Starting phenix.real_space_refine on Wed Feb 14 05:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/02_2024/6utj_20881.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.208 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 231 5.16 5 C 36911 2.51 5 N 9968 2.21 5 O 11249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Z TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58359 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "O" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "P" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "Q" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "T" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "U" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "b" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "c" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "d" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "e" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "f" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1760 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ARG A 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 28 " occ=0.50 residue: pdb=" N VAL A 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A 77 " occ=0.50 residue: pdb=" N ARG B 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 28 " occ=0.50 residue: pdb=" N VAL B 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B 77 " occ=0.50 residue: pdb=" N ARG C 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 28 " occ=0.50 residue: pdb=" N VAL C 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C 77 " occ=0.50 residue: pdb=" N ARG D 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 28 " occ=0.50 residue: pdb=" N VAL D 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D 77 " occ=0.50 residue: pdb=" N ARG E 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG E 28 " occ=0.50 residue: pdb=" N VAL E 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL E 77 " occ=0.50 residue: pdb=" N ARG F 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG F 28 " occ=0.50 residue: pdb=" N ARG G 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG G 28 " occ=0.50 Time building chain proxies: 22.45, per 1000 atoms: 0.38 Number of scatterers: 58359 At special positions: 0 Unit cell: (133.272, 133.272, 236.928, 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 231 16.00 O 11249 8.00 N 9968 7.00 C 36911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.47 Conformation dependent library (CDL) restraints added in 7.9 seconds 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13902 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 56 sheets defined 50.1% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.649A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.621A pdb=" N ILE A 64 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.314A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.612A pdb=" N ARG A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.588A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.604A pdb=" N ILE B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.331A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.644A pdb=" N ARG B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.659A pdb=" N LYS C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.622A pdb=" N ILE C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.226A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.615A pdb=" N ARG C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.657A pdb=" N LYS D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.631A pdb=" N ILE D 64 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 109 through 123 removed outlier: 4.003A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.627A pdb=" N ARG D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'E' and resid 21 through 33 removed outlier: 3.644A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.598A pdb=" N ILE E 64 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 109 through 123 removed outlier: 3.986A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.618A pdb=" N ARG E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 199 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'F' and resid 21 through 33 removed outlier: 3.638A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.608A pdb=" N ILE F 64 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 109 through 123 removed outlier: 3.980A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.609A pdb=" N ARG F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.577A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.652A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.589A pdb=" N ILE G 64 " --> pdb=" O GLN G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.225A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.607A pdb=" N ARG G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 199 Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 231 through 233 No H-bonds generated for 'chain 'G' and resid 231 through 233' Processing helix chain 'O' and resid 5 through 16 Processing helix chain 'O' and resid 17 through 52 removed outlier: 4.056A pdb=" N THR O 32 " --> pdb=" O TRP O 28 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 61 Processing helix chain 'O' and resid 64 through 94 Processing helix chain 'O' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'O' and resid 143 through 161 removed outlier: 3.775A pdb=" N VAL O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 221 removed outlier: 3.578A pdb=" N LEU O 180 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS O 217 " --> pdb=" O LEU O 213 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 231 removed outlier: 4.114A pdb=" N LEU O 230 " --> pdb=" O HIS O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 16 Processing helix chain 'P' and resid 17 through 52 removed outlier: 4.056A pdb=" N THR P 32 " --> pdb=" O TRP P 28 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 61 Processing helix chain 'P' and resid 64 through 94 Processing helix chain 'P' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL P 109 " --> pdb=" O LEU P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 142 No H-bonds generated for 'chain 'P' and resid 140 through 142' Processing helix chain 'P' and resid 143 through 161 removed outlier: 3.776A pdb=" N VAL P 155 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 221 removed outlier: 3.578A pdb=" N LEU P 180 " --> pdb=" O SER P 176 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS P 217 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 231 removed outlier: 4.113A pdb=" N LEU P 230 " --> pdb=" O HIS P 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 16 Processing helix chain 'Q' and resid 17 through 52 removed outlier: 4.056A pdb=" N THR Q 32 " --> pdb=" O TRP Q 28 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU Q 33 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 61 Processing helix chain 'Q' and resid 64 through 94 Processing helix chain 'Q' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 142 No H-bonds generated for 'chain 'Q' and resid 140 through 142' Processing helix chain 'Q' and resid 143 through 161 removed outlier: 3.776A pdb=" N VAL Q 155 " --> pdb=" O ALA Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 221 removed outlier: 3.579A pdb=" N LEU Q 180 " --> pdb=" O SER Q 176 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS Q 217 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 231 removed outlier: 4.114A pdb=" N LEU Q 230 " --> pdb=" O HIS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 Processing helix chain 'R' and resid 17 through 52 removed outlier: 4.055A pdb=" N THR R 32 " --> pdb=" O TRP R 28 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 61 Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL R 109 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 143 through 161 removed outlier: 3.776A pdb=" N VAL R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 221 removed outlier: 3.578A pdb=" N LEU R 180 " --> pdb=" O SER R 176 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS R 217 " --> pdb=" O LEU R 213 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 231 removed outlier: 4.113A pdb=" N LEU R 230 " --> pdb=" O HIS R 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 16 Processing helix chain 'S' and resid 17 through 52 removed outlier: 4.056A pdb=" N THR S 32 " --> pdb=" O TRP S 28 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU S 33 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN S 34 " --> pdb=" O ALA S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 61 Processing helix chain 'S' and resid 64 through 94 Processing helix chain 'S' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL S 109 " --> pdb=" O LEU S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 142 No H-bonds generated for 'chain 'S' and resid 140 through 142' Processing helix chain 'S' and resid 143 through 161 removed outlier: 3.776A pdb=" N VAL S 155 " --> pdb=" O ALA S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 221 removed outlier: 3.578A pdb=" N LEU S 180 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS S 218 " --> pdb=" O LEU S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 removed outlier: 4.114A pdb=" N LEU S 230 " --> pdb=" O HIS S 226 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 16 Processing helix chain 'T' and resid 17 through 52 removed outlier: 4.055A pdb=" N THR T 32 " --> pdb=" O TRP T 28 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN T 34 " --> pdb=" O ALA T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 61 Processing helix chain 'T' and resid 64 through 94 Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL T 109 " --> pdb=" O LEU T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 142 No H-bonds generated for 'chain 'T' and resid 140 through 142' Processing helix chain 'T' and resid 143 through 161 removed outlier: 3.776A pdb=" N VAL T 155 " --> pdb=" O ALA T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 221 removed outlier: 3.579A pdb=" N LEU T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS T 218 " --> pdb=" O LEU T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 231 removed outlier: 4.114A pdb=" N LEU T 230 " --> pdb=" O HIS T 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 16 Processing helix chain 'U' and resid 17 through 52 removed outlier: 4.056A pdb=" N THR U 32 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 61 Processing helix chain 'U' and resid 64 through 94 Processing helix chain 'U' and resid 104 through 123 removed outlier: 3.505A pdb=" N VAL U 109 " --> pdb=" O LEU U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 142 No H-bonds generated for 'chain 'U' and resid 140 through 142' Processing helix chain 'U' and resid 143 through 161 removed outlier: 3.775A pdb=" N VAL U 155 " --> pdb=" O ALA U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 221 removed outlier: 3.579A pdb=" N LEU U 180 " --> pdb=" O SER U 176 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS U 217 " --> pdb=" O LEU U 213 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS U 218 " --> pdb=" O LEU U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 226 through 231 removed outlier: 4.114A pdb=" N LEU U 230 " --> pdb=" O HIS U 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 3.927A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 166 Processing helix chain '1' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 3.925A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 166 Processing helix chain '2' and resid 188 through 200 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.925A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.925A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.927A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 3.705A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.926A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 3.706A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'a' and resid 21 through 33 Processing helix chain 'a' and resid 81 through 104 Processing helix chain 'a' and resid 108 through 126 removed