7695 (tp30) REVERT: C 584 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8642 (mt) REVERT: C 681 THR cc_start: 0.9165 (m) cc_final: 0.8785 (p) REVERT: C 709 ASN cc_start: 0.8539 (m110) cc_final: 0.8253 (m-40) REVERT: C 823 ILE cc_start: 0.9559 (mt) cc_final: 0.9228 (tt) REVERT: D 15 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7144 (tp-100) REVERT: D 19 ASP cc_start: 0.7525 (m-30) cc_final: 0.7083 (m-30) REVERT: D 49 LYS cc_start: 0.8827 (mttt) cc_final: 0.7939 (tmtt) REVERT: D 124 TYR cc_start: 0.8075 (m-80) cc_final: 0.7807 (m-80) REVERT: D 206 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.7444 (mmt180) REVERT: D 338 LYS cc_start: 0.8350 (tptp) cc_final: 0.7821 (mptt) REVERT: D 643 GLN cc_start: 0.8813 (tt0) cc_final: 0.8409 (tt0) REVERT: D 740 ARG cc_start: 0.7401 (ttt90) cc_final: 0.7105 (ttm170) REVERT: D 809 GLU cc_start: 0.8708 (tt0) cc_final: 0.8300 (tt0) REVERT: E 49 LYS cc_start: 0.9062 (mttt) cc_final: 0.8423 (tptt) REVERT: E 68 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8302 (pp) REVERT: E 262 LYS cc_start: 0.7652 (tptt) cc_final: 0.5936 (tptt) REVERT: E 307 ILE cc_start: 0.9077 (mm) cc_final: 0.8768 (mt) REVERT: E 484 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7888 (tp30) REVERT: E 569 SER cc_start: 0.8408 (t) cc_final: 0.7726 (p) REVERT: E 740 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7011 (ttm170) REVERT: E 746 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (p0) REVERT: F 18 MET cc_start: 0.8806 (tpp) cc_final: 0.8443 (tpp) REVERT: F 29 ASN cc_start: 0.8551 (m-40) cc_final: 0.8346 (m-40) REVERT: F 36 SER cc_start: 0.9235 (m) cc_final: 0.8873 (t) REVERT: F 49 LYS cc_start: 0.8723 (mttt) cc_final: 0.8116 (tptt) REVERT: F 95 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8440 (mt) REVERT: F 162 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7430 (mtt) REVERT: F 210 GLU cc_start: 0.6392 (mp0) cc_final: 0.5000 (mp0) REVERT: F 338 LYS cc_start: 0.8681 (tptp) cc_final: 0.8216 (mptt) REVERT: F 488 GLU cc_start: 0.7951 (tp30) cc_final: 0.7271 (tp30) REVERT: A 21 GLU cc_start: 0.8368 (tp30) cc_final: 0.8111 (tp30) REVERT: A 49 LYS cc_start: 0.8614 (mttt) cc_final: 0.7864 (mtpp) REVERT: A 95 ILE cc_start: 0.8543 (pp) cc_final: 0.8278 (mt) REVERT: A 210 GLU cc_start: 0.6030 (mp0) cc_final: 0.5074 (mp0) REVERT: A 338 LYS cc_start: 0.8453 (tptp) cc_final: 0.8009 (mptt) REVERT: A 569 SER cc_start: 0.8629 (t) cc_final: 0.8265 (p) REVERT: A 583 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8559 (tppt) REVERT: A 740 ARG cc_start: 0.7481 (ttt90) cc_final: 0.6706 (ttm170) REVERT: G 49 LYS cc_start: 0.9103 (mttt) cc_final: 0.8146 (tmtt) REVERT: G 210 GLU cc_start: 0.6328 (mp0) cc_final: 0.5270 (mp0) REVERT: G 230 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6989 (mm-30) REVERT: G 338 LYS cc_start: 0.8733 (tptp) cc_final: 0.8326 (mptt) REVERT: G 600 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7134 (mm-30) REVERT: G 683 LYS cc_start: 0.8509 (mttt) cc_final: 0.8200 (mttm) REVERT: G 740 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: G 773 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8721 (pp) REVERT: G 809 GLU cc_start: 0.8543 (tt0) cc_final: 0.8149 (tt0) REVERT: H 49 LYS cc_start: 0.9223 (mttt) cc_final: 0.8219 (tptt) REVERT: H 219 TYR cc_start: 0.8083 (p90) cc_final: 0.7844 (p90) REVERT: H 338 LYS cc_start: 0.8442 (tptp) cc_final: 0.7926 (mmtm) REVERT: H 740 ARG cc_start: 0.7676 (ttt90) cc_final: 0.6873 (ttm170) REVERT: I 1 MET cc_start: 0.6133 (tpp) cc_final: 0.5894 (mmm) REVERT: I 68 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8790 (pp) REVERT: I 211 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7366 (t160) REVERT: I 390 PHE cc_start: 0.7583 (m-80) cc_final: 0.7376 (m-80) REVERT: I 484 GLU cc_start: 0.7914 (tp30) cc_final: 0.7598 (tp30) REVERT: I 740 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6567 (ttm170) REVERT: I 809 GLU cc_start: 0.8957 (tt0) cc_final: 0.8413 (tt0) REVERT: J 49 LYS cc_start: 0.9021 (mttt) cc_final: 0.8238 (tmtt) REVERT: J 120 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8523 (ptpt) REVERT: J 298 LEU cc_start: 0.8544 (pt) cc_final: 0.8190 (pp) REVERT: J 338 LYS cc_start: 0.8821 (tptp) cc_final: 0.7972 (mptt) REVERT: J 641 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7612 (mm-30) REVERT: J 790 ILE cc_start: 0.8537 (mp) cc_final: 0.8208 (mm) REVERT: J 809 GLU cc_start: 0.8908 (tt0) cc_final: 0.8692 (tt0) REVERT: J 819 LEU cc_start: 0.8873 (mt) cc_final: 0.8492 (mp) REVERT: J 833 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9123 (p) REVERT: K 68 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8861 (pp) REVERT: K 219 TYR cc_start: 0.7790 (p90) cc_final: 0.7196 (p90) REVERT: K 224 ASN cc_start: 0.8096 (t0) cc_final: 0.7879 (t0) REVERT: K 319 ILE cc_start: 0.9286 (mm) cc_final: 0.9059 (mm) REVERT: K 356 ASP cc_start: 0.7497 (p0) cc_final: 0.7152 (p0) REVERT: K 362 MET cc_start: 0.8666 (mmt) cc_final: 0.8390 (mmt) REVERT: K 474 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8296 (p0) REVERT: K 484 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7673 (tp30) REVERT: K 584 ILE cc_start: 0.9276 (pt) cc_final: 0.9001 (mt) REVERT: K 740 ARG cc_start: 0.7256 (ttt90) cc_final: 0.6548 (ttm170) REVERT: K 806 SER cc_start: 0.9048 (t) cc_final: 0.8753 (p) outliers start: 503 outliers final: 356 residues processed: 2182 average time/residue: 0.6226 time to fit residues: 2375.4706 Evaluate side-chains 2112 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 1741 time to evaluate : 5.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 686 ASN Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 593 VAL Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain E residue 633 SER Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain E residue 746 ASN Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 668 THR Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 555 THR Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 584 ILE Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 735 LYS Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain H residue 3 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 512 THR Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 617 ASP Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 705 THR Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 756 THR Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 637 ASP Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 720 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 845 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 576 SER Chi-restraints excluded: chain J residue 601 SER Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 637 ASP Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 833 SER Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 415 GLN Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 525 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 576 SER Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 593 VAL Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 720 THR Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 756 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 805 THR Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 837 SER Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 752 optimal weight: 10.0000 chunk 513 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 672 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 chunk 771 optimal weight: 0.9990 chunk 624 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 461 optimal weight: 30.0000 chunk 811 optimal weight: 5.9990 chunk 228 optimal weight: 0.0870 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 201 ASN B 217 GLN B 252 GLN B 285 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 154 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 ASN C 643 GLN ** C 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 301 ASN D 370 ASN D 538 ASN D 716 ASN E 27 ASN E 211 ASN E 309 ASN E 353 ASN E 560 ASN E 623 HIS E 640 ASN F 183 ASN F 283 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 ASN A 14 HIS ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 211 ASN A 242 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 716 ASN G 27 ASN G 177 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 564 ASN H 27 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 841 GLN ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN ** I 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 564 ASN I 596 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN I 841 GLN ** I 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 303 ASN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 ASN J 520 GLN ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN J 632 GLN K 27 ASN K 311 ASN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 ASN ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 643 GLN K 696 ASN K 716 ASN K 832 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 71115 Z= 0.207 Angle : 0.662 14.602 96723 Z= 0.348 Chirality : 0.045 0.199 11022 Planarity : 0.003 0.040 13068 Dihedral : 5.520 31.486 9845 