outlier: 3.833A pdb=" N LEU a 112 " --> pdb=" O ASN a 108 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR a 123 " --> pdb=" O GLN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 180 Processing helix chain 'a' and resid 185 through 202 removed outlier: 3.573A pdb=" N SER a 200 " --> pdb=" O ALA a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 225 through 233 removed outlier: 3.657A pdb=" N VAL a 229 " --> pdb=" O ASP a 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS a 230 " --> pdb=" O GLN a 226 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS a 231 " --> pdb=" O GLU a 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE a 232 " --> pdb=" O GLU a 228 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 33 Processing helix chain 'b' and resid 81 through 104 Processing helix chain 'b' and resid 108 through 126 removed outlier: 3.845A pdb=" N LEU b 112 " --> pdb=" O ASN b 108 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 185 through 202 removed outlier: 3.570A pdb=" N SER b 200 " --> pdb=" O ALA b 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 225 through 233 removed outlier: 3.663A pdb=" N VAL b 229 " --> pdb=" O ASP b 225 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS b 230 " --> pdb=" O GLN b 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS b 231 " --> pdb=" O GLU b 227 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE b 232 " --> pdb=" O GLU b 228 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 33 Processing helix chain 'c' and resid 81 through 104 Processing helix chain 'c' and resid 108 through 126 removed outlier: 3.848A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR c 123 " --> pdb=" O GLN c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 180 Processing helix chain 'c' and resid 185 through 202 removed outlier: 3.567A pdb=" N SER c 200 " --> pdb=" O ALA c 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 233 removed outlier: 3.655A pdb=" N VAL c 229 " --> pdb=" O ASP c 225 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS c 230 " --> pdb=" O GLN c 226 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE c 232 " --> pdb=" O GLU c 228 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 33 Processing helix chain 'd' and resid 81 through 104 Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.839A pdb=" N LEU d 112 " --> pdb=" O ASN d 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 180 Processing helix chain 'd' and resid 185 through 202 removed outlier: 3.564A pdb=" N SER d 200 " --> pdb=" O ALA d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 225 through 233 removed outlier: 3.655A pdb=" N VAL d 229 " --> pdb=" O ASP d 225 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS d 230 " --> pdb=" O GLN d 226 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS d 231 " --> pdb=" O GLU d 227 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 33 Processing helix chain 'e' and resid 81 through 104 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.837A pdb=" N LEU e 112 " --> pdb=" O ASN e 108 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR e 123 " --> pdb=" O GLN e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 180 Processing helix chain 'e' and resid 185 through 202 removed outlier: 3.562A pdb=" N SER e 200 " --> pdb=" O ALA e 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 225 through 233 removed outlier: 3.659A pdb=" N VAL e 229 " --> pdb=" O ASP e 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS e 230 " --> pdb=" O GLN e 226 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS e 231 " --> pdb=" O GLU e 227 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE e 232 " --> pdb=" O GLU e 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 33 Processing helix chain 'f' and resid 81 through 104 Processing helix chain 'f' and resid 108 through 126 removed outlier: 3.834A pdb=" N LEU f 112 " --> pdb=" O ASN f 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR f 123 " --> pdb=" O GLN f 119 " (cutoff:3.500A) Processing helix chain 'f' and resid 169 through 180 Processing helix chain 'f' and resid 185 through 202 removed outlier: 3.576A pdb=" N SER f 200 " --> pdb=" O ALA f 196 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 233 removed outlier: 3.658A pdb=" N VAL f 229 " --> pdb=" O ASP f 225 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS f 230 " --> pdb=" O GLN f 226 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS f 231 " --> pdb=" O GLU f 227 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE f 232 " --> pdb=" O GLU f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 33 Processing helix chain 'g' and resid 81 through 104 Processing helix chain 'g' and resid 108 through 126 removed outlier: 3.842A pdb=" N LEU g 112 " --> pdb=" O ASN g 108 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR g 123 " --> pdb=" O GLN g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 180 Processing helix chain 'g' and resid 185 through 202 removed outlier: 3.572A pdb=" N SER g 200 " --> pdb=" O ALA g 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 225 through 233 removed outlier: 3.664A pdb=" N VAL g 229 " --> pdb=" O ASP g 225 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS g 230 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS g 231 " --> pdb=" O GLU g 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE g 232 " --> pdb=" O GLU g 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.503A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE A 212 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.579A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 removed outlier: 4.834A pdb=" N ILE B 212 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 removed outlier: 3.573A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.529A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE C 212 " --> pdb=" O TYR C 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.566A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.519A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE D 212 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.564A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.525A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.592A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.507A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.583A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.525A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE G 212 " --> pdb=" O TYR G 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.592A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Z' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA M 11 " --> pdb=" O LEU M 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 100 " --> pdb=" O THR M 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '1' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA 1 11 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU 1 100 " --> pdb=" O THR 1 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA N 11 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.604A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU N 100 " --> pdb=" O THR N 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA 2 11 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '2' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 2 100 " --> pdb=" O THR 2 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA H 11 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU H 100 " --> pdb=" O THR H 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA V 11 " --> pdb=" O LEU V 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU V 100 " --> pdb=" O THR V 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 125 removed outlier: 3.663A pdb=" N ALA I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.606A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 100 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA W 11 " --> pdb=" O LEU W 8 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU W 100 " --> pdb=" O THR W 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA J 11 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU J 100 " --> pdb=" O THR J 44 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU X 100 " --> pdb=" O THR X 44 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA K 11 " --> pdb=" O LEU K 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 124 through 125 removed outlier: 3.662A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 124 through 125 removed outlier: 3.663A pdb=" N ALA L 11 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.605A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'a' and resid 162 through 165 Processing sheet with id=AE8, first strand: chain 'a' and resid 67 through 71 removed outlier: 6.064A pdb=" N VAL a 74 " --> pdb=" O ILE a 70 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN a 158 " --> pdb=" O ASP a 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 162 through 165 Processing sheet with id=AF1, first strand: chain 'b' and resid 67 through 71 removed outlier: 6.084A pdb=" N VAL b 74 " --> pdb=" O ILE b 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 136 " --> pdb=" O CYS b 151 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE b 138 " --> pdb=" O PHE b 149 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN b 158 " --> pdb=" O ASP b 150 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 162 through 165 Processing sheet with id=AF3, first strand: chain 'c' and resid 67 through 71 removed outlier: 6.019A pdb=" N VAL c 74 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU c 136 " --> pdb=" O CYS c 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN c 158 " --> pdb=" O ASP c 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'd' and resid 67 through 71 removed outlier: 5.958A pdb=" N VAL d 74 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU d 136 " --> pdb=" O CYS d 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE d 138 " --> pdb=" O PHE d 149 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN d 158 " --> pdb=" O ASP d 150 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'e' and resid 162 through 165 Processing sheet with id=AF7, first strand: chain 'e' and resid 67 through 71 removed outlier: 6.068A pdb=" N VAL e 74 " --> pdb=" O ILE e 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU e 136 " --> pdb=" O CYS e 151 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE e 138 " --> pdb=" O PHE e 149 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN e 158 " --> pdb=" O ASP e 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'f' and resid 162 through 165 Processing sheet with id=AF9, first strand: chain 'f' and resid 67 through 71 removed outlier: 5.997A pdb=" N VAL f 74 " --> pdb=" O ILE f 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU f 136 " --> pdb=" O CYS f 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE f 138 " --> pdb=" O PHE f 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN f 158 " --> pdb=" O ASP f 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 162 through 165 Processing sheet with id=AG2, first strand: chain 'g' and resid 67 through 71 removed outlier: 6.044A pdb=" N VAL g 74 " --> pdb=" O ILE g 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU g 136 " --> pdb=" O CYS g 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE g 138 " --> pdb=" O PHE g 149 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN g 158 " --> pdb=" O ASP g 150 " (cutoff:3.500A) 3594 hydrogen bonds defined for protein. 