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.89 % Favored : 92.73 % Rotamer: Outliers : 6.57 % Allowed : 19.20 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 0.97 % 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: -1.68 (0.08), residues: 9339 helix: 2.34 (0.14), residues: 1166 sheet: -1.67 (0.10), residues: 2123 loop : -1.69 (0.07), residues: 6050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 406 HIS 0.003 0.001 HIS E 623 PHE 0.019 0.001 PHE J 513 TYR 0.021 0.001 TYR D 464 ARG 0.009 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2338 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 498 poor density : 1840 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8108 (tp-100) cc_final: 0.6941 (tp40) REVERT: B 19 ASP cc_start: 0.7870 (m-30) cc_final: 0.7104 (m-30) REVERT: B 37 ARG cc_start: 0.8700 (ptt90) cc_final: 0.8376 (ptt90) REVERT: B 205 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7516 (tt0) REVERT: B 338 LYS cc_start: 0.8623 (tptp) cc_final: 0.8192 (mptt) REVERT: B 740 ARG cc_start: 0.7758 (ttt90) cc_final: 0.7189 (ttm170) REVERT: B 782 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8237 (ttpt) REVERT: B 830 GLN cc_start: 0.8619 (mm110) cc_final: 0.8413 (mt0) REVERT: C 36 SER cc_start: 0.9056 (m) cc_final: 0.8738 (t) REVERT: C 68 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8588 (pp) REVERT: C 105 ASP cc_start: 0.6448 (t70) cc_final: 0.6168 (t70) REVERT: C 128 VAL cc_start: 0.8756 (t) cc_final: 0.8504 (m) REVERT: C 292 LYS cc_start: 0.5677 (tttt) cc_final: 0.4616 (tttp) REVERT: C 338 LYS cc_start: 0.8874 (tptp) cc_final: 0.8415 (mptt) REVERT: C 484 GLU cc_start: 0.8056 (tp30) cc_final: 0.7843 (tp30) REVERT: C 488 GLU cc_start: 0.8132 (tp30) cc_final: 0.7754 (tp30) REVERT: C 598 ILE cc_start: 0.9087 (mt) cc_final: 0.8754 (tt) REVERT: C 681 THR cc_start: 0.9307 (m) cc_final: 0.8927 (p) REVERT: C 709 ASN cc_start: 0.8535 (m110) cc_final: 0.8185 (m-40) REVERT: C 823 ILE cc_start: 0.9566 (mt) cc_final: 0.9363 (tt) REVERT: D 15 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7972 (tp-100) REVERT: D 49 LYS cc_start: 0.8818 (mttt) cc_final: 0.7943 (tmtt) REVERT: D 124 TYR cc_start: 0.7832 (m-80) cc_final: 0.7525 (m-80) REVERT: D 338 LYS cc_start: 0.8291 (tptp) cc_final: 0.7816 (mptt) REVERT: D 484 GLU cc_start: 0.8363 (tp30) cc_final: 0.8071 (tp30) REVERT: D 508 ASN cc_start: 0.7405 (p0) cc_final: 0.7118 (p0) REVERT: D 560 ASN cc_start: 0.7949 (m-40) cc_final: 0.7485 (m110) REVERT: D 576 SER cc_start: 0.8113 (m) cc_final: 0.7873 (p) REVERT: D 643 GLN cc_start: 0.8853 (tt0) cc_final: 0.8471 (tt0) REVERT: D 688 SER cc_start: 0.8947 (m) cc_final: 0.8662 (t) REVERT: D 809 GLU cc_start: 0.8698 (tt0) cc_final: 0.8073 (tt0) REVERT: E 49 LYS cc_start: 0.9019 (mttt) cc_final: 0.8364 (tptp) REVERT: E 68 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8286 (pp) REVERT: E 401 GLN cc_start: 0.5783 (OUTLIER) cc_final: 0.4457 (mt0) REVERT: E 569 SER cc_start: 0.8470 (t) cc_final: 0.7872 (p) REVERT: E 655 ASN cc_start: 0.6954 (p0) cc_final: 0.6585 (t0) REVERT: E 740 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7040 (ttm170) REVERT: E 808 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8789 (mp) REVERT: F 18 MET cc_start: 0.8707 (tpp) cc_final: 0.8223 (tpp) REVERT: F 36 SER cc_start: 0.9076 (m) cc_final: 0.8823 (t) REVERT: F 49 LYS cc_start: 0.8765 (mttt) cc_final: 0.8143 (tptt) REVERT: F 95 ILE cc_start: 0.8695 (pp) cc_final: 0.8356 (mt) REVERT: F 210 GLU cc_start: 0.6324 (mp0) cc_final: 0.5801 (mp0) REVERT: F 338 LYS cc_start: 0.8605 (tptp) cc_final: 0.8208 (mptt) REVERT: F 569 SER cc_start: 0.8214 (t) cc_final: 0.7722 (p) REVERT: F 681 THR cc_start: 0.9212 (m) cc_final: 0.8992 (p) REVERT: F 809 GLU cc_start: 0.8786 (tt0) cc_final: 0.8495 (tt0) REVERT: A 18 MET cc_start: 0.8664 (mmm) cc_final: 0.8131 (tpp) REVERT: A 21 GLU cc_start: 0.8387 (tp30) cc_final: 0.8139 (tp30) REVERT: A 49 LYS cc_start: 0.8544 (mttt) cc_final: 0.7777 (mtpp) REVERT: A 210 GLU cc_start: 0.6221 (mp0) cc_final: 0.4564 (mp0) REVERT: A 338 LYS cc_start: 0.8503 (tptp) cc_final: 0.8027 (mptt) REVERT: A 569 SER cc_start: 0.8592 (t) cc_final: 0.8332 (p) REVERT: A 740 ARG cc_start: 0.7378 (ttt90) cc_final: 0.6857 (ttm170) REVERT: A 809 GLU cc_start: 0.8584 (tt0) cc_final: 0.8268 (tt0) REVERT: G 37 ARG cc_start: 0.8268 (ptt90) cc_final: 0.8052 (ptt90) REVERT: G 210 GLU cc_start: 0.6392 (mp0) cc_final: 0.5829 (mp0) REVERT: G 230 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6908 (mm-30) REVERT: G 338 LYS cc_start: 0.8771 (tptp) cc_final: 0.8348 (mptt) REVERT: G 600 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7195 (mm-30) REVERT: G 683 LYS cc_start: 0.8548 (mttt) cc_final: 0.8257 (mttm) REVERT: G 740 ARG cc_start: 0.8568 (ttt90) cc_final: 0.6997 (ttm110) REVERT: G 746 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7647 (p0) REVERT: G 773 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8680 (pp) REVERT: G 809 GLU cc_start: 0.8526 (tt0) cc_final: 0.8023 (tt0) REVERT: H 49 LYS cc_start: 0.9215 (mttt) cc_final: 0.8194 (tptt) REVERT: H 292 LYS cc_start: 0.6336 (tptt) cc_final: 0.5800 (tptm) REVERT: H 338 LYS cc_start: 0.8333 (tptp) cc_final: 0.7962 (mmtm) REVERT: H 740 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7028 (ttm170) REVERT: H 844 GLN cc_start: 0.8824 (tp40) cc_final: 0.8498 (tp40) REVERT: I 15 GLN cc_start: 0.8617 (tp40) cc_final: 0.8302 (tp40) REVERT: I 21 GLU cc_start: 0.8238 (tp30) cc_final: 0.7989 (tp30) REVERT: I 68 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8800 (pp) REVERT: I 211 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7461 (t160) REVERT: I 740 ARG cc_start: 0.6850 (ttt90) cc_final: 0.6573 (ttm110) REVERT: J 49 LYS cc_start: 0.9020 (mttt) cc_final: 0.8210 (tmtt) REVERT: J 298 LEU cc_start: 0.8632 (pt) cc_final: 0.8358 (pp) REVERT: J 338 LYS cc_start: 0.8882 (tptp) cc_final: 0.8054 (mptt) REVERT: J 606 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8171 (pp) REVERT: J 641 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7817 (mm-30) REVERT: J 790 ILE cc_start: 0.8477 (mp) cc_final: 0.8178 (mm) REVERT: J 833 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.9135 (p) REVERT: K 68 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8864 (pp) REVERT: K 219 TYR cc_start: 0.7814 (p90) cc_final: 0.7272 (p90) REVERT: K 338 LYS cc_start: 0.8520 (tppt) cc_final: 0.8257 (tppt) REVERT: K 356 ASP cc_start: 0.7520 (p0) cc_final: 0.7147 (p0) REVERT: K 362 MET cc_start: 0.8684 (mmt) cc_final: 0.8406 (mmt) REVERT: K 473 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8493 (mmtm) REVERT: K 474 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8417 (p0) REVERT: K 584 ILE cc_start: 0.9222 (pt) cc_final: 0.9013 (mt) REVERT: K 740 ARG cc_start: 0.7281 (ttt90) cc_final: 0.6644 (ttm170) REVERT: K 806 SER cc_start: 0.8914 (t) cc_final: 0.8700 (p) outliers start: 498 outliers final: 374 residues processed: 2106 average time/residue: 0.6049 time to fit residues: 2222.7800 Evaluate side-chains 2127 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1741 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain C residue 727 ASP Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 401 GLN Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 535 SER Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 560 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 668 THR Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 341 LYS Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 617 ASP Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 705 THR Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 756 THR Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 341 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 633 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 805 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 529 ASN Chi-restraints excluded: chain J residue 576 SER Chi-restraints excluded: chain J residue 582 THR Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 637 ASP Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 770 ASN Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 833 SER Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 177 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 311 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 384 ASN Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 525 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 576 SER Chi-restraints excluded: chain K residue 592 LEU Chi-restraints excluded: chain K residue 593 VAL Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 632 GLN Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 662 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 805 THR Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 837 SER Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 304 optimal weight: 10.0000 chunk 813 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 530 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 904 optimal weight: 8.9990 chunk 750 optimal weight: 20.0000 chunk 418 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 474 optimal weight: 9.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN C 139 ASN ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 GLN ** C 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN D 205 GLN D 538 ASN D 716 ASN E 27 ASN E 126 ASN E 401 GLN E 696 ASN ** E 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 145 GLN F 538 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 ASN ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 716 ASN G 177 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 709 ASN H 29 ASN H 145 GLN H 177 ASN H 198 HIS ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 596 ASN ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 560 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 ASN ** I 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 303 ASN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 520 GLN ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 71115 Z= 0.245 Angle : 0.679 16.161 96723 Z= 0.356 Chirality : 0.046 0.215 11022 Planarity : 0.004 0.044 13068 Dihedral : 5.588 31.511 9845 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.13 % Favored : 92.48 % Rotamer: Outliers : 6.70 % Allowed : 19.99 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 1.62 % 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: -1.75 (0.08), residues: 9339 helix: 2.26 (0.14), residues: 1166 sheet: -1.60 (0.10), residues: 2288 loop : -1.78 (0.07), residues: 5885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 200 HIS 0.004 0.001 HIS K 623 PHE 0.022 0.001 PHE I 588 TYR 0.039 0.002 TYR D 383 ARG 0.010 0.001 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2296 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 508 poor density : 1788 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8080 (tp-100) cc_final: 0.6882 (tp40) REVERT: B 19 ASP cc_start: 0.7813 (m-30) cc_final: 0.6914 (m-30) REVERT: B 37 ARG cc_start: 0.8715 (ptt90) cc_final: 0.8300 (ptt90) REVERT: B 205 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7179 (tt0) REVERT: B 338 LYS cc_start: 0.8652 (tptp) cc_final: 0.8257 (mptt) REVERT: B 740 ARG cc_start: 0.7697 (ttt90) cc_final: 0.7079 (ttm170) REVERT: C 36 SER cc_start: 0.9102 (m) cc_final: 0.8758 (t) REVERT: C 68 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (pp) REVERT: C 128 VAL cc_start: 0.8753 (t) cc_final: 0.8530 (m) REVERT: C 292 LYS cc_start: 0.5734 (tttt) cc_final: 0.5205 (tttt) REVERT: C 338 LYS cc_start: 0.8962 (tptp) cc_final: 0.8476 (mptt) REVERT: C 569 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 598 ILE cc_start: 0.9082 (mt) cc_final: 0.8717 (tt) REVERT: C 681 THR cc_start: 0.9265 (m) cc_final: 0.8883 (p) REVERT: C 709 ASN cc_start: 0.8569 (m110) cc_final: 0.8295 (m-40) REVERT: D 15 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7227 (tp-100) REVERT: D 19 ASP cc_start: 0.7562 (m-30) cc_final: 0.7170 (m-30) REVERT: D 49 LYS cc_start: 0.8840 (mttt) cc_final: 0.7961 (tmtt) REVERT: D 338 LYS cc_start: 0.8548 (tptp) cc_final: 0.8020 (mptt) REVERT: D 508 ASN cc_start: 0.7684 (p0) cc_final: 0.7441 (p0) REVERT: D 560 ASN cc_start: 0.7963 (m-40) cc_final: 0.7350 (m-40) REVERT: D 576 SER cc_start: 0.8373 (m) cc_final: 0.8156 (p) REVERT: D 643 GLN cc_start: 0.8872 (tt0) cc_final: 0.7995 (tt0) REVERT: D 740 ARG cc_start: 0.5308 (ttm170) cc_final: 0.3463 (ttm170) REVERT: E 27 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7773 (p0) REVERT: E 49 LYS cc_start: 0.9006 (mttt) cc_final: 0.8375 (tptp) REVERT: E 68 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8347 (pp) REVERT: E 307 ILE cc_start: 0.9240 (mm) cc_final: 0.8936 (mt) REVERT: E 569 SER cc_start: 0.8444 (t) cc_final: 0.7858 (p) REVERT: E 655 ASN cc_start: 0.6988 (p0) cc_final: 0.6690 (t0) REVERT: E 740 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7084 (ttm170) REVERT: E 743 ASP cc_start: 0.7719 (t0) cc_final: 0.6600 (t70) REVERT: E 808 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8863 (mp) REVERT: E 830 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7829 (mp10) REVERT: F 18 MET cc_start: 0.8838 (tpp) cc_final: 0.8211 (tpp) REVERT: F 36 SER cc_start: 0.9191 (m) cc_final: 0.8868 (t) REVERT: F 49 LYS cc_start: 0.8774 (mttt) cc_final: 0.8133 (tptt) REVERT: F 162 MET cc_start: 0.7701 (mtp) cc_final: 0.7428 (mtp) REVERT: F 210 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: F 338 LYS cc_start: 0.8699 (tptp) cc_final: 0.8383 (mptt) REVERT: F 569 SER cc_start: 0.8116 (t) cc_final: 0.7654 (p) REVERT: A 21 GLU cc_start: 0.8380 (tp30) cc_final: 0.8104 (tp30) REVERT: A 210 GLU cc_start: 0.6204 (mp0) cc_final: 0.5476 (mp0) REVERT: A 230 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 338 LYS cc_start: 0.8528 (tptp) cc_final: 0.8078 (mptt) REVERT: A 740 ARG cc_start: 0.7674 (ttt90) cc_final: 0.6727 (ttm170) REVERT: A 809 GLU cc_start: 0.8605 (tt0) cc_final: 0.8236 (tt0) REVERT: G 49 LYS cc_start: 0.9090 (mttm) cc_final: 0.8069 (tmtm) REVERT: G 210 GLU cc_start: 0.6434 (mp0) cc_final: 0.5650 (mp0) REVERT: G 338 LYS cc_start: 0.8736 (tptp) cc_final: 0.8463 (mptt) REVERT: G 600 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 683 LYS cc_start: 0.8625 (mttt) cc_final: 0.8392 (mttm) REVERT: G 740 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7246 (ttm170) REVERT: G 746 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7623 (p0) REVERT: G 773 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8748 (pp) REVERT: G 809 GLU cc_start: 0.8569 (tt0) cc_final: 0.8098 (tt0) REVERT: H 49 LYS cc_start: 0.9198 (mttt) cc_final: 0.8181 (tptt) REVERT: H 292 LYS cc_start: 0.6246 (tptt) cc_final: 0.5760 (mmtp) REVERT: H 740 ARG cc_start: 0.7920 (ttt90) cc_final: 0.7024 (ttm170) REVERT: H 809 GLU cc_start: 0.8961 (tt0) cc_final: 0.7958 (tt0) REVERT: H 844 GLN cc_start: 0.8861 (tp40) cc_final: 0.8556 (tp40) REVERT: I 15 GLN cc_start: 0.8649 (tp40) cc_final: 0.8309 (tp40) REVERT: I 21 GLU cc_start: 0.8188 (tp30) cc_final: 0.7938 (tp30) REVERT: I 68 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8825 (pp) REVERT: I 338 LYS cc_start: 0.6964 (mptt) cc_final: 0.5969 (mptt) REVERT: I 740 ARG cc_start: 0.7058 (ttt90) cc_final: 0.6650 (ttm110) REVERT: J 49 LYS cc_start: 0.8999 (mttt) cc_final: 0.8190 (tmtt) REVERT: J 120 LYS cc_start: 0.8771 (ptpt) cc_final: 0.8531 (ptpt) REVERT: J 183 ASN cc_start: 0.8450 (m-40) cc_final: 0.8224 (p0) REVERT: J 298 LEU cc_start: 0.8690 (pt) cc_final: 0.8408 (pp) REVERT: J 338 LYS cc_start: 0.8974 (tptp) cc_final: 0.8071 (mptt) REVERT: J 488 GLU cc_start: 0.8171 (tp30) cc_final: 0.7840 (tp30) REVERT: J 606 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8264 (pp) REVERT: J 790 ILE cc_start: 0.8427 (mp) cc_final: 0.8134 (mm) REVERT: J 809 GLU cc_start: 0.9006 (tt0) cc_final: 0.8726 (tt0) REVERT: J 833 SER cc_start: 0.9381 (OUTLIER) cc_final: 0.9105 (p) REVERT: K 68 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8886 (pp) REVERT: K 230 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7754 (mm-30) REVERT: K 341 LYS cc_start: 0.8539 (tttp) cc_final: 0.8310 (tttt) REVERT: K 356 ASP cc_start: 0.7670 (p0) cc_final: 0.7326 (p0) REVERT: K 362 MET cc_start: 0.8745 (mmt) cc_final: 0.8512 (mmt) REVERT: K 406 TRP cc_start: 0.7917 (p90) cc_final: 0.7684 (p90) REVERT: K 474 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8496 (p0) REVERT: K 740 ARG cc_start: 0.7498 (ttt90) cc_final: 0.6661 (ttm170) REVERT: K 806 SER cc_start: 0.9032 (t) cc_final: 0.8780 (p) outliers start: 508 outliers final: 401 residues processed: 2076 average time/residue: 0.6269 time to fit residues: 2269.0259 Evaluate side-chains 2117 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1702 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 727 ASP Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 770 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 401 GLN Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain E residue 633 SER Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 665 ILE Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 808 LEU Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 716 ASN Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 766 SER Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 835 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 766 SER Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 341 LYS Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 562 SER Chi-restraints excluded: chain H residue 577 THR Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 617 ASP Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 696 ASN Chi-restraints excluded: chain H residue 705 THR Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 756 THR Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 341 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 461 SER Chi-restraints excluded: chain I residue 557 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 633 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 720 THR Chi-restraints excluded: chain I residue 730 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 770 ASN Chi-restraints excluded: chain I residue 805 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 417 GLN Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 525 VAL Chi-restraints excluded: chain J residue 576 SER Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 637 ASP Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 717 SER Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 770 ASN Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 833 SER Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 144 ASP Chi-restraints excluded: chain K residue 177 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 415 GLN Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 525 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 632 GLN Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 805 THR Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 837 SER Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 872 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 515 optimal weight: 4.9990 chunk 660 optimal weight: 30.0000 chunk 511 optimal weight: 5.9990 chunk 761 optimal weight: 0.9980 chunk 505 optimal weight: 20.0000 chunk 901 optimal weight: 0.0020 chunk 563 optimal weight: 20.0000 chunk 549 optimal weight: 30.0000 chunk 416 optimal weight: 6.