10443 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: 19.63 Time building geometry restraints manager: 19.20 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: 13776 1.33 - 1.45: 10932 1.45 - 1.57: 33951 1.57 - 1.68: 36 1.68 - 1.80: 434 Bond restraints: 59129 Sorted by residual: bond pdb=" CA LEU B 21 " pdb=" CB LEU B 21 " ideal model delta sigma weight residual 1.525 1.441 0.084 1.47e-02 4.63e+03 3.25e+01 bond pdb=" CA LEU D 21 " pdb=" CB LEU D 21 " ideal model delta sigma weight residual 1.528 1.384 0.145 2.61e-02 1.47e+03 3.07e+01 bond pdb=" CA LEU F 21 " pdb=" CB LEU F 21 " ideal model delta sigma weight residual 1.525 1.450 0.074 1.47e-02 4.63e+03 2.55e+01 bond pdb=" CG ARG g 10 " pdb=" CD ARG g 10 " ideal model delta sigma weight residual 1.520 1.666 -0.146 3.00e-02 1.11e+03 2.37e+01 bond pdb=" CA LEU A 21 " pdb=" CB LEU A 21 " ideal model delta sigma weight residual 1.525 1.453 0.071 1.47e-02 4.63e+03 2.35e+01 ... (remaining 59124 not shown) Histogram of bond angle deviations from ideal: 94.28 - 103.50: 625 103.50 - 112.72: 30872 112.72 - 121.94: 36324 121.94 - 131.16: 11922 131.16 - 140.38: 113 Bond angle restraints: 79856 Sorted by residual: angle pdb=" CA TYR g 8 " pdb=" CB TYR g 8 " pdb=" CG TYR g 8 " ideal model delta sigma weight residual 113.90 135.29 -21.39 1.80e+00 3.09e-01 1.41e+02 angle pdb=" CA TYR e 8 " pdb=" CB TYR e 8 " pdb=" CG TYR e 8 " ideal model delta sigma weight residual 113.90 135.20 -21.30 1.80e+00 3.09e-01 1.40e+02 angle pdb=" CA TYR c 8 " pdb=" CB TYR c 8 " pdb=" CG TYR c 8 " ideal model delta sigma weight residual 113.90 134.25 -20.35 1.80e+00 3.09e-01 1.28e+02 angle pdb=" CA TYR a 8 " pdb=" CB TYR a 8 " pdb=" CG TYR a 8 " ideal model delta sigma weight residual 113.90 133.98 -20.08 1.80e+00 3.09e-01 1.24e+02 angle pdb=" C THR W 21 " pdb=" N MET W 22 " pdb=" CA MET W 22 " ideal model delta sigma weight residual 121.70 140.38 -18.68 1.80e+00 3.09e-01 1.08e+02 ... (remaining 79851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 34312 15.66 - 31.31: 1331 31.31 - 46.97: 372 46.97 - 62.63: 63 62.63 - 78.28: 63 Dihedral angle restraints: 36141 sinusoidal: 14399 harmonic: 21742 Sorted by residual: dihedral pdb=" CA ASN 2 24 " pdb=" C ASN 2 24 " pdb=" N PHE 2 25 " pdb=" CA PHE 2 25 " ideal model delta harmonic sigma weight residual 180.00 122.32 57.68 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA ASN X 24 " pdb=" C ASN X 24 " pdb=" N PHE X 25 " pdb=" CA PHE X 25 " ideal model delta harmonic sigma weight residual 180.00 122.34 57.66 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA ASN K 24 " pdb=" C ASN K 24 " pdb=" N PHE K 25 " pdb=" CA PHE K 25 " ideal model delta harmonic sigma weight residual 180.00 122.34 57.66 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 36138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 7708 0.077 - 0.155: 1321 0.155 - 0.232: 223 0.232 - 0.309: 64 0.309 - 0.386: 22 Chirality restraints: 9338 Sorted by residual: chirality pdb=" CB ILE M 178 " pdb=" CA ILE M 178 " pdb=" CG1 ILE M 178 " pdb=" CG2 ILE M 178 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB ILE H 178 " pdb=" CA ILE H 178 " pdb=" CG1 ILE H 178 " pdb=" CG2 ILE H 178 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CB ILE N 178 " pdb=" CA ILE N 178 " pdb=" CG1 ILE N 178 " pdb=" CG2 ILE N 178 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 9335 not shown) Planarity restraints: 10255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR g 8 " -0.071 2.00e-02 2.50e+03 4.69e-02 4.39e+01 pdb=" CG TYR g 8 " 0.094 2.00e-02 2.50e+03 pdb=" CD1 TYR g 8 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR g 8 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR g 8 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR g 8 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR g 8 " -0.045 2.00e-02 2.50e+03 pdb=" OH TYR g 8 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 8 " 0.071 2.00e-02 2.50e+03 4.44e-02 3.93e+01 pdb=" CG TYR d 8 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TYR d 8 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR d 8 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR d 8 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR d 8 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR d 8 " 0.045 2.00e-02 2.50e+03 pdb=" OH TYR d 8 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR e 8 " 0.068 2.00e-02 2.50e+03 4.40e-02 3.87e+01 pdb=" CG TYR e 8 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 TYR e 8 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR e 8 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR e 8 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR e 8 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR e 8 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR e 8 " -0.006 2.00e-02 2.50e+03 ... (remaining 10252 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6757 2.75 - 3.29: 56077 3.29 - 3.82: 100394 3.82 - 4.36: 119983 4.36 - 4.90: 205890 Nonbonded interactions: 489101 Sorted by model distance: nonbonded pdb=" O LYS B 41 " pdb=" OH TYR B 180 " model vdw 2.212 2.440 nonbonded pdb=" O LYS D 41 " pdb=" OH TYR D 180 " model vdw 2.212 2.440 nonbonded pdb=" O LYS F 41 " pdb=" OH TYR F 180 " model vdw 2.212 2.440 nonbonded pdb=" O LYS A 41 " pdb=" OH TYR A 180 " model vdw 2.215 2.440 nonbonded pdb=" O LYS C 41 " pdb=" OH TYR C 180 " model vdw 2.218 2.440 ... (remaining 489096 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 '1' selection = chain '2' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'B' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'C' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'D' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'E' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'F' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'G' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'a' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'b' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'c' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'd' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'e' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'f' and (resid 8 through 65 or resid 67 through 233)) selection = (chain 'g' and (resid 8 through 65 or resid 67 through 233)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.030 Extract box with map and model: 9.030 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 115.920 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.390 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.009 0.146 59129 Z= 0.608 Angle : 1.344 21.393 79856 Z= 0.768 Chirality : 0.066 0.386 9338 Planarity : 0.007 0.060 10255 Dihedral : 10.474 78.284 22239 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.07 % Favored : 94.65 % Rotamer: Outliers : 1.01 % Allowed : 4.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -2.93 (0.08), residues: 7462 helix: -1.51 (0.07), residues: 3430 sheet: -1.69 (0.13), residues: 1414 loop : -2.44 (0.10), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 28 HIS 0.010 0.004 HIS Q 111 PHE 0.040 0.005 PHE J 111 TYR 0.094 0.005 TYR g 8 ARG 0.028 0.002 ARG g 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2483 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 2420 time to evaluate : 5.116 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: A 231 LYS cc_start: 0.8240 (mtpm) cc_final: 0.7833 (tttm) REVERT: B 177 GLU cc_start: 0.7218 (tp30) cc_final: 0.6930 (tp30) REVERT: C 231 LYS cc_start: 0.8018 (mtpm) cc_final: 0.7431 (ttpp) REVERT: D 170 ASP cc_start: 0.7424 (m-30) cc_final: 0.7106 (m-30) REVERT: D 177 GLU cc_start: 0.7458 (tp30) cc_final: 0.7255 (tp30) REVERT: D 231 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7893 (tttp) REVERT: E 173 VAL cc_start: 0.8447 (t) cc_final: 0.8212 (m) REVERT: E 177 GLU cc_start: 0.7427 (tp30) cc_final: 0.7155 (mm-30) REVERT: E 231 LYS cc_start: 0.8034 (mtpm) cc_final: 0.7808 (ttpp) REVERT: F 103 TYR cc_start: 0.8845 (m-80) cc_final: 0.8422 (m-10) REVERT: F 177 GLU cc_start: 0.7452 (tp30) cc_final: 0.7218 (tp30) REVERT: F 231 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7782 (tttp) REVERT: G 9 ASP cc_start: 0.7539 (p0) cc_final: 0.7332 (p0) REVERT: G 118 ASP cc_start: 0.8068 (m-30) cc_final: 0.7842 (m-30) REVERT: G 170 ASP cc_start: 0.7473 (m-30) cc_final: 0.7219 (m-30) REVERT: O 182 GLU cc_start: 0.7821 (tt0) cc_final: 0.7594 (tp30) REVERT: P 152 ARG cc_start: 0.8267 (ttt90) cc_final: 0.7875 (ttt180) REVERT: P 184 ARG cc_start: 0.8745 (ttt-90) cc_final: 0.8474 (ttt-90) REVERT: Q 34 GLN cc_start: 0.8586 (mp10) cc_final: 0.8154 (mp10) REVERT: Q 119 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7232 (mt-10) REVERT: Q 156 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7731 (mt-10) REVERT: R 119 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7509 (mt-10) REVERT: R 121 GLU cc_start: 0.8217 (pt0) cc_final: 0.7800 (pt0) REVERT: R 229 VAL cc_start: 0.8770 (t) cc_final: 0.8563 (p) REVERT: S 34 GLN cc_start: 0.8610 (mp10) cc_final: 0.8285 (mp-120) REVERT: S 156 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7598 (mt-10) REVERT: S 229 VAL cc_start: 0.8631 (t) cc_final: 0.8345 (p) REVERT: T 16 TYR cc_start: 0.7325 (m-10) cc_final: 0.7109 (m-80) REVERT: T 182 GLU cc_start: 0.7484 (tt0) cc_final: 0.7182 (tp30) REVERT: T 191 MET cc_start: 0.9090 (mmp) cc_final: 0.8394 (mmp) REVERT: U 55 TYR cc_start: 0.7741 (m-10) cc_final: 0.7361 (m-10) REVERT: U 156 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7834 (mt-10) REVERT: U 191 MET cc_start: 0.8407 (mmp) cc_final: 0.7833 (mmp) REVERT: U 212 TYR cc_start: 0.8910 (t80) cc_final: 0.8619 (t80) REVERT: Z 146 MET cc_start: 0.8752 (mtt) cc_final: 0.8513 (mtm) REVERT: M 27 MET cc_start: 0.8731 (ttt) cc_final: 0.8224 (ttt) REVERT: M 153 ASP cc_start: 0.7845 (m-30) cc_final: 0.7567 (m-30) REVERT: 1 55 LEU cc_start: 0.8629 (mm) cc_final: 0.8419 (mt) REVERT: 1 112 SER cc_start: 0.8442 (t) cc_final: 0.8208 (m) REVERT: 1 156 ILE cc_start: 0.8851 (mt) cc_final: 0.8631 (mm) REVERT: N 8 LEU cc_start: 0.8113 (pp) cc_final: 0.7906 (mt) REVERT: N 153 ASP cc_start: 0.7841 (m-30) cc_final: 0.7565 (m-30) REVERT: 2 164 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7669 (mm-40) REVERT: H 43 MET cc_start: 0.8320 (ttm) cc_final: 0.8098 (ttm) REVERT: H 123 ILE cc_start: 0.8748 (pt) cc_final: 0.8509 (mp) REVERT: H 153 ASP cc_start: 0.7874 (m-30) cc_final: 0.7491 (m-30) REVERT: V 27 MET cc_start: 0.7924 (ttt) cc_final: 0.7667 (ttt) REVERT: I 27 MET cc_start: 0.8663 (ttt) cc_final: 0.8257 (ttp) REVERT: I 153 ASP cc_start: 0.7759 (m-30) cc_final: 0.7404 (m-30) REVERT: J 95 TYR cc_start: 0.8499 (m-80) cc_final: 0.8291 (m-80) REVERT: J 99 LEU cc_start: 0.8707 (mt) cc_final: 0.8478 (mt) REVERT: J 105 ASP cc_start: 0.8313 (p0) cc_final: 0.8024 (p0) REVERT: X 27 MET cc_start: 0.7998 (ttt) cc_final: 0.7730 (ttt) REVERT: X 150 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7834 (mt-10) REVERT: K 153 ASP cc_start: 0.7824 (m-30) cc_final: 0.7520 (m-30) REVERT: K 175 VAL cc_start: 0.8772 (p) cc_final: 0.8518 (t) REVERT: Y 124 TYR cc_start: 0.8258 (p90) cc_final: 0.7531 (p90) REVERT: L 99 LEU cc_start: 0.8798 (mt) cc_final: 0.8593 (mt) REVERT: L 112 SER cc_start: 0.8552 (t) cc_final: 0.8326 (t) REVERT: L 153 ASP cc_start: 0.7611 (m-30) cc_final: 0.6946 (m-30) REVERT: a 18 ASP cc_start: 0.7586 (p0) cc_final: 0.6909 (p0) REVERT: a 90 ASP cc_start: 0.6988 (m-30) cc_final: 0.6515 (m-30) REVERT: a 120 MET cc_start: 0.9166 (mtp) cc_final: 0.8903 (mtp) REVERT: b 18 ASP cc_start: 0.7608 (p0) cc_final: 0.7098 (p0) REVERT: b 191 THR cc_start: 0.8284 (m) cc_final: 0.7762 (p) REVERT: c 18 ASP cc_start: 0.7740 (p0) cc_final: 0.7194 (OUTLIER) REVERT: c 141 ILE cc_start: 0.8562 (pp) cc_final: 0.8343 (pp) REVERT: c 191 THR cc_start: 0.8443 (m) cc_final: 0.7839 (p) REVERT: d 18 ASP cc_start: 0.7896 (p0) cc_final: 0.7274 (p0) REVERT: d 108 ASN cc_start: 0.7853 (t0) cc_final: 0.7408 (t0) REVERT: d 120 MET cc_start: 0.9151 (mtp) cc_final: 0.8279 (mtp) REVERT: d 180 TYR cc_start: 0.7458 (t80) cc_final: 0.6819 (t80) REVERT: e 18 ASP cc_start: 0.8242 (p0) cc_final: 0.7733 (p0) REVERT: e 33 LYS cc_start: 0.8211 (mtpp) cc_final: 0.8009 (mtpm) REVERT: e 60 GLU cc_start: 0.7155 (tp30) cc_final: 0.6889 (tp30) REVERT: e 71 ASP cc_start: 0.7657 (t70) cc_final: 0.7326 (t0) REVERT: e 120 MET cc_start: 0.9103 (mtp) cc_final: 0.8848 (mtp) REVERT: e 159 GLU cc_start: 0.7087 (tt0) cc_final: 0.6761 (tt0) REVERT: e 191 THR cc_start: 0.8450 (m) cc_final: 0.7878 (p) REVERT: f 18 ASP cc_start: 0.7624 (p0) cc_final: 0.7064 (p0) REVERT: f 52 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7145 (tttt) REVERT: f 60 GLU cc_start: 0.7198 (tp30) cc_final: 0.6914 (tp30) REVERT: f 120 MET cc_start: 0.9106 (mtp) cc_final: 0.8656 (mtm) REVERT: f 161 LYS cc_start: 0.7270 (mttm) cc_final: 0.7033 (mmmt) REVERT: f 180 TYR cc_start: 