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 ASN C 538 ASN ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 ASN D 538 ASN D 716 ASN E 27 ASN E 126 ASN F 538 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 ASN A 130 ASN A 242 ASN A 529 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN G 177 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN H 198 HIS H 384 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 841 GLN I 24 ASN I 27 ASN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN I 415 GLN ** I 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN ** I 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 303 ASN J 384 ASN J 560 ASN ** J 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 ASN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 ASN ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 71115 Z= 0.172 Angle : 0.651 15.544 96723 Z= 0.338 Chirality : 0.045 0.208 11022 Planarity : 0.003 0.042 13068 Dihedral : 5.270 30.613 9845 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.80 % Favored : 92.83 % Rotamer: Outliers : 5.50 % Allowed : 21.89 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 0.65 % 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: -1.60 (0.08), residues: 9339 helix: 2.39 (0.14), residues: 1166 sheet: -1.41 (0.10), residues: 2200 loop : -1.72 (0.07), residues: 5973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 200 HIS 0.003 0.000 HIS K 623 PHE 0.018 0.001 PHE B 588 TYR 0.029 0.001 TYR D 383 ARG 0.011 0.000 ARG K 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2231 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1814 time to evaluate : 5.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7046 (tp40) REVERT: B 19 ASP cc_start: 0.7781 (m-30) cc_final: 0.7010 (m-30) REVERT: B 205 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7137 (tt0) REVERT: B 338 LYS cc_start: 0.8679 (tptp) cc_final: 0.8205 (mptt) REVERT: B 681 THR cc_start: 0.9209 (m) cc_final: 0.8906 (p) REVERT: B 740 ARG cc_start: 0.7366 (ttt90) cc_final: 0.6998 (ttm170) REVERT: C 36 SER cc_start: 0.9038 (m) cc_final: 0.8711 (t) REVERT: C 68 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8669 (pp) REVERT: C 128 VAL cc_start: 0.8754 (t) cc_final: 0.8529 (m) REVERT: C 292 LYS cc_start: 0.5818 (tttt) cc_final: 0.4709 (tttp) REVERT: C 338 LYS cc_start: 0.8901 (tptp) cc_final: 0.8422 (mptt) REVERT: C 484 GLU cc_start: 0.8384 (tp30) cc_final: 0.8173 (tp30) REVERT: C 598 ILE cc_start: 0.9070 (mt) cc_final: 0.8719 (tt) REVERT: C 681 THR cc_start: 0.9224 (m) cc_final: 0.8868 (p) REVERT: D 15 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7100 (tp-100) REVERT: D 19 ASP cc_start: 0.7456 (m-30) cc_final: 0.6983 (m-30) REVERT: D 49 LYS cc_start: 0.8786 (mttt) cc_final: 0.8209 (tmtt) REVERT: D 338 LYS cc_start: 0.8513 (tptp) cc_final: 0.7879 (mptt) REVERT: D 508 ASN cc_start: 0.7748 (p0) cc_final: 0.7544 (p0) REVERT: D 576 SER cc_start: 0.8485 (m) cc_final: 0.8200 (p) REVERT: D 688 SER cc_start: 0.9046 (m) cc_final: 0.8686 (t) REVERT: D 740 ARG cc_start: 0.5435 (ttm170) cc_final: 0.3397 (ttm170) REVERT: E 49 LYS cc_start: 0.8962 (mttt) cc_final: 0.8319 (tptt) REVERT: E 68 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8249 (pp) REVERT: E 307 ILE cc_start: 0.9223 (mm) cc_final: 0.8872 (mt) REVERT: E 309 ASN cc_start: 0.8640 (t0) cc_final: 0.8424 (m-40) REVERT: E 523 LYS cc_start: 0.5489 (tptt) cc_final: 0.5066 (tptp) REVERT: E 569 SER cc_start: 0.8395 (t) cc_final: 0.7820 (p) REVERT: E 655 ASN cc_start: 0.6970 (p0) cc_final: 0.6638 (t0) REVERT: E 740 ARG cc_start: 0.7907 (ttt90) cc_final: 0.7047 (ttm170) REVERT: E 743 ASP cc_start: 0.7718 (t0) cc_final: 0.7253 (t70) REVERT: E 830 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7838 (mp10) REVERT: F 18 MET cc_start: 0.8766 (tpp) cc_final: 0.8166 (tpp) REVERT: F 36 SER cc_start: 0.9082 (m) cc_final: 0.8784 (t) REVERT: F 49 LYS cc_start: 0.8794 (mttt) cc_final: 0.8148 (tptt) REVERT: F 162 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: F 338 LYS cc_start: 0.8619 (tptp) cc_final: 0.8349 (mptt) REVERT: F 569 SER cc_start: 0.8094 (t) cc_final: 0.7653 (p) REVERT: A 21 GLU cc_start: 0.8374 (tp30) cc_final: 0.8091 (tp30) REVERT: A 338 LYS cc_start: 0.8517 (tptp) cc_final: 0.8031 (mptt) REVERT: A 576 SER cc_start: 0.8418 (p) cc_final: 0.8065 (p) REVERT: A 740 ARG cc_start: 0.7463 (ttt90) cc_final: 0.6846 (ttm110) REVERT: A 803 MET cc_start: 0.9027 (mmm) cc_final: 0.8826 (mmt) REVERT: G 210 GLU cc_start: 0.6366 (mp0) cc_final: 0.5695 (mp0) REVERT: G 230 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6838 (mm-30) REVERT: G 338 LYS cc_start: 0.8749 (tptp) cc_final: 0.8414 (mptt) REVERT: G 600 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7308 (mm-30) REVERT: G 683 LYS cc_start: 0.8602 (mttt) cc_final: 0.8375 (mttm) REVERT: G 740 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7009 (ttm170) REVERT: G 746 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7553 (p0) REVERT: G 773 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8649 (pp) REVERT: G 809 GLU cc_start: 0.8585 (tt0) cc_final: 0.8133 (tt0) REVERT: H 49 LYS cc_start: 0.9166 (mttt) cc_final: 0.8163 (tptt) REVERT: H 338 LYS cc_start: 0.8488 (tptp) cc_final: 0.7969 (mmtm) REVERT: H 740 ARG cc_start: 0.7675 (ttt90) cc_final: 0.7027 (ttm110) REVERT: H 809 GLU cc_start: 0.8880 (tt0) cc_final: 0.7850 (tt0) REVERT: H 844 GLN cc_start: 0.8906 (tp40) cc_final: 0.8596 (tp40) REVERT: I 15 GLN cc_start: 0.8652 (tp40) cc_final: 0.8329 (tp40) REVERT: I 21 GLU cc_start: 0.8188 (tp30) cc_final: 0.7987 (tp30) REVERT: I 68 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8859 (pp) REVERT: I 338 LYS cc_start: 0.6952 (mptt) cc_final: 0.5953 (mptt) REVERT: I 746 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7855 (p0) REVERT: J 49 LYS cc_start: 0.8957 (mttt) cc_final: 0.8154 (tmtt) REVERT: J 298 LEU cc_start: 0.8657 (pt) cc_final: 0.8376 (pp) REVERT: J 338 LYS cc_start: 0.8960 (tptp) cc_final: 0.8037 (mptt) REVERT: J 374 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8224 (t) REVERT: J 489 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8697 (mp) REVERT: J 606 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8114 (pp) REVERT: J 641 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7826 (mm-30) REVERT: J 790 ILE cc_start: 0.8370 (mp) cc_final: 0.8099 (mm) REVERT: J 809 GLU cc_start: 0.8963 (tt0) cc_final: 0.8710 (tt0) REVERT: K 49 LYS cc_start: 0.9240 (mttt) cc_final: 0.8196 (tptp) REVERT: K 68 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8874 (pp) REVERT: K 356 ASP cc_start: 0.7614 (p0) cc_final: 0.7198 (p0) REVERT: K 362 MET cc_start: 0.8704 (mmt) cc_final: 0.8430 (mmt) REVERT: K 406 TRP cc_start: 0.7892 (p90) cc_final: 0.7650 (p90) REVERT: K 474 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8452 (p0) REVERT: K 740 ARG cc_start: 0.7397 (ttt90) cc_final: 0.6490 (ttm170) outliers start: 417 outliers final: 320 residues processed: 2041 average time/residue: 0.6087 time to fit residues: 2158.7379 Evaluate side-chains 2038 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1705 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 27 ASN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 665 ILE Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 783 VAL Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 560 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 766 SER Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 701 LEU Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 735 LYS Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 766 SER Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain G residue 846 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 384 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 562 SER Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 632 GLN Chi-restraints excluded: chain H residue 637 ASP Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 701 LEU Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 341 LYS Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 461 SER Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 633 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 417 GLN Chi-restraints excluded: chain J residue 461 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 601 SER Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 311 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 557 optimal weight: 20.0000 chunk 359 optimal weight: 0.7980 chunk 538 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 chunk 177 optimal weight: 0.0040 chunk 174 optimal weight: 10.0000 chunk 572 optimal weight: 7.9990 chunk 613 optimal weight: 10.0000 chunk 445 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 708 optimal weight: 8.9990 overall best weight: 2.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 HIS C 242 ASN C 538 ASN C 640 ASN ** C 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 ASN D 183 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 560 ASN E 27 ASN E 126 ASN E 686 ASN E 696 ASN E 698 GLN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 848 GLN A 154 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 716 ASN G 177 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 596 ASN H 198 HIS H 384 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 564 ASN H 643 GLN I 29 ASN I 211 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 323 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN I 841 GLN J 384 ASN J 402 ASN ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 311 ASN ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 71115 Z= 0.172 Angle : 0.645 15.353 96723 Z= 0.334 Chirality : 0.044 0.205 11022 Planarity : 0.003 0.042 13068 Dihedral : 5.109 30.631 9845 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.79 % Favored : 92.84 % Rotamer: Outliers : 5.52 % Allowed : 22.47 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 0.32 % 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: -1.55 (0.08), residues: 9339 helix: 2.40 (0.14), residues: 1166 sheet: -1.26 (0.10), residues: 2255 loop : -1.74 (0.07), residues: 5918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 200 HIS 0.003 0.000 HIS K 623 PHE 0.018 0.001 PHE B 588 TYR 0.025 0.001 TYR F 568 ARG 0.009 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2186 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 418 poor density : 1768 time to evaluate : 6.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7070 (tp40) REVERT: B 19 ASP cc_start: 0.7786 (m-30) cc_final: 0.7001 (m-30) REVERT: B 338 LYS cc_start: 0.8657 (tptp) cc_final: 0.8287 (mptt) REVERT: B 415 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6185 (pp30) REVERT: B 681 THR cc_start: 0.9218 (m) cc_final: 0.8910 (p) REVERT: B 740 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7255 (ttm170) REVERT: C 36 SER cc_start: 0.9036 (m) cc_final: 0.8718 (t) REVERT: C 68 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (pp) REVERT: C 128 VAL cc_start: 0.8742 (t) cc_final: 0.8508 (m) REVERT: C 292 LYS cc_start: 0.5679 (tttt) cc_final: 0.4776 (tttp) REVERT: C 338 LYS cc_start: 0.8898 (tptp) cc_final: 0.8419 (mptt) REVERT: C 484 GLU cc_start: 0.8435 (tp30) cc_final: 0.8216 (tp30) REVERT: C 569 SER cc_start: 0.8704 (t) cc_final: 0.7853 (p) REVERT: C 598 ILE cc_start: 0.9075 (mt) cc_final: 0.8718 (tt) REVERT: C 681 THR cc_start: 0.9205 (m) cc_final: 0.8862 (p) REVERT: D 15 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7912 (tp-100) REVERT: D 49 LYS cc_start: 0.9011 (mttt) cc_final: 0.8203 (tmtt) REVERT: D 338 LYS cc_start: 0.8514 (tptp) cc_final: 0.7938 (mptt) REVERT: D 508 ASN cc_start: 0.7807 (p0) cc_final: 0.7597 (p0) REVERT: D 560 ASN cc_start: 0.8202 (m-40) cc_final: 0.7930 (m-40) REVERT: D 576 SER cc_start: 0.8458 (m) cc_final: 0.8205 (p) REVERT: D 688 SER cc_start: 0.9095 (m) cc_final: 0.8714 (t) REVERT: D 740 ARG cc_start: 0.5470 (ttm170) cc_final: 0.5062 (ttp-170) REVERT: E 18 MET cc_start: 0.8663 (mmm) cc_final: 0.8417 (tpp) REVERT: E 49 LYS cc_start: 0.8960 (mttt) cc_final: 0.8338 (tptp) REVERT: E 68 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8239 (pp) REVERT: E 307 ILE cc_start: 0.9221 (mm) cc_final: 0.8885 (mt) REVERT: E 523 LYS cc_start: 0.5664 (tptt) cc_final: 0.5180 (tptp) REVERT: E 569 SER cc_start: 0.8377 (t) cc_final: 0.7810 (p) REVERT: E 740 ARG cc_start: 0.7906 (ttt90) cc_final: 0.7076 (ttm170) REVERT: E 743 ASP cc_start: 0.7744 (t0) cc_final: 0.7336 (t70) REVERT: F 18 MET cc_start: 0.8775 (tpp) cc_final: 0.8152 (tpp) REVERT: F 36 SER cc_start: 0.9026 (m) cc_final: 0.8735 (t) REVERT: F 49 LYS cc_start: 0.8795 (mttt) cc_final: 0.8144 (tptt) REVERT: F 162 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7398 (mtp) REVERT: F 338 LYS cc_start: 0.8598 (tptp) cc_final: 0.8369 (mptt) REVERT: F 569 SER cc_start: 0.8086 (t) cc_final: 0.7666 (p) REVERT: F 681 THR cc_start: 0.9203 (m) cc_final: 0.8959 (p) REVERT: A 21 GLU cc_start: 0.8310 (tp30) cc_final: 0.8092 (tp30) REVERT: A 310 ASP cc_start: 0.7983 (p0) cc_final: 0.7735 (p0) REVERT: A 338 LYS cc_start: 0.8559 (tptp) cc_final: 0.8056 (mptt) REVERT: A 484 GLU cc_start: 0.7607 (tp30) cc_final: 0.7073 (tp30) REVERT: A 576 SER cc_start: 0.8368 (p) cc_final: 0.8036 (p) REVERT: A 740 ARG cc_start: 0.7350 (ttt90) cc_final: 0.6861 (ttm110) REVERT: A 809 GLU cc_start: 0.8681 (tt0) cc_final: 0.8338 (tt0) REVERT: G 210 GLU cc_start: 0.6464 (mp0) cc_final: 0.6154 (mp0) REVERT: G 230 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7296 (mm-30) REVERT: G 338 LYS cc_start: 0.8752 (tptp) cc_final: 0.8418 (mptt) REVERT: G 600 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7294 (mm-30) REVERT: G 683 LYS cc_start: 0.8598 (mttt) cc_final: 0.8344 (mttm) REVERT: G 740 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6983 (ttm170) REVERT: G 746 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7632 (p0) REVERT: G 773 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8679 (pp) REVERT: G 809 GLU cc_start: 0.8617 (tt0) cc_final: 0.8166 (tt0) REVERT: H 49 LYS cc_start: 0.9115 (mttt) cc_final: 0.8128 (tptt) REVERT: H 65 GLN cc_start: 0.8751 (pt0) cc_final: 0.8509 (pt0) REVERT: H 338 LYS cc_start: 0.8440 (tptp) cc_final: 0.7899 (mmtm) REVERT: H 564 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.7787 (m110) REVERT: H 740 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7040 (ttm170) REVERT: H 809 GLU cc_start: 0.8881 (tt0) cc_final: 0.7825 (tt0) REVERT: H 844 GLN cc_start: 0.8914 (tp40) cc_final: 0.8566 (tp40) REVERT: I 15 GLN cc_start: 0.8648 (tp40) cc_final: 0.8320 (tp40) REVERT: I 68 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8938 (pp) REVERT: I 338 LYS cc_start: 0.6919 (mptt) cc_final: 0.5905 (mptt) REVERT: I 670 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7643 (ttm170) REVERT: I 740 ARG cc_start: 0.5370 (ttm170) cc_final: 0.2882 (ttm170) REVERT: I 809 GLU cc_start: 0.8869 (tt0) cc_final: 0.8205 (tt0) REVERT: J 49 LYS cc_start: 0.8943 (mttt) cc_final: 0.8139 (tmtt) REVERT: J 247 ASN cc_start: 0.8486 (t0) cc_final: 0.8099 (t0) REVERT: J 298 LEU cc_start: 0.8663 (pt) cc_final: 0.8381 (pp) REVERT: J 338 LYS cc_start: 0.8981 (tptp) cc_final: 0.8036 (mptt) REVERT: J 374 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8326 (t) REVERT: J 489 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (mp) REVERT: J 606 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8048 (pp) REVERT: J 790 ILE cc_start: 0.8367 (mp) cc_final: 0.8095 (mm) REVERT: J 809 GLU cc_start: 0.8972 (tt0) cc_final: 0.8730 (tt0) REVERT: K 27 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: K 49 LYS cc_start: 0.9226 (mttt) cc_final: 0.8178 (tptp) REVERT: K 68 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8783 (pp) REVERT: K 356 ASP cc_start: 0.7592 (p0) cc_final: 0.7231 (p0) REVERT: K 406 TRP cc_start: 0.7928 (p90) cc_final: 0.7646 (p90) REVERT: K 474 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8452 (p0) REVERT: K 740 ARG cc_start: 0.7320 (ttt90) cc_final: 0.6423 (ttm170) REVERT: K 844 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8427 (tm-30) outliers start: 418 outliers final: 348 residues processed: 1991 average time/residue: 0.6179 time to fit residues: 2141.9243 Evaluate side-chains 2055 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1693 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 727 ASP Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 401 GLN Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 596 ASN Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 624 THR Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 665 ILE Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 686 ASN Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 560 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 766 SER Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 452 ASN Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 653 GLU Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 701 LEU Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 735 LYS Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 766 SER Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 384 ASN Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 461 SER Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 562 SER Chi-restraints excluded: chain H residue 564 ASN Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 632 GLN Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 701 LEU Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 830 GLN Chi-restraints excluded: chain H residue 835 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 461 SER Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 730 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 805 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 417 GLN Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain J residue 582 THR Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 601 SER Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 614 GLU Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 662 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 835 THR Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 819 optimal weight: 8.9990 chunk 863 optimal weight: 9.9990 chunk 787 optimal weight: 20.0000 chunk 839 optimal weight: 20.0000 chunk 505 optimal weight: 20.0000 chunk 365 optimal weight: 30.0000 chunk 659 optimal weight: 0.0870 chunk 257 optimal weight: 7.9990 chunk 758 optimal weight: 8.9990 chunk 794 optimal weight: 0.6980 chunk 836 optimal weight: 30.0000 overall best weight: 5.