0.7456 (t80) cc_final: 0.7154 (t80) REVERT: f 191 THR cc_start: 0.8539 (m) cc_final: 0.7884 (p) REVERT: g 18 ASP cc_start: 0.7991 (p0) cc_final: 0.7144 (p0) REVERT: g 33 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8232 (mtmm) REVERT: g 60 GLU cc_start: 0.7264 (tp30) cc_final: 0.7024 (tp30) REVERT: g 120 MET cc_start: 0.9131 (mtp) cc_final: 0.8906 (mtm) REVERT: g 180 TYR cc_start: 0.7593 (t80) cc_final: 0.7333 (t80) outliers start: 63 outliers final: 46 residues processed: 2462 average time/residue: 1.4803 time to fit residues: 4546.3858 Evaluate side-chains 1387 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1342 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 111 PHE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain g residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 10.0000 chunk 557 optimal weight: 4.9990 chunk 309 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 576 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 428 optimal weight: 2.9990 chunk 667 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 158 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN B 158 ASN C 23 GLN C 119 GLN C 158 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 158 ASN G 23 GLN G 108 ASN O 79 HIS O 111 HIS ** O 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 HIS P 79 HIS P 99 HIS P 111 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Q 72 GLN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 HIS Q 185 GLN R 99 HIS R 111 HIS S 111 HIS S 200 HIS T 59 GLN T 72 GLN T 79 HIS T 111 HIS T 200 HIS U 59 GLN U 66 GLN U 79 HIS U 111 HIS U 200 HIS Z 69 GLN Z 141 GLN Z 186 GLN 1 88 ASN 1 186 GLN N 88 ASN N 141 GLN 2 88 ASN 2 141 GLN 2 186 GLN H 30 ASN H 36 GLN H 85 ASN V 88 ASN V 89 GLN V 141 GLN V 186 GLN W 88 ASN J 30 ASN X 73 ASN X 88 ASN X 141 GLN K 141 GLN L 36 GLN ** a 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 97 GLN a 98 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 121 GLN a 125 GLN ** b 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 23 GLN f 108 ASN ** f 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 59129 Z= 0.309 Angle : 0.711 13.679 79856 Z= 0.384 Chirality : 0.046 0.260 9338 Planarity : 0.005 0.075 10255 Dihedral : 6.708 83.070 8355 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 6.92 % Allowed : 18.90 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.04 (0.09), residues: 7462 helix: 0.62 (0.08), residues: 3430 sheet: -1.16 (0.12), residues: 1407 loop : -2.14 (0.10), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 216 HIS 0.008 0.002 HIS U 79 PHE 0.029 0.002 PHE a 42 TYR 0.026 0.002 TYR M 66 ARG 0.011 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1862 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 1429 time to evaluate : 5.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7199 (pt0) cc_final: 0.6983 (pt0) REVERT: A 177 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: A 187 LYS cc_start: 0.7865 (tttt) cc_final: 0.7641 (mmmt) REVERT: A 231 LYS cc_start: 0.8222 (mtpm) cc_final: 0.7718 (ttpp) REVERT: B 32 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7605 (ttmt) REVERT: B 40 MET cc_start: 0.8324 (ptp) cc_final: 0.8116 (ptp) REVERT: B 52 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7878 (ptmt) REVERT: B 84 ASP cc_start: 0.8587 (m-30) cc_final: 0.8237 (m-30) REVERT: B 94 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8670 (mp) REVERT: C 106 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.7959 (tp) REVERT: C 231 LYS cc_start: 0.8059 (mtpm) cc_final: 0.7482 (ttpp) REVERT: D 40 MET cc_start: 0.8372 (ptp) cc_final: 0.7792 (ptp) REVERT: D 170 ASP cc_start: 0.7708 (m-30) cc_final: 0.7489 (m-30) REVERT: E 40 MET cc_start: 0.8287 (ptt) cc_final: 0.7960 (ptp) REVERT: E 231 LYS cc_start: 0.7850 (mtpm) cc_final: 0.7341 (ttpp) REVERT: F 94 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8532 (mp) REVERT: F 103 TYR cc_start: 0.8792 (m-80) cc_final: 0.8494 (m-80) REVERT: F 118 ASP cc_start: 0.8529 (m-30) cc_final: 0.8051 (m-30) REVERT: F 187 LYS cc_start: 0.8125 (tttt) cc_final: 0.7893 (mptp) REVERT: F 208 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7699 (mtmt) REVERT: F 211 GLU cc_start: 0.7686 (pt0) cc_final: 0.7404 (pt0) REVERT: G 52 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7666 (ptpp) REVERT: G 98 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: G 118 ASP cc_start: 0.8409 (m-30) cc_final: 0.7675 (m-30) REVERT: G 208 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7939 (mtmm) REVERT: G 211 GLU cc_start: 0.7600 (pt0) cc_final: 0.7329 (pt0) REVERT: O 37 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: O 59 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: O 204 MET cc_start: 0.8092 (ttp) cc_final: 0.7844 (mtt) REVERT: P 142 MET cc_start: 0.8039 (mmt) cc_final: 0.7824 (mpt) REVERT: P 187 ASP cc_start: 0.8656 (m-30) cc_final: 0.8436 (m-30) REVERT: Q 34 GLN cc_start: 0.8524 (mp10) cc_final: 0.8127 (mp10) REVERT: Q 37 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: Q 204 MET cc_start: 0.7363 (mtm) cc_final: 0.7075 (mtt) REVERT: Q 221 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: R 119 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7543 (mt-10) REVERT: R 221 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7932 (mp10) REVERT: R 229 VAL cc_start: 0.8711 (t) cc_final: 0.8433 (p) REVERT: S 119 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7470 (mt-10) REVERT: T 125 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7874 (tt) REVERT: T 182 GLU cc_start: 0.7559 (tt0) cc_final: 0.7279 (tp30) REVERT: T 204 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7325 (mtt) REVERT: U 191 MET cc_start: 0.8787 (mmp) cc_final: 0.8161 (mmp) REVERT: U 204 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7499 (mtt) REVERT: Z 26 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7425 (pt) REVERT: Z 62 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7344 (mm-30) REVERT: Z 96 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7318 (mtp) REVERT: Z 146 MET cc_start: 0.8775 (mtt) cc_final: 0.8494 (mtm) REVERT: M 93 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.4622 (pmt) REVERT: M 153 ASP cc_start: 0.7868 (m-30) cc_final: 0.7530 (m-30) REVERT: 1 26 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7425 (pt) REVERT: 1 51 ASP cc_start: 0.8212 (m-30) cc_final: 0.7991 (m-30) REVERT: 1 64 GLU cc_start: 0.7198 (tt0) cc_final: 0.6996 (tt0) REVERT: 1 96 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: 1 177 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8571 (t) REVERT: N 153 ASP cc_start: 0.7825 (m-30) cc_final: 0.7538 (m-30) REVERT: 2 21 THR cc_start: 0.4765 (OUTLIER) cc_final: 0.4408 (t) REVERT: 2 93 MET cc_start: 0.6550 (pmm) cc_final: 0.6296 (pmm) REVERT: 2 173 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8579 (mt) REVERT: H 33 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8487 (mttp) REVERT: H 153 ASP cc_start: 0.7862 (m-30) cc_final: 0.7506 (m-30) REVERT: V 26 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7271 (pt) REVERT: V 27 MET cc_start: 0.8171 (ttt) cc_final: 0.7957 (ttt) REVERT: V 51 ASP cc_start: 0.8315 (m-30) cc_final: 0.8042 (m-30) REVERT: V 96 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: V 144 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: V 165 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8000 (mmt-90) REVERT: V 172 MET cc_start: 0.7568 (tpt) cc_final: 0.7366 (tpp) REVERT: V 177 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8780 (m) REVERT: I 93 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.4491 (pmt) REVERT: I 123 ILE cc_start: 0.8702 (pt) cc_final: 0.8479 (mp) REVERT: I 153 ASP cc_start: 0.7686 (m-30) cc_final: 0.7258 (m-30) REVERT: W 93 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6244 (pmm) REVERT: W 96 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: W 145 LYS cc_start: 0.8512 (mppt) cc_final: 0.8245 (mmtm) REVERT: W 173 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8562 (mt) REVERT: W 177 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8508 (p) REVERT: J 93 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5075 (mpp) REVERT: J 95 TYR cc_start: 0.8678 (m-80) cc_final: 0.8460 (m-80) REVERT: X 26 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7424 (pt) REVERT: X 30 ASN cc_start: 0.8078 (t0) cc_final: 0.7872 (t0) REVERT: X 51 ASP cc_start: 0.8127 (m-30) cc_final: 0.7889 (m-30) REVERT: X 156 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8576 (mm) REVERT: X 177 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8756 (m) REVERT: K 88 ASN cc_start: 0.8720 (t0) cc_final: 0.8454 (t0) REVERT: K 96 MET cc_start: 0.7796 (mpp) cc_final: 0.7514 (mtm) REVERT: K 131 SER cc_start: 0.8583 (t) cc_final: 0.8365 (p) REVERT: K 153 ASP cc_start: 0.7766 (m-30) cc_final: 0.7440 (m-30) REVERT: K 178 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8335 (tp) REVERT: Y 51 ASP cc_start: 0.8186 (m-30) cc_final: 0.7977 (m-30) REVERT: Y 145 LYS cc_start: 0.8368 (mppt) cc_final: 0.8149 (mmtm) REVERT: L 93 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.4446 (mpp) REVERT: L 105 ASP cc_start: 0.8357 (p0) cc_final: 0.8138 (p0) REVERT: L 153 ASP cc_start: 0.7684 (m-30) cc_final: 0.7061 (m-30) REVERT: a 29 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: a 48 LEU cc_start: 0.8731 (mt) cc_final: 0.8525 (mt) REVERT: a 72 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7771 (t0) REVERT: a 108 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8051 (t0) REVERT: a 120 MET cc_start: 0.9064 (mtp) cc_final: 0.8863 (mtp) REVERT: a 152 ASP cc_start: 0.8036 (t0) cc_final: 0.7780 (t0) REVERT: a 212 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8440 (mt) REVERT: b 72 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7662 (t0) REVERT: b 147 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8138 (mmm-85) REVERT: b 161 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6753 (mmtp) REVERT: b 188 GLU cc_start: 0.7504 (tp30) cc_final: 0.7089 (tp30) REVERT: b 191 THR cc_start: 0.8266 (m) cc_final: 0.7665 (p) REVERT: c 90 ASP cc_start: 0.7032 (m-30) cc_final: 0.6688 (m-30) REVERT: c 115 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7363 (mtp180) REVERT: c 152 ASP cc_start: 0.7808 (t0) cc_final: 0.7592 (t0) REVERT: c 184 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6977 (mm) REVERT: c 191 THR cc_start: 0.8450 (m) cc_final: 0.7852 (p) REVERT: d 49 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7491 (pp) REVERT: d 120 MET cc_start: 0.9066 (mtp) cc_final: 0.8361 (mtp) REVERT: d 125 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8160 (tp40) REVERT: d 180 TYR cc_start: 0.7413 (t80) cc_final: 0.6702 (t80) REVERT: e 49 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7326 (pp) REVERT: e 184 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7205 (mm) REVERT: f 68 GLN cc_start: 0.7769 (mp10) cc_final: 0.7503 (mp10) REVERT: f 94 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (mm) REVERT: f 120 MET cc_start: 0.9026 (mtp) cc_final: 0.8695 (mtm) REVERT: f 125 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8418 (tp40) REVERT: f 161 LYS cc_start: 0.7429 (mttm) cc_final: 0.7177 (mtmt) REVERT: f 180 TYR cc_start: 0.7439 (t80) cc_final: 0.7025 (t80) REVERT: f 191 THR cc_start: 0.8352 (m) cc_final: 0.8135 (m) REVERT: f 222 ARG cc_start: 0.7721 (ptm-80) cc_final: 0.7477 (ttp-110) REVERT: g 49 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7566 (mt) REVERT: g 72 ASP cc_start: 0.7877 (m-30) cc_final: 0.7655 (m-30) REVERT: g 125 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8483 (tp-100) REVERT: g 180 TYR cc_start: 0.7571 (t80) cc_final: 0.7261 (t80) outliers start: 433 outliers final: 153 residues processed: 1687 average time/residue: 1.2772 time to fit residues: 2787.9095 Evaluate side-chains 1424 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1215 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 59 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 96 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 177 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 182 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 165 ARG Chi-restraints excluded: chain V residue 177 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 93 MET Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 140 SER Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 177 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 84 SER Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 177 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 29 GLU Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 212 ILE Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 142 ASP Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 212 ILE Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 184 LEU Chi-restraints excluded: chain e residue 212 ILE Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain f residue 125 GLN Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 125 GLN Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 555 optimal weight: 3.9990 chunk 454 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 668 optimal weight: 6.9990 chunk 722 optimal weight: 2.9990 chunk 595 optimal weight: 0.0770 chunk 663 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 536 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 98 GLN C 108 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS R 72 GLN R 79 HIS S 79 HIS T 59 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN 1 30 ASN 1 89 GLN N 88 ASN 2 73 ASN 2 141 GLN H 30 ASN H 36 GLN V 89 GLN V 141 GLN J 30 ASN J 88 ASN X 69 GLN X 141 GLN Y 30 ASN L 36 GLN a 23 GLN a 97 GLN a 98 GLN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 GLN b 98 GLN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 23 GLN ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 GLN d 98 GLN ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 ASN ** f 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 23 GLN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 59129 Z= 0.254 Angle : 0.649 13.810 79856 Z= 0.350 Chirality : 0.044 0.241 9338 Planarity : 0.004 0.061 10255 Dihedral : 6.166 55.144 8347 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.22 % Rotamer: Outliers : 7.08 % Allowed : 20.84 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 7462 helix: 1.55 (0.09), residues: 3430 sheet: -0.85 (0.12), residues: 1421 loop : -1.94 (0.10), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 28 HIS 0.010 0.002 HIS S 79 PHE 0.027 0.002 PHE e 42 TYR 0.022 0.002 TYR K 184 ARG 0.012 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 443 poor density : 1312 time to evaluate : 5.135 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: A 99 GLU cc_start: 0.7834 (tp30) cc_final: 0.7561 (mm-30) REVERT: A 177 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: A 187 LYS cc_start: 0.7819 (tttt) cc_final: 0.7584 (mmmt) REVERT: A 231 LYS cc_start: 0.8140 (mtpm) cc_final: 0.7848 (tttm) REVERT: B 94 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 187 LYS cc_start: 0.8248 (tttp) cc_final: 0.7811 (mptp) REVERT: C 177 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: C 208 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7673 (ttmt) REVERT: C 231 LYS cc_start: 0.7866 (mtpm) cc_final: 0.7246 (ttpp) REVERT: D 40 MET cc_start: 0.8513 (ptp) cc_final: 0.8058 (ptp) REVERT: D 56 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7827 (t) REVERT: D 178 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7428 (ptp90) REVERT: E 28 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7741 (mtp-110) REVERT: E 40 MET cc_start: 0.8261 (ptt) cc_final: 0.7890 (ptp) REVERT: E 78 THR cc_start: 0.8411 (p) cc_final: 0.8166 (p) REVERT: F 94 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8604 (mp) REVERT: F 103 TYR cc_start: 0.8837 (m-80) cc_final: 0.8378 (m-80) REVERT: F 118 ASP cc_start: 0.8544 (m-30) cc_final: 0.8092 (m-30) REVERT: F 187 LYS cc_start: 0.8115 (tttt) cc_final: 0.7826 (mmtt) REVERT: F 208 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7678 (mtmt) REVERT: F 211 GLU cc_start: 0.7679 (pt0) cc_final: 0.7421 (pt0) REVERT: G 118 ASP cc_start: 0.8423 (m-30) cc_final: 0.7878 (m-30) REVERT: G 198 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: G 208 LYS cc_start: 0.8312 (mtpt) cc_final: 0.8012 (mtmm) REVERT: O 37 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: O 204 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7545 (mtt) REVERT: P 16 TYR cc_start: 0.7244 (m-10) cc_final: 0.7025 (m-10) REVERT: P 18 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7779 (tp30) REVERT: P 142 MET cc_start: 0.8220 (mmt) cc_final: 0.7967 (mpt) REVERT: P 221 GLN cc_start: 0.8099 (mp10) cc_final: 0.7872 (mp10) REVERT: Q 82 TYR cc_start: 0.8662 (t80) cc_final: 0.8409 (t80) REVERT: Q 204 MET cc_start: 0.7427 (mtm) cc_final: 0.7093 (mtt) REVERT: Q 221 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: R 86 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8464 (mm-30) REVERT: R 101 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: R 154 THR cc_start: 0.8480 (m) cc_final: 0.8250 (p) REVERT: S 119 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7513 (mt-10) REVERT: S 125 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7569 (tp) REVERT: S 140 ILE cc_start: 0.7844 (pt) cc_final: 0.7639 (pt) REVERT: T 204 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7484 (mtt) REVERT: U 100 LYS cc_start: 0.8773 (mttm) cc_final: 0.8491 (mttt) REVERT: U 185 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8415 (tp40) REVERT: Z 26 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7564 (pt) REVERT: Z 96 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7234 (mtp) REVERT: Z 146 MET cc_start: 0.8614 (mtt) cc_final: 0.8213 (mtm) REVERT: M 93 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.4424 (pmt) REVERT: M 153 ASP cc_start: 0.7877 (m-30) cc_final: 0.7528 (m-30) REVERT: 1 17 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: 1 51 ASP cc_start: 0.8279 (m-30) cc_final: 0.8043 (m-30) REVERT: 1 96 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7776 (mtp) REVERT: 1 122 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: N 96 MET cc_start: 0.7632 (mpp) cc_final: 0.7419 (mtm) REVERT: N 153 ASP cc_start: 0.7826 (m-30) cc_final: 0.7526 (m-30) REVERT: 2 21 THR cc_start: 0.4537 (OUTLIER) cc_final: 0.4132 (t) REVERT: 2 93 MET cc_start: 0.6806 (pmm) cc_final: 0.6397 (pmm) REVERT: H 96 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7298 (mtp) REVERT: H 149 ASP cc_start: 0.6981 (p0) cc_final: 0.6445 (p0) REVERT: H 153 ASP cc_start: 0.7884 (m-30) cc_final: 0.7478 (m-30) REVERT: V 26 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7291 (pt) REVERT: V 51 ASP cc_start: 0.8367 (m-30) cc_final: 0.8076 (m-30) REVERT: V 96 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7813 (mtp) REVERT: V 139 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7736 (mm-30) REVERT: V 144 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: V 165 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7904 (mmt-90) REVERT: V 172 MET cc_start: 0.7569 (tpt) cc_final: 0.7360 (tpp) REVERT: I 67 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7579 (ttp-110) REVERT: I 93 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.4194 (pmt) REVERT: I 114 ASP cc_start: 0.8203 (p0) cc_final: 0.7990 (p0) REVERT: I 153 ASP cc_start: 0.7678 (m-30) cc_final: 0.7251 (m-30) REVERT: W 93 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6251 (pmm) REVERT: W 173 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8591 (mt) REVERT: J 77 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: J 93 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.4942 (mpp) REVERT: J 105 ASP cc_start: 0.8319 (p0) cc_final: 0.7912 (p0) REVERT: J 172 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: J 180 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.7879 (tpp-160) REVERT: X 26 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7381 (pt) REVERT: X 30 ASN cc_start: 0.8146 (t0) cc_final: 0.7839 (t0) REVERT: X 51 ASP cc_start: 0.8220 (m-30) cc_final: 0.7953 (m-30) REVERT: K 96 MET cc_start: 0.7732 (mpp) cc_final: 0.7493 (mtm) REVERT: K 153 ASP cc_start: 0.7735 (m-30) cc_final: 0.7414 (m-30) REVERT: Y 51 ASP cc_start: 0.8279 (m-30) cc_final: 0.8037 (m-30) REVERT: Y 59 MET cc_start: 0.8322 (mmp) cc_final: 0.8069 (mmp) REVERT: L 26 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7515 (pt) REVERT: L 67 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7996 (ttp-110) REVERT: L 71 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7807 (mtm110) REVERT: L 77 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: L 93 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.4556 (mpp) REVERT: L 105 ASP cc_start: 0.8280 (p0) cc_final: 0.8020 (p0) REVERT: L 153 ASP cc_start: 0.7665 (m-30) cc_final: 0.7037 (m-30) REVERT: a 72 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7655 (t0) REVERT: a 184 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7150 (mm) REVERT: b 72 ASP cc_start: 0.7893 (t0) cc_final: 0.7628 (t0) REVERT: b 120 MET cc_start: 0.8955 (mtp) cc_final: 0.8704 (mtp) REVERT: b 161 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7006 (mmtp) REVERT: b 188 GLU cc_start: 0.7452 (tp30) cc_final: 0.7052 (tp30) REVERT: b 191 THR cc_start: 0.8119 (m) cc_final: 0.7560 (p) REVERT: c 90 ASP cc_start: 0.7013 (m-30) cc_final: 0.6632 (m-30) REVERT: c 180 TYR cc_start: 0.7592 (t80) cc_final: 0.7132 (t80) REVERT: d 120 MET cc_start: 0.8954 (mtp) cc_final: 0.8436 (mtp) REVERT: d 125 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: d 198 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7792 (tptt) REVERT: e 100 LYS cc_start: 0.8565 (mptm) cc_final: 0.8354 (ttmm) REVERT: f 68 GLN cc_start: 0.7740 (mp10) cc_final: 0.7529 (mp10) REVERT: f 94 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9006 (mm) REVERT: f 120 MET cc_start: 0.8818 (mtp) cc_final: 0.8614 (mtt) REVERT: f 161 LYS cc_start: 0.7360 (mttm) cc_final: 0.7079 (mtmt) REVERT: f 178 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7714 (ttm110) REVERT: f 180 TYR cc_start: 0.7371 (t80) cc_final: 0.7048 (t80) REVERT: f 191 THR cc_start: 0.8372 (m) cc_final: 0.8164 (m) REVERT: f 208 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4818 (mtmm) REVERT: f 212 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (tp) REVERT: g 125 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: g 180 TYR cc_start: 0.7336 (t80) cc_final: 0.7110 (t80) outliers start: 443 outliers final: 185 residues processed: 1578 average time/residue: 1.2342 time to fit residues: 2534.5471 Evaluate side-chains 1412 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1182 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 100 LYS Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 79 HIS Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 17 GLU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 96 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 165 ARG Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 93 MET Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 144 GLU Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain a residue 72 ASP Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 201 LEU Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 208 LYS Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 125 GLN Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 212 ILE Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 3.9990 chunk 502 optimal weight: 4.9990 chunk 347 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 449 optimal weight: 0.9990 chunk 671 optimal weight: 9.9990 chunk 710 optimal weight: 0.6980 chunk 350 optimal weight: 0.9990 chunk 636 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS S 79 HIS S 99 HIS T 59 GLN T 75 GLN T 79 HIS U 79 HIS ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN M 30 ASN 1 88 ASN 1 89 GLN N 88 ASN 2 141 GLN H 30 ASN H 36 GLN V 89 GLN I 88 ASN J 30 ASN X 141 GLN Y 30 ASN L 36 GLN L 88 ASN ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 108 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 23 GLN e 98 GLN ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 ASN f 121 GLN f 125 GLN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59129 Z= 0.201 Angle : 0.617 13.506 79856 