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 ASN B 412 GLN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN C 79 HIS C 538 ASN C 643 GLN D 183 ASN D 396 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN E 183 ASN E 508 ASN E 686 ASN E 696 ASN E 786 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 716 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 596 ASN H 177 ASN H 198 HIS H 384 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 ASN I 211 ASN I 560 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN J 154 GLN J 384 ASN ** J 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 154 GLN K 211 ASN K 311 ASN ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 71115 Z= 0.246 Angle : 0.675 15.013 96723 Z= 0.352 Chirality : 0.045 0.220 11022 Planarity : 0.003 0.040 13068 Dihedral : 5.309 31.198 9845 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.43 % Favored : 92.18 % Rotamer: Outliers : 6.14 % Allowed : 22.01 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 1.30 % 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: -1.62 (0.08), residues: 9339 helix: 2.28 (0.14), residues: 1166 sheet: -1.28 (0.10), residues: 2288 loop : -1.78 (0.07), residues: 5885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 200 HIS 0.005 0.001 HIS K 623 PHE 0.018 0.001 PHE B 588 TYR 0.025 0.001 TYR D 829 ARG 0.009 0.001 ARG H 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2159 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 465 poor density : 1694 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7132 (tp40) REVERT: B 19 ASP cc_start: 0.7848 (m-30) cc_final: 0.7088 (m-30) REVERT: B 338 LYS cc_start: 0.8620 (tptp) cc_final: 0.8203 (mptt) REVERT: B 681 THR cc_start: 0.9237 (m) cc_final: 0.8958 (p) REVERT: B 740 ARG cc_start: 0.7570 (ttt90) cc_final: 0.7042 (ttm110) REVERT: B 830 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: C 36 SER cc_start: 0.9081 (m) cc_final: 0.8753 (t) REVERT: C 68 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8615 (pp) REVERT: C 128 VAL cc_start: 0.8749 (t) cc_final: 0.8544 (m) REVERT: C 210 GLU cc_start: 0.6678 (mp0) cc_final: 0.6046 (mp0) REVERT: C 292 LYS cc_start: 0.5842 (tttt) cc_final: 0.4948 (tttp) REVERT: C 338 LYS cc_start: 0.8952 (tptp) cc_final: 0.8505 (mptt) REVERT: C 523 LYS cc_start: 0.5653 (tptt) cc_final: 0.5345 (mttp) REVERT: C 569 SER cc_start: 0.8719 (t) cc_final: 0.7904 (p) REVERT: C 598 ILE cc_start: 0.9088 (mt) cc_final: 0.8733 (tt) REVERT: C 681 THR cc_start: 0.9219 (m) cc_final: 0.8897 (p) REVERT: D 15 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7131 (tp-100) REVERT: D 19 ASP cc_start: 0.7447 (m-30) cc_final: 0.6976 (m-30) REVERT: D 49 LYS cc_start: 0.9028 (mttt) cc_final: 0.8217 (tmtt) REVERT: D 338 LYS cc_start: 0.8590 (tptp) cc_final: 0.7943 (mptt) REVERT: D 560 ASN cc_start: 0.8226 (m-40) cc_final: 0.7696 (m110) REVERT: D 576 SER cc_start: 0.8474 (m) cc_final: 0.8241 (p) REVERT: D 677 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8934 (tp) REVERT: D 740 ARG cc_start: 0.5548 (ttm170) cc_final: 0.5175 (ttp-170) REVERT: E 49 LYS cc_start: 0.8975 (mttt) cc_final: 0.8335 (tptp) REVERT: E 68 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8343 (pp) REVERT: E 523 LYS cc_start: 0.5688 (tptt) cc_final: 0.5188 (tptp) REVERT: E 569 SER cc_start: 0.8129 (t) cc_final: 0.7548 (p) REVERT: E 740 ARG cc_start: 0.8241 (ttt90) cc_final: 0.7133 (ttm170) REVERT: F 18 MET cc_start: 0.8824 (tpp) cc_final: 0.8164 (tpp) REVERT: F 36 SER cc_start: 0.9083 (m) cc_final: 0.8757 (t) REVERT: F 49 LYS cc_start: 0.8798 (mttt) cc_final: 0.8140 (tptt) REVERT: F 162 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7421 (mtp) REVERT: F 230 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7671 (mm-30) REVERT: F 338 LYS cc_start: 0.8608 (tptp) cc_final: 0.8387 (mptt) REVERT: F 569 SER cc_start: 0.8035 (t) cc_final: 0.7715 (p) REVERT: A 21 GLU cc_start: 0.8340 (tp30) cc_final: 0.8083 (tp30) REVERT: A 230 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7367 (tp30) REVERT: A 338 LYS cc_start: 0.8638 (tptp) cc_final: 0.8172 (mptt) REVERT: A 576 SER cc_start: 0.8494 (p) cc_final: 0.8142 (p) REVERT: A 737 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.6827 (p0) REVERT: A 740 ARG cc_start: 0.7730 (ttt90) cc_final: 0.6733 (ttm170) REVERT: G 210 GLU cc_start: 0.6601 (mp0) cc_final: 0.5886 (mp0) REVERT: G 338 LYS cc_start: 0.8772 (tptp) cc_final: 0.8426 (mptt) REVERT: G 600 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7327 (mm-30) REVERT: G 683 LYS cc_start: 0.8600 (mttt) cc_final: 0.8384 (mttm) REVERT: G 740 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7119 (ttm170) REVERT: G 746 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7557 (p0) REVERT: G 773 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8722 (pp) REVERT: G 809 GLU cc_start: 0.8631 (tt0) cc_final: 0.8215 (tt0) REVERT: H 49 LYS cc_start: 0.9137 (mttt) cc_final: 0.8115 (tptt) REVERT: H 338 LYS cc_start: 0.8555 (tptp) cc_final: 0.7964 (mmtm) REVERT: H 740 ARG cc_start: 0.7949 (ttt90) cc_final: 0.7039 (ttm110) REVERT: H 809 GLU cc_start: 0.8935 (tt0) cc_final: 0.7924 (tt0) REVERT: H 844 GLN cc_start: 0.8930 (tp40) cc_final: 0.8587 (tp40) REVERT: I 68 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8822 (pp) REVERT: I 338 LYS cc_start: 0.6928 (mptt) cc_final: 0.5918 (mptt) REVERT: I 390 PHE cc_start: 0.7872 (m-80) cc_final: 0.7478 (m-80) REVERT: I 670 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7848 (ttt-90) REVERT: I 740 ARG cc_start: 0.5504 (ttm170) cc_final: 0.4992 (ttp-110) REVERT: I 809 GLU cc_start: 0.8900 (tt0) cc_final: 0.8242 (tt0) REVERT: J 49 LYS cc_start: 0.8945 (mttt) cc_final: 0.8119 (tmtt) REVERT: J 120 LYS cc_start: 0.8777 (ptpt) cc_final: 0.8536 (ptpt) REVERT: J 247 ASN cc_start: 0.8542 (t0) cc_final: 0.8174 (t0) REVERT: J 298 LEU cc_start: 0.8685 (pt) cc_final: 0.8397 (pp) REVERT: J 338 LYS cc_start: 0.9046 (tptp) cc_final: 0.8150 (mptt) REVERT: J 606 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8179 (pp) REVERT: J 790 ILE cc_start: 0.8407 (mp) cc_final: 0.8122 (mm) REVERT: J 809 GLU cc_start: 0.9046 (tt0) cc_final: 0.8750 (tt0) REVERT: J 833 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9160 (p) REVERT: K 68 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8844 (pp) REVERT: K 356 ASP cc_start: 0.7681 (p0) cc_final: 0.7372 (p0) REVERT: K 406 TRP cc_start: 0.8186 (p90) cc_final: 0.7796 (p90) REVERT: K 474 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8511 (p0) REVERT: K 740 ARG cc_start: 0.7539 (ttt90) cc_final: 0.6538 (ttm170) outliers start: 465 outliers final: 395 residues processed: 1962 average time/residue: 0.6268 time to fit residues: 2145.5342 Evaluate side-chains 2064 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 1655 time to evaluate : 5.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 830 GLN Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 727 ASP Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 ASN Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 316 ASP Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 401 GLN Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 596 ASN Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 665 ILE Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 783 VAL Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 560 ASN Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain F residue 681 THR Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 727 ASP Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 461 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 602 GLU Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 701 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 766 SER Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 384 ASN Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 461 SER Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 617 ASP Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 701 LEU Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 764 MET Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 835 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 341 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 461 SER Chi-restraints excluded: chain I residue 557 ASN Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 730 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 770 ASN Chi-restraints excluded: chain I residue 805 THR Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 417 GLN Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 461 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain J residue 582 THR Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 601 SER Chi-restraints excluded: chain J residue 602 GLU Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 614 GLU Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 770 ASN Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 833 SER Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 311 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 835 THR Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 843 LEU Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 551 optimal weight: 10.0000 chunk 888 optimal weight: 9.9990 chunk 542 optimal weight: 6.9990 chunk 421 optimal weight: 5.9990 chunk 617 optimal weight: 30.0000 chunk 931 optimal weight: 20.0000 chunk 857 optimal weight: 10.0000 chunk 741 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 572 optimal weight: 5.9990 chunk 454 optimal weight: 0.2980 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 ASN C 538 ASN C 640 ASN C 709 ASN D 183 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN ** E 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 716 ASN G 177 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 596 ASN G 686 ASN H 177 ASN H 198 HIS H 384 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 826 GLN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN I 841 GLN J 384 ASN ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 560 ASN ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN K 311 ASN ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 716 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 71115 Z= 0.243 Angle : 0.680 14.830 96723 Z= 0.354 Chirality : 0.045 0.231 11022 Planarity : 0.003 0.038 13068 Dihedral : 5.344 31.462 9845 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.40 % Favored : 92.24 % Rotamer: Outliers : 5.79 % Allowed : 22.50 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 1.30 % 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: -1.62 (0.08), residues: 9339 helix: 2.22 (0.14), residues: 1166 sheet: -1.20 (0.11), residues: 2233 loop : -1.80 (0.07), residues: 5940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 200 HIS 0.004 0.001 HIS K 623 PHE 0.021 0.001 PHE I 588 TYR 0.024 0.001 TYR D 829 ARG 0.008 0.001 ARG B 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18678 Ramachandran restraints generated. 9339 Oldfield, 0 Emsley, 9339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2129 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 439 poor density : 1690 time to evaluate : 6.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7133 (tp40) REVERT: B 19 ASP cc_start: 0.7803 (m-30) cc_final: 0.6897 (m-30) REVERT: B 338 LYS cc_start: 0.8670 (tptp) cc_final: 0.8213 (mptt) REVERT: B 681 THR cc_start: 0.9227 (m) cc_final: 0.8972 (p) REVERT: B 740 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7125 (ttm170) REVERT: C 36 SER cc_start: 0.9093 (m) cc_final: 0.8741 (t) REVERT: C 68 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 128 VAL cc_start: 0.8744 (t) cc_final: 0.8542 (m) REVERT: C 198 HIS cc_start: 0.8053 (t70) cc_final: 0.7782 (t-90) REVERT: C 203 LYS cc_start: 0.8537 (mmtm) cc_final: 0.7767 (tptt) REVERT: C 210 GLU cc_start: 0.6569 (mp0) cc_final: 0.5438 (mp0) REVERT: C 292 LYS cc_start: 0.5900 (tttt) cc_final: 0.4929 (tttp) REVERT: C 338 LYS cc_start: 0.8982 (tptp) cc_final: 0.8535 (mptt) REVERT: C 484 GLU cc_start: 0.8488 (tp30) cc_final: 0.8274 (tp30) REVERT: C 523 LYS cc_start: 0.5302 (tptt) cc_final: 0.5051 (mttp) REVERT: C 569 SER cc_start: 0.8712 (t) cc_final: 0.7943 (p) REVERT: C 598 ILE cc_start: 0.9076 (mt) cc_final: 0.8717 (tt) REVERT: C 681 THR cc_start: 0.9200 (m) cc_final: 0.8868 (p) REVERT: D 15 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7212 (tp-100) REVERT: D 19 ASP cc_start: 0.7455 (m-30) cc_final: 0.6957 (m-30) REVERT: D 49 LYS cc_start: 0.9026 (mttt) cc_final: 0.8213 (tmtt) REVERT: D 338 LYS cc_start: 0.8650 (tptp) cc_final: 0.7974 (mptt) REVERT: D 560 ASN cc_start: 0.8266 (m-40) cc_final: 0.7844 (m110) REVERT: D 576 SER cc_start: 0.8510 (m) cc_final: 0.8241 (p) REVERT: D 677 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8904 (tp) REVERT: D 740 ARG cc_start: 0.5574 (ttm170) cc_final: 0.5235 (ttp-170) REVERT: D 743 ASP cc_start: 0.7900 (t0) cc_final: 0.7592 (t70) REVERT: E 49 LYS cc_start: 0.8955 (mttt) cc_final: 0.8331 (tptp) REVERT: E 68 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8370 (pp) REVERT: E 523 LYS cc_start: 0.5513 (tptt) cc_final: 0.5058 (tptp) REVERT: E 569 SER cc_start: 0.8028 (t) cc_final: 0.7415 (p) REVERT: E 740 ARG cc_start: 0.8326 (ttt90) cc_final: 0.7171 (ttm170) REVERT: E 830 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7969 (mp10) REVERT: F 18 MET cc_start: 0.8812 (tpp) cc_final: 0.8168 (tpp) REVERT: F 49 LYS cc_start: 0.8803 (mttt) cc_final: 0.8154 (tptt) REVERT: F 162 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7417 (mtp) REVERT: F 230 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7655 (mm-30) REVERT: F 338 LYS cc_start: 0.8617 (tptp) cc_final: 0.8371 (mptt) REVERT: F 569 SER cc_start: 0.7986 (t) cc_final: 0.7700 (p) REVERT: A 21 GLU cc_start: 0.8328 (tp30) cc_final: 0.8081 (tp30) REVERT: A 210 GLU cc_start: 0.6066 (mp0) cc_final: 0.5456 (mp0) REVERT: A 310 ASP cc_start: 0.8069 (p0) cc_final: 0.7820 (p0) REVERT: A 338 LYS cc_start: 0.8642 (tptp) cc_final: 0.8152 (mptt) REVERT: A 528 GLU cc_start: 0.8629 (pm20) cc_final: 0.8400 (pm20) REVERT: A 576 SER cc_start: 0.8489 (p) cc_final: 0.8132 (p) REVERT: A 737 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 740 ARG cc_start: 0.7761 (ttt90) cc_final: 0.6851 (ttm110) REVERT: G 124 TYR cc_start: 0.8012 (m-80) cc_final: 0.7721 (m-80) REVERT: G 209 ASP cc_start: 0.7451 (m-30) cc_final: 0.7235 (m-30) REVERT: G 210 GLU cc_start: 0.6815 (mp0) cc_final: 0.6052 (mp0) REVERT: G 230 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7044 (mm-30) REVERT: G 338 LYS cc_start: 0.8808 (tptp) cc_final: 0.8426 (mptt) REVERT: G 484 GLU cc_start: 0.8290 (tp30) cc_final: 0.7941 (tp30) REVERT: G 600 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7341 (mm-30) REVERT: G 683 LYS cc_start: 0.8615 (mttt) cc_final: 0.8368 (mttm) REVERT: G 740 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: G 746 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7754 (p0) REVERT: G 773 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8696 (pp) REVERT: G 809 GLU cc_start: 0.8639 (tt0) cc_final: 0.8213 (tt0) REVERT: H 49 LYS cc_start: 0.9133 (mttt) cc_final: 0.8133 (tptt) REVERT: H 292 LYS cc_start: 0.6131 (tptt) cc_final: 0.5441 (mmtp) REVERT: H 338 LYS cc_start: 0.8545 (tptp) cc_final: 0.7888 (mmtm) REVERT: H 412 GLN cc_start: 0.5365 (tm-30) cc_final: 0.5035 (tm-30) REVERT: H 740 ARG cc_start: 0.8196 (ttt90) cc_final: 0.7080 (ttm170) REVERT: H 809 GLU cc_start: 0.8941 (tt0) cc_final: 0.7917 (tt0) REVERT: H 844 GLN cc_start: 0.8923 (tp40) cc_final: 0.8614 (tp40) REVERT: I 68 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8845 (pp) REVERT: I 338 LYS cc_start: 0.6914 (mptt) cc_final: 0.5900 (mptt) REVERT: I 670 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7835 (ttm-80) REVERT: I 809 GLU cc_start: 0.8898 (tt0) cc_final: 0.8234 (tt0) REVERT: I 815 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (mp) REVERT: I 829 TYR cc_start: 0.8524 (t80) cc_final: 0.8208 (t80) REVERT: J 49 LYS cc_start: 0.8936 (mttt) cc_final: 0.8101 (tmtt) REVERT: J 120 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8546 (ptpt) REVERT: J 247 ASN cc_start: 0.8515 (t0) cc_final: 0.8138 (t0) REVERT: J 298 LEU cc_start: 0.8684 (pt) cc_final: 0.8379 (pp) REVERT: J 338 LYS cc_start: 0.9075 (tptp) cc_final: 0.8157 (mptt) REVERT: J 606 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8163 (pp) REVERT: J 790 ILE cc_start: 0.8446 (mp) cc_final: 0.8123 (mm) REVERT: J 833 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.9136 (p) REVERT: K 68 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8852 (pp) REVERT: K 740 ARG cc_start: 0.7593 (ttt90) cc_final: 0.6734 (ttm170) outliers start: 439 outliers final: 394 residues processed: 1947 average time/residue: 0.6305 time to fit residues: 2143.6234 Evaluate side-chains 2046 residues out of total 7579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 1639 time to evaluate : 5.