Z= 0.331 Chirality : 0.043 0.228 9338 Planarity : 0.004 0.062 10255 Dihedral : 5.711 52.632 8332 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.11 % Rotamer: Outliers : 6.41 % Allowed : 23.23 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.09), residues: 7462 helix: 2.00 (0.09), residues: 3423 sheet: -0.70 (0.12), residues: 1421 loop : -1.80 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 28 HIS 0.018 0.002 HIS S 79 PHE 0.028 0.002 PHE e 42 TYR 0.026 0.002 TYR J 66 ARG 0.007 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1261 time to evaluate : 5.133 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: A 99 GLU cc_start: 0.7745 (tp30) cc_final: 0.7521 (mm-30) REVERT: A 177 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: A 187 LYS cc_start: 0.7756 (tttt) cc_final: 0.7536 (mmmt) REVERT: A 231 LYS cc_start: 0.8136 (mtpm) cc_final: 0.7877 (tttm) REVERT: B 94 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 231 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8408 (ptmm) REVERT: C 94 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8655 (mp) REVERT: C 177 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: C 208 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7906 (mtmm) REVERT: C 231 LYS cc_start: 0.7765 (mtpm) cc_final: 0.7343 (ttpp) REVERT: D 40 MET cc_start: 0.8491 (ptp) cc_final: 0.8134 (ptp) REVERT: D 94 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8475 (mp) REVERT: D 98 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: D 178 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7473 (ptp90) REVERT: E 28 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7690 (mtp-110) REVERT: E 40 MET cc_start: 0.8196 (ptt) cc_final: 0.7825 (ptp) REVERT: E 55 ARG cc_start: 0.7440 (pmm-80) cc_final: 0.7171 (ptp-170) REVERT: F 94 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8611 (mp) REVERT: F 103 TYR cc_start: 0.8878 (m-80) cc_final: 0.8360 (m-80) REVERT: F 208 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7705 (mtmt) REVERT: G 118 ASP cc_start: 0.8463 (m-30) cc_final: 0.7920 (m-30) REVERT: G 208 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7975 (mtmm) REVERT: G 211 GLU cc_start: 0.7517 (pt0) cc_final: 0.7276 (pt0) REVERT: O 59 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: O 90 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8284 (m) REVERT: O 140 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7453 (pt) REVERT: O 204 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: P 16 TYR cc_start: 0.7228 (m-10) cc_final: 0.6966 (m-10) REVERT: P 18 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7709 (tp30) REVERT: P 51 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7549 (ttp80) REVERT: P 77 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (tp) REVERT: P 142 MET cc_start: 0.8138 (mmt) cc_final: 0.7859 (mpt) REVERT: Q 61 GLU cc_start: 0.7834 (tp30) cc_final: 0.7590 (tp30) REVERT: Q 204 MET cc_start: 0.7434 (mtm) cc_final: 0.7071 (mtt) REVERT: Q 221 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: R 101 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: R 232 ARG cc_start: 0.7166 (ptt90) cc_final: 0.6608 (mtm180) REVERT: S 119 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7398 (mt-10) REVERT: S 140 ILE cc_start: 0.7860 (pt) cc_final: 0.7596 (pt) REVERT: S 191 MET cc_start: 0.9026 (mmm) cc_final: 0.8677 (mmp) REVERT: T 204 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7469 (mtt) REVERT: U 119 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7488 (mt-10) REVERT: U 185 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8488 (tp40) REVERT: U 204 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: Z 96 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7260 (mtp) REVERT: Z 146 MET cc_start: 0.8561 (mtt) cc_final: 0.8231 (mtm) REVERT: Z 150 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: M 27 MET cc_start: 0.8696 (ttt) cc_final: 0.8441 (ttt) REVERT: M 38 ASP cc_start: 0.8160 (t70) cc_final: 0.7628 (t70) REVERT: M 43 MET cc_start: 0.7996 (ttm) cc_final: 0.7728 (ptp) REVERT: M 74 MET cc_start: 0.8017 (ttm) cc_final: 0.7749 (ttp) REVERT: M 93 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.4349 (pmt) REVERT: M 105 ASP cc_start: 0.8297 (p0) cc_final: 0.7956 (p0) REVERT: M 153 ASP cc_start: 0.7849 (m-30) cc_final: 0.7534 (m-30) REVERT: M 173 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8411 (mt) REVERT: 1 51 ASP cc_start: 0.8236 (m-30) cc_final: 0.7976 (m-30) REVERT: 1 96 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: 1 122 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: N 96 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: N 114 ASP cc_start: 0.8475 (p0) cc_final: 0.8271 (p0) REVERT: N 120 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8854 (t) REVERT: N 153 ASP cc_start: 0.7904 (m-30) cc_final: 0.7592 (m-30) REVERT: 2 21 THR cc_start: 0.4546 (OUTLIER) cc_final: 0.4123 (t) REVERT: 2 93 MET cc_start: 0.6809 (pmm) cc_final: 0.6350 (pmm) REVERT: H 38 ASP cc_start: 0.8028 (t70) cc_final: 0.7407 (t0) REVERT: H 96 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: H 153 ASP cc_start: 0.7873 (m-30) cc_final: 0.7476 (m-30) REVERT: V 51 ASP cc_start: 0.8358 (m-30) cc_final: 0.8067 (m-30) REVERT: V 96 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7778 (mtp) REVERT: V 172 MET cc_start: 0.7632 (tpt) cc_final: 0.7428 (tpp) REVERT: I 67 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7678 (ttp-110) REVERT: I 93 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4237 (pmt) REVERT: I 114 ASP cc_start: 0.8191 (p0) cc_final: 0.7983 (p0) REVERT: I 153 ASP cc_start: 0.7676 (m-30) cc_final: 0.7240 (m-30) REVERT: W 17 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.5754 (pp20) REVERT: W 71 ARG cc_start: 0.7351 (mtm110) cc_final: 0.7051 (mtm-85) REVERT: W 93 MET cc_start: 0.6709 (pmm) cc_final: 0.6423 (pmm) REVERT: J 77 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: J 93 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.4886 (mpp) REVERT: J 139 GLU cc_start: 0.8137 (tp30) cc_final: 0.7898 (mm-30) REVERT: J 146 MET cc_start: 0.8940 (mtm) cc_final: 0.8718 (mtp) REVERT: X 6 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8876 (pt) REVERT: X 26 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7321 (pt) REVERT: X 51 ASP cc_start: 0.8218 (m-30) cc_final: 0.7943 (m-30) REVERT: X 156 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8597 (mm) REVERT: X 177 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8676 (m) REVERT: K 96 MET cc_start: 0.7723 (mpp) cc_final: 0.7476 (mtm) REVERT: K 153 ASP cc_start: 0.7730 (m-30) cc_final: 0.7406 (m-30) REVERT: Y 45 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6759 (mm) REVERT: Y 51 ASP cc_start: 0.8264 (m-30) cc_final: 0.8061 (m-30) REVERT: Y 138 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8231 (tp) REVERT: L 26 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7438 (pt) REVERT: L 67 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7989 (ttp-110) REVERT: L 74 MET cc_start: 0.8076 (ttm) cc_final: 0.7788 (ttp) REVERT: L 77 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: L 105 ASP cc_start: 0.8264 (p0) cc_final: 0.8032 (p0) REVERT: L 153 ASP cc_start: 0.7640 (m-30) cc_final: 0.7035 (m-30) REVERT: a 184 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (mm) REVERT: a 222 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7649 (ttp80) REVERT: b 53 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5746 (ptpp) REVERT: b 72 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7608 (t0) REVERT: b 144 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8049 (mp) REVERT: b 161 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6596 (mmpt) REVERT: b 182 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6718 (tp30) REVERT: b 208 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.4750 (mmmm) REVERT: c 90 ASP cc_start: 0.7008 (m-30) cc_final: 0.6607 (m-30) REVERT: c 120 MET cc_start: 0.8948 (mtp) cc_final: 0.8737 (mtm) REVERT: c 180 TYR cc_start: 0.7374 (t80) cc_final: 0.6847 (t80) REVERT: c 197 LEU cc_start: 0.8209 (tp) cc_final: 0.7990 (tt) REVERT: d 120 MET cc_start: 0.8870 (mtp) cc_final: 0.8565 (mtp) REVERT: d 125 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: d 198 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7809 (tptt) REVERT: e 208 LYS cc_start: 0.5356 (OUTLIER) cc_final: 0.5026 (mtmm) REVERT: f 53 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.4631 (ptmm) REVERT: f 94 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9019 (mm) REVERT: f 161 LYS cc_start: 0.7452 (mttm) cc_final: 0.7225 (mtmt) REVERT: f 208 LYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4737 (mtmm) REVERT: f 212 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8321 (tp) REVERT: f 228 GLU cc_start: 0.6982 (tp30) cc_final: 0.6749 (tp30) REVERT: g 100 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (mmtp) REVERT: g 152 ASP cc_start: 0.7940 (t0) cc_final: 0.7392 (t0) REVERT: g 188 GLU cc_start: 0.7222 (tp30) cc_final: 0.6955 (tp30) REVERT: g 191 THR cc_start: 0.8219 (m) cc_final: 0.7778 (p) outliers start: 401 outliers final: 173 residues processed: 1504 average time/residue: 1.2326 time to fit residues: 2413.1300 Evaluate side-chains 1397 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1168 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain O residue 59 GLN Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 122 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 223 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 96 MET Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 217 VAL Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 208 LYS Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 100 LYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 1.9990 chunk 403 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 528 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 606 optimal weight: 0.9990 chunk 491 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 637 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN G 122 GLN O 79 HIS P 72 GLN P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS T 59 GLN T 75 GLN T 79 HIS U 79 HIS ** U 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN M 30 ASN N 88 ASN 2 141 GLN V 89 GLN V 141 GLN I 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN K 88 ASN L 36 GLN L 88 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 ASN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59129 Z= 0.227 Angle : 0.617 13.679 79856 Z= 0.330 Chirality : 0.043 0.244 9338 Planarity : 0.004 0.050 10255 Dihedral : 5.602 52.754 8329 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 6.97 % Allowed : 23.03 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 7462 helix: 2.18 (0.09), residues: 3416 sheet: -0.64 (0.12), residues: 1421 loop : -1.66 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 28 HIS 0.011 0.002 HIS R 79 PHE 0.029 0.002 PHE g 42 TYR 0.022 0.002 TYR K 184 ARG 0.008 0.000 ARG Z 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1226 time to evaluate : 5.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7769 (tp30) cc_final: 0.7530 (mm-30) REVERT: B 94 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 231 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8268 (ptpp) REVERT: C 94 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8563 (mp) REVERT: C 208 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7961 (mtmm) REVERT: C 231 LYS cc_start: 0.7618 (mtpm) cc_final: 0.7399 (ttpp) REVERT: D 40 MET cc_start: 0.8577 (ptp) cc_final: 0.8136 (ptp) REVERT: D 52 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7861 (ptpt) REVERT: D 94 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8373 (mp) REVERT: D 98 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: E 40 MET cc_start: 0.8266 (ptt) cc_final: 0.7892 (ptp) REVERT: E 100 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8366 (mttt) REVERT: F 93 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8146 (mtt-85) REVERT: F 94 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8614 (mp) REVERT: F 103 TYR cc_start: 0.8934 (m-80) cc_final: 0.8428 (m-80) REVERT: G 52 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8036 (ptpp) REVERT: G 118 ASP cc_start: 0.8490 (m-30) cc_final: 0.7946 (m-30) REVERT: G 208 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7896 (mtmm) REVERT: O 51 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6453 (tpp80) REVERT: O 90 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8272 (m) REVERT: O 204 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: P 16 TYR cc_start: 0.7169 (m-10) cc_final: 0.6902 (m-10) REVERT: P 18 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7543 (tp30) REVERT: P 51 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7518 (ttp80) REVERT: P 77 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8914 (tp) REVERT: P 142 MET cc_start: 0.8263 (mmt) cc_final: 0.7985 (mpt) REVERT: P 232 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6298 (ptt90) REVERT: Q 61 GLU cc_start: 0.7896 (tp30) cc_final: 0.7686 (tp30) REVERT: Q 204 MET cc_start: 0.7437 (mtm) cc_final: 0.7218 (mtt) REVERT: Q 221 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: R 51 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7118 (ttp-170) REVERT: R 101 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: R 232 ARG cc_start: 0.7067 (ptt90) cc_final: 0.6553 (mtm180) REVERT: S 41 LYS cc_start: 0.7956 (mptt) cc_final: 0.7754 (mptt) REVERT: S 119 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7418 (mt-10) REVERT: S 140 ILE cc_start: 0.7772 (pt) cc_final: 0.7568 (pt) REVERT: S 191 MET cc_start: 0.8917 (mmm) cc_final: 0.8705 (mmp) REVERT: T 204 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7472 (mtt) REVERT: T 217 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8355 (mmmm) REVERT: U 51 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7109 (ttp-170) REVERT: U 119 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7492 (mt-10) REVERT: U 185 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (tp40) REVERT: U 204 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7606 (mtt) REVERT: Z 26 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7504 (pt) REVERT: Z 96 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7273 (mtp) REVERT: Z 150 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: M 27 MET cc_start: 0.8743 (ttt) cc_final: 0.8541 (ttt) REVERT: M 38 ASP cc_start: 0.8124 (t70) cc_final: 0.7540 (t70) REVERT: M 74 MET cc_start: 0.8107 (ttm) cc_final: 0.7793 (ttp) REVERT: M 77 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: M 93 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.4176 (pmt) REVERT: M 153 ASP cc_start: 0.7780 (m-30) cc_final: 0.7467 (m-30) REVERT: M 173 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8422 (mt) REVERT: 1 26 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7377 (pt) REVERT: 1 51 ASP cc_start: 0.8271 (m-30) cc_final: 0.7978 (m-30) REVERT: 1 122 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: 1 152 VAL cc_start: 0.8494 (p) cc_final: 0.8177 (t) REVERT: N 38 ASP cc_start: 0.7992 (t70) cc_final: 0.7350 (t0) REVERT: N 96 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7459 (mtm) REVERT: N 153 ASP cc_start: 0.7864 (m-30) cc_final: 0.7574 (m-30) REVERT: 2 21 THR cc_start: 0.4537 (OUTLIER) cc_final: 0.4162 (t) REVERT: 2 93 MET cc_start: 0.6716 (pmm) cc_final: 0.6272 (pmm) REVERT: 2 150 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: H 33 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: H 38 ASP cc_start: 0.7943 (t70) cc_final: 0.7348 (t0) REVERT: H 96 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7205 (mtp) REVERT: H 153 ASP cc_start: 0.7887 (m-30) cc_final: 0.7481 (m-30) REVERT: V 51 ASP cc_start: 0.8393 (m-30) cc_final: 0.8117 (m-30) REVERT: V 71 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7321 (mtm110) REVERT: V 96 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7764 (mpp) REVERT: V 106 THR cc_start: 0.8688 (p) cc_final: 0.8319 (m) REVERT: I 21 THR cc_start: 0.4207 (OUTLIER) cc_final: 0.4003 (t) REVERT: I 93 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.4250 (pmt) REVERT: I 153 ASP cc_start: 0.7680 (m-30) cc_final: 0.7255 (m-30) REVERT: W 55 LEU cc_start: 0.8692 (mm) cc_final: 0.8472 (tp) REVERT: W 71 ARG cc_start: 0.7400 (mtm110) cc_final: 0.7151 (mtm110) REVERT: W 86 MET cc_start: 0.7978 (ttm) cc_final: 0.7763 (ttm) REVERT: W 90 VAL cc_start: 0.8546 (p) cc_final: 0.8285 (p) REVERT: W 105 ASP cc_start: 0.8378 (p0) cc_final: 0.7959 (p0) REVERT: W 122 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: J 77 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: J 105 ASP cc_start: 0.8472 (p0) cc_final: 0.8268 (p0) REVERT: J 139 GLU cc_start: 0.8135 (tp30) cc_final: 0.7903 (mm-30) REVERT: J 146 MET cc_start: 0.9030 (mtm) cc_final: 0.8767 (mtp) REVERT: J 186 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: X 6 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8919 (pt) REVERT: X 26 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7328 (pt) REVERT: X 51 ASP cc_start: 0.8236 (m-30) cc_final: 0.7977 (m-30) REVERT: X 122 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: X 177 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (m) REVERT: K 74 MET cc_start: 0.8071 (ttp) cc_final: 0.7742 (ttp) REVERT: K 96 MET cc_start: 0.7742 (mpp) cc_final: 0.7493 (mtm) REVERT: K 153 ASP cc_start: 0.7782 (m-30) cc_final: 0.7458 (m-30) REVERT: Y 45 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6845 (mm) REVERT: Y 51 ASP cc_start: 0.8309 (m-30) cc_final: 0.8085 (m-30) REVERT: Y 165 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8208 (tpp-160) REVERT: L 26 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7462 (pt) REVERT: L 67 ARG cc_start: 0.8335 (ttm110) cc_final: 0.7956 (ttp-110) REVERT: L 77 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: L 105 ASP cc_start: 0.8293 (p0) cc_final: 0.7987 (p0) REVERT: L 153 ASP cc_start: 0.7708 (m-30) cc_final: 0.7081 (m-30) REVERT: a 184 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7333 (mm) REVERT: a 222 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7767 (ttp80) REVERT: b 53 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5869 (ptpp) REVERT: b 72 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7569 (t0) REVERT: b 126 TYR cc_start: 0.7305 (m-80) cc_final: 0.7073 (m-80) REVERT: b 144 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7951 (mp) REVERT: b 161 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6693 (mmpt) REVERT: b 182 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6724 (tp30) REVERT: b 208 LYS cc_start: 0.5541 (OUTLIER) cc_final: 0.4919 (mmmm) REVERT: c 47 LEU cc_start: 0.8671 (pp) cc_final: 0.8458 (pp) REVERT: c 90 ASP cc_start: 0.7004 (m-30) cc_final: 0.6577 (m-30) REVERT: c 120 MET cc_start: 0.8945 (mtp) cc_final: 0.8735 (mtm) REVERT: c 180 TYR cc_start: 0.7343 (t80) cc_final: 0.6904 (t80) REVERT: d 120 MET cc_start: 0.8817 (mtp) cc_final: 0.8489 (mtp) REVERT: d 198 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7907 (tptt) REVERT: e 208 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5338 (mtmm) REVERT: f 53 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.4662 (ptmm) REVERT: f 94 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9031 (mm) REVERT: f 161 LYS cc_start: 0.7559 (mttm) cc_final: 0.7207 (mtmt) REVERT: f 208 LYS cc_start: 0.4901 (OUTLIER) cc_final: 0.4584 (mtmm) REVERT: f 212 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8286 (tp) REVERT: f 228 GLU cc_start: 0.6993 (tp30) cc_final: 0.6765 (tp30) REVERT: g 100 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8361 (mmtp) REVERT: g 152 ASP cc_start: 0.7836 (t0) cc_final: 0.7351 (t0) REVERT: g 191 THR cc_start: 0.8316 (m) cc_final: 0.7883 (p) outliers start: 436 outliers final: 212 residues processed: 1500 average time/residue: 1.2646 time to fit residues: 2457.3116 Evaluate side-chains 1457 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1183 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 225 ASP Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 223 ARG Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 51 ARG Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 96 MET Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 150 GLU Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 51 ASP Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 208 LYS Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 100 LYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 201 LEU Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 7.9990 chunk 639 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 417 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 711 optimal weight: 7.9990 chunk 590 optimal weight: 0.8980 chunk 329 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 235 optimal weight: 3.9990 chunk 373 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN O 79 HIS P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 79 HIS Q 84 GLN R 79 HIS T 47 HIS T 59 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN N 88 ASN 2 141 GLN H 36 GLN V 89 GLN V 141 GLN I 88 ASN J 30 ASN J 88 ASN K 141 GLN L 36 GLN L 88 ASN a 108 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 121 GLN ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 108 ASN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 59129 Z= 0.275 Angle : 0.640 13.779 79856 Z= 0.341 Chirality : 0.044 0.300 9338 Planarity : 0.004 0.049 10255 Dihedral : 5.664 54.496 8329 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.85 % Favored : 95.99 % Rotamer: Outliers : 7.43 % Allowed : 23.12 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 7462 helix: 2.15 (0.09), residues: 3444 sheet: -0.59 (0.13), residues: 1421 loop : -1.57 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 28 HIS 0.012 0.002 HIS R 79 PHE 0.030 0.002 PHE g 42 TYR 0.024 0.002 TYR K 184 ARG 0.013 0.001 ARG Z 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 465 poor density : 1231 time to evaluate : 6.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7276 (pt0) cc_final: 0.7032 (pt0) REVERT: A 221 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7272 (t80) REVERT: B 94 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 221 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7216 (t80) REVERT: B 231 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8098 (ptpp) REVERT: C 68 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: C 72 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7322 (t0) REVERT: C 94 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 177 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 208 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7990 (mtmm) REVERT: C 219 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: D 40 MET cc_start: 0.8591 (ptp) cc_final: 0.8105 (ptp) REVERT: D 52 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7883 (ptpt) REVERT: D 56 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7849 (t) REVERT: D 94 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8516 (mp) REVERT: E 28 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7765 (mtp-110) REVERT: E 40 MET cc_start: 0.8316 (ptt) cc_final: 0.7960 (ptp) REVERT: E 100 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8361 (mttt) REVERT: E 221 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7300 (t80) REVERT: F 93 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8170 (mtt-85) REVERT: F 94 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8631 (mp) REVERT: F 103 TYR cc_start: 0.8949 (m-80) cc_final: 0.8482 (m-80) REVERT: G 52 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7950 (ptpp) REVERT: G 118 ASP cc_start: 0.8479 (m-30) cc_final: 0.7974 (m-30) REVERT: O 51 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: O 204 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7389 (mtt) REVERT: P 18 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7442 (tp30) REVERT: P 51 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7550 (ttp80) REVERT: P 77 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8916 (tp) REVERT: P 221 GLN cc_start: 0.8099 (mp10) cc_final: 0.7858 (mp10) REVERT: P 232 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6063 (ptt90) REVERT: Q 37 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: Q 204 MET cc_start: 0.7451 (mtm) cc_final: 0.7202 (mtt) REVERT: Q 221 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: R 55 TYR cc_start: 0.8191 (m-10) cc_final: 0.7841 (m-10) REVERT: R 101 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: R 232 ARG cc_start: 0.7260 (ptt90) cc_final: 0.6712 (mtm180) REVERT: S 34 GLN cc_start: 0.8663 (mp10) cc_final: 0.8340 (mp-120) REVERT: S 41 LYS cc_start: 0.8006 (mptt) cc_final: 0.7503 (mmtm) REVERT: S 119 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7358 (mt-10) REVERT: T 204 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7609 (mtt) REVERT: U 51 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7228 (ttp-170) REVERT: U 100 LYS cc_start: 0.8830 (mttm) cc_final: 0.8541 (mttp) REVERT: U 119 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7594 (mt-10) REVERT: U 185 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8383 (tp40) REVERT: Z 10 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6841 (t0) REVERT: Z 26 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7484 (pt) REVERT: Z 96 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7311 (mtp) REVERT: Z 105 ASP cc_start: 0.8345 (p0) cc_final: 0.8126 (p0) REVERT: Z 150 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: M 27 MET cc_start: 0.8822 (ttt) cc_final: 0.8464 (ttt) REVERT: M 38 ASP cc_start: 0.7984 (t70) cc_final: 0.7403 (t70) REVERT: M 74 MET cc_start: 0.8102 (ttm) cc_final: 0.7811 (ttp) REVERT: M 93 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.4289 (pmt) REVERT: M 153 ASP cc_start: 0.7800 (m-30) cc_final: 0.7484 (m-30) REVERT: 1 51 ASP cc_start: 0.8385 (m-30) cc_final: 0.8112 (m-30) REVERT: 1 122 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: 1 152 VAL cc_start: 0.8543 (p) cc_final: 0.8239 (t) REVERT: N 38 ASP cc_start: 0.7846 (t70) cc_final: 0.7279 (t0) REVERT: N 71 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7024 (mtt90) REVERT: N 96 MET cc_start: 0.7690 (mpp) cc_final: 0.7462 (mtm) REVERT: N 153 ASP cc_start: 0.7885 (m-30) cc_final: 0.7532 (m-30) REVERT: 2 21 THR cc_start: 0.4615 (OUTLIER) cc_final: 0.4263 (t) REVERT: 2 26 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7436 (pt) REVERT: 2 90 VAL cc_start: 0.8314 (p) cc_final: 0.8098 (p) REVERT: 2 93 MET cc_start: 0.6618 (pmm) cc_final: 0.6280 (pmm) REVERT: H 33 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8574 (mttp) REVERT: H 38 ASP cc_start: 0.7915 (t70) cc_final: 0.7357 (t0) REVERT: H 96 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7257 (mtp) REVERT: H 153 ASP cc_start: 0.7891 (m-30) cc_final: 0.7486 (m-30) REVERT: V 71 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7373 (mtm110) REVERT: V 96 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: V 106 THR cc_start: 0.8588 (p) cc_final: 0.8309 (m) REVERT: V 138 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8420 (mt) REVERT: V 139 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7855 (mm-30) REVERT: V 165 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7647 (mmt-90) REVERT: I 153 ASP cc_start: 0.7715 (m-30) cc_final: 0.7286 (m-30) REVERT: W 26 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7555 (pt) REVERT: W 71 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7206 (mtm110) REVERT: W 90 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8135 (p) REVERT: W 93 MET cc_start: 0.6729 (pmm) cc_final: 0.6310 (pmm) REVERT: W 105 ASP cc_start: 0.8435 (p0) cc_final: 0.8137 (p0) REVERT: W 122 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: W 124 TYR cc_start: 0.8905 (p90) cc_final: 0.8609 (p90) REVERT: W 145 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8241 (mmtm) REVERT: J 27 MET cc_start: 0.8858 (ttt) cc_final: 0.8640 (ttt) REVERT: J 77 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: J 139 GLU cc_start: 0.8132 (tp30) cc_final: 0.7882 (mm-30) REVERT: J 146 MET cc_start: 0.8988 (mtm) cc_final: 0.8745 (mtp) REVERT: J 186 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7901 (mm-40) REVERT: X 6 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8949 (pt) REVERT: X 51 ASP cc_start: 0.8416 (m-30) cc_final: 0.8170 (m-30) REVERT: X 96 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7763 (mtp) REVERT: X 122 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: X 177 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8660 (m) REVERT: K 96 MET cc_start: 0.7764 (mpp) cc_final: 0.7534 (mtm) REVERT: K 153 ASP cc_start: 0.7760 (m-30) cc_final: 0.7431 (m-30) REVERT: Y 10 ASP cc_start: 0.7135 (m-30) cc_final: 0.6916 (t70) REVERT: Y 51 ASP cc_start: 0.8369 (m-30) cc_final: 0.8105 (m-30) REVERT: Y 122 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7338 (m-30) REVERT: Y 138 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8275 (tp) REVERT: Y 165 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8232 (tpp-160) REVERT: L 22 MET cc_start: 0.1502 (OUTLIER) cc_final: 0.1111 (tmt) REVERT: L 26 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7555 (pt) REVERT: L 33 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8373 (mttp) REVERT: L 74 MET cc_start: 0.8179 (ttp) cc_final: 0.7896 (ttp) REVERT: L 77 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: L 105 ASP cc_start: 0.8436 (p0) cc_final: 0.8135 (p0) REVERT: L 153 ASP cc_start: 0.7720 (m-30) cc_final: 0.7080 (m-30) REVERT: a 108 ASN cc_start: 0.8590 (t0) cc_final: 0.8361 (t160) REVERT: a 142 ASP cc_start: 0.8497 (p0) cc_final: 0.8265 (p0) REVERT: a 222 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7711 (ttp80) REVERT: b 72 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7579 (t0) REVERT: b 161 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.6775 (mmpt) REVERT: b 179 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: b 182 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6913 (tp30) REVERT: b 208 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.4843 (mmmm) REVERT: c 12 ILE cc_start: 0.6454 (tp) cc_final: 0.6018 (tt) REVERT: c 90 ASP cc_start: 0.7006 (m-30) cc_final: 0.6563 (m-30) REVERT: c 125 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7946 (tp-100) REVERT: c 180 TYR cc_start: 0.7590 (t80) cc_final: 0.7126 (t80) REVERT: d 120 MET cc_start: 0.8834 (mtp) cc_final: 0.8511 (mtp) REVERT: e 150 ASP cc_start: 0.7932 (t70) cc_final: 0.7713 (t0) REVERT: e 208 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.5564 (mtmm) REVERT: f 94 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9033 (mm) REVERT: f 125 GLN cc_start: 0.8691 (tp40) cc_final: 0.8476 (tp40) REVERT: f 212 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8196 (tp) REVERT: f 228 GLU cc_start: 0.7044 (tp30) cc_final: 0.6803 (tp30) REVERT: g 142 ASP cc_start: 0.7742 (p0) cc_final: 0.7511 (p0) REVERT: g 152 ASP cc_start: 0.7853 (t0) cc_final: 0.7402 (t0) REVERT: g 191 THR cc_start: 0.8376 (m) cc_final: 0.7940 (p) outliers start: 465 outliers final: 251 residues processed: 1525 average time/residue: 1.2370 time to fit residues: 2458.9032 Evaluate side-chains 1492 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1176 time to evaluate : 4.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain G residue 225 ASP Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 51 ARG Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 51 ARG Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 10 ASP Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 123 ILE Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 165 ARG Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 145 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 122 ASP Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 SER Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain b residue 217 VAL Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 GLN Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 223 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 181 LYS Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 191 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 216 THR Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 405 optimal weight: 4.9990 chunk 519 optimal weight: 0.8980 chunk 402 optimal weight: 3.9990 chunk 598 optimal weight: 7.9990 chunk 397 optimal weight: 1.9990 chunk 708 optimal weight: 6.9990 chunk 443 optimal weight: 0.2980 chunk 431 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN G 122 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 79 HIS R 79 HIS T 47 HIS T 59 GLN T 75 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN N 88 ASN N 141 GLN 2 141 GLN H 36 GLN H 88 ASN H 89 GLN V 89 GLN V 141 GLN I 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN J 36 GLN J 88 ASN X 141 GLN K 141 GLN Y 30 ASN Y 88 ASN L 36 GLN L 88 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 59129 Z= 0.216 Angle : 0.613 13.467 79856 Z= 0.328 Chirality : 0.043 0.312 9338 Planarity : 0.004 0.052 10255 Dihedral : 5.511 53.991 8329 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 6.30 % Allowed : 24.90 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 7462 helix: 2.32 (0.09), residues: 3423 sheet: -0.64 (0.13), residues: 1463 loop : -1.49 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 28 HIS 0.013 0.001 HIS R 79 PHE 0.029 0.002 PHE g 42 TYR 0.024 0.001 TYR K 184 ARG 0.008 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 1210 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8681 (mp) REVERT: B 101 VAL cc_start: 0.8702 (m) cc_final: 0.8479 (t) REVERT: B 221 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7242 (t80) REVERT: B 231 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8152 (ptpp) REVERT: C 94 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8574 (mp) REVERT: C 177 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7862 (mm-30) REVERT: C 208 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: D 40 MET cc_start: 0.8542 (ptp) cc_final: 0.7978 (ptp) REVERT: D 52 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7849 (ptpt) REVERT: D 56 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (t) REVERT: D 94 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8434 (mp) REVERT: E 28 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7786 (mtp-110) REVERT: E 40 MET cc_start: 0.8264 (ptt) cc_final: 0.7880 (ptp) REVERT: E 81 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8621 (mt) REVERT: E 100 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (mttt) REVERT: E 221 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7252 (t80) REVERT: F 93 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8106 (mtt-85) REVERT: F 94 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8619 (mp) REVERT: F 103 TYR cc_start: 0.8952 (m-80) cc_final: 0.8461 (m-80) REVERT: F 178 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8377 (ttp-110) REVERT: F 198 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8583 (mtmm) REVERT: F 227 GLU cc_start: 0.7830 (pm20) cc_final: 0.7557 (pm20) REVERT: F 231 LYS cc_start: 0.8373 (ptpp) cc_final: 0.7562 (pttp) REVERT: G 118 ASP cc_start: 0.8490 (m-30) cc_final: 0.7976 (m-30) REVERT: O 51 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7431 (ttp-170) REVERT: O 59 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: O 204 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: P 77 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8906 (tp) REVERT: P 232 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6057 (ptt90) REVERT: Q 37 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: Q 204 MET cc_start: 0.7439 (mtm) cc_final: 0.7228 (mtt) REVERT: Q 221 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: R 55 TYR cc_start: 0.8232 (m-10) cc_final: 0.8031 (m-10) REVERT: R 101 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: R 232 ARG cc_start: 0.7174 (ptt90) cc_final: 0.6651 (mtm180) REVERT: S 18 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: S 41 LYS cc_start: 0.7954 (mptt) cc_final: 0.7511 (mmtm) REVERT: S 119 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7314 (mt-10) REVERT: S 204 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: T 160 LEU cc_start: 0.7595 (mt) cc_final: 0.7340 (mt) REVERT: T 204 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: U 100 LYS cc_start: 0