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 835 THR Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 138 TRP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 727 ASP Chi-restraints excluded: chain C residue 746 ASN Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 617 ASP Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 756 THR Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 790 ILE Chi-restraints excluded: chain D residue 802 GLU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain E residue 596 ASN Chi-restraints excluded: chain E residue 606 LEU Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 665 ILE Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 705 THR Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 752 THR Chi-restraints excluded: chain E residue 756 THR Chi-restraints excluded: chain E residue 783 VAL Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 846 LEU Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 138 TRP Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 431 SER Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 477 GLU Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 560 ASN Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 665 ILE Chi-restraints excluded: chain F residue 681 THR Chi-restraints excluded: chain F residue 705 THR Chi-restraints excluded: chain F residue 730 THR Chi-restraints excluded: chain F residue 735 LYS Chi-restraints excluded: chain F residue 746 ASN Chi-restraints excluded: chain F residue 756 THR Chi-restraints excluded: chain F residue 766 SER Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain F residue 805 THR Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 138 TRP Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 226 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 316 ASP Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 512 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 606 LEU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 641 GLU Chi-restraints excluded: chain G residue 665 ILE Chi-restraints excluded: chain G residue 688 SER Chi-restraints excluded: chain G residue 701 LEU Chi-restraints excluded: chain G residue 709 ASN Chi-restraints excluded: chain G residue 720 THR Chi-restraints excluded: chain G residue 727 ASP Chi-restraints excluded: chain G residue 730 THR Chi-restraints excluded: chain G residue 740 ARG Chi-restraints excluded: chain G residue 746 ASN Chi-restraints excluded: chain G residue 756 THR Chi-restraints excluded: chain G residue 766 SER Chi-restraints excluded: chain G residue 773 LEU Chi-restraints excluded: chain G residue 805 THR Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 138 TRP Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 356 ASP Chi-restraints excluded: chain H residue 384 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 477 GLU Chi-restraints excluded: chain H residue 606 LEU Chi-restraints excluded: chain H residue 618 SER Chi-restraints excluded: chain H residue 641 GLU Chi-restraints excluded: chain H residue 665 ILE Chi-restraints excluded: chain H residue 701 LEU Chi-restraints excluded: chain H residue 717 SER Chi-restraints excluded: chain H residue 730 THR Chi-restraints excluded: chain H residue 737 ASP Chi-restraints excluded: chain H residue 756 THR Chi-restraints excluded: chain H residue 764 MET Chi-restraints excluded: chain H residue 766 SER Chi-restraints excluded: chain H residue 773 LEU Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain H residue 805 THR Chi-restraints excluded: chain H residue 830 GLN Chi-restraints excluded: chain H residue 835 THR Chi-restraints excluded: chain H residue 846 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 138 TRP Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 341 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 430 SER Chi-restraints excluded: chain I residue 431 SER Chi-restraints excluded: chain I residue 461 SER Chi-restraints excluded: chain I residue 576 SER Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 617 ASP Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 705 THR Chi-restraints excluded: chain I residue 709 ASN Chi-restraints excluded: chain I residue 717 SER Chi-restraints excluded: chain I residue 730 THR Chi-restraints excluded: chain I residue 737 ASP Chi-restraints excluded: chain I residue 746 ASN Chi-restraints excluded: chain I residue 770 ASN Chi-restraints excluded: chain I residue 805 THR Chi-restraints excluded: chain I residue 815 LEU Chi-restraints excluded: chain I residue 846 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 GLN Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 138 TRP Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 380 THR Chi-restraints excluded: chain J residue 384 ASN Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain J residue 461 SER Chi-restraints excluded: chain J residue 477 GLU Chi-restraints excluded: chain J residue 498 VAL Chi-restraints excluded: chain J residue 582 THR Chi-restraints excluded: chain J residue 584 ILE Chi-restraints excluded: chain J residue 601 SER Chi-restraints excluded: chain J residue 606 LEU Chi-restraints excluded: chain J residue 614 GLU Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 633 SER Chi-restraints excluded: chain J residue 657 THR Chi-restraints excluded: chain J residue 665 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 730 THR Chi-restraints excluded: chain J residue 737 ASP Chi-restraints excluded: chain J residue 756 THR Chi-restraints excluded: chain J residue 764 MET Chi-restraints excluded: chain J residue 766 SER Chi-restraints excluded: chain J residue 770 ASN Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 LEU Chi-restraints excluded: chain J residue 833 SER Chi-restraints excluded: chain J residue 835 THR Chi-restraints excluded: chain J residue 846 LEU Chi-restraints excluded: chain K residue 12 GLN Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 138 TRP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 311 ASN Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain K residue 351 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 422 VAL Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 477 GLU Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 575 VAL Chi-restraints excluded: chain K residue 584 ILE Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 617 ASP Chi-restraints excluded: chain K residue 624 THR Chi-restraints excluded: chain K residue 632 GLN Chi-restraints excluded: chain K residue 633 SER Chi-restraints excluded: chain K residue 657 THR Chi-restraints excluded: chain K residue 665 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 717 SER Chi-restraints excluded: chain K residue 737 ASP Chi-restraints excluded: chain K residue 752 THR Chi-restraints excluded: chain K residue 766 SER Chi-restraints excluded: chain K residue 773 LEU Chi-restraints excluded: chain K residue 805 THR Chi-restraints excluded: chain K residue 814 ASP Chi-restraints excluded: chain K residue 839 SER Chi-restraints excluded: chain K residue 846 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 589 optimal weight: 30.0000 chunk 790 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 683 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 742 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 chunk 762 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN B 538 ASN C 79 HIS C 242 ASN C 283 GLN C 538 ASN C 560 ASN C 640 ASN D 183 ASN D 396 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN E 686 ASN E 696 ASN ** F 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN ** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 786 ASN ** F 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN G 177 ASN ** G 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 596 ASN H 198 HIS H 384 ASN ** H 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 643 GLN I 560 ASN ** I 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 643 GLN J 217 GLN J 384 ASN ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN K 311 ASN ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 716 ASN K 844 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127142 restraints weight = 158175.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129755 restraints weight = 74026.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131484 restraints weight = 43240.381| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71115 Z= 0.231 Angle : 0.678 14.766 96723 Z= 0.352 Chirality : 0.045 0.266 11022 Planarity : 0.003 0.038 13068 Dihedral : 5.307 31.209 9845 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.61 % Favored : 92.02 % Rotamer: Outliers : 5.75 % Allowed : 22.69 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 1.22 % Twisted Proline : 1.30 % 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: -1.65 (0.08), residues: 9339 helix: 2.21 (0.14), residues: 1166 sheet: -1.21 (0.10), residues: 2288 loop : -1.83 (0.07), residues: 5885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 200 HIS 0.004 0.001 HIS K 623 PHE 0.018 0.001 PHE B 588 TYR 0.018 0.001 TYR D 383 ARG 0.008 0.001 ARG B 332 =============================================================================== Job complete usr+sys time: 29852.41 seconds wall clock time: 517 minutes 10.21 seconds (31030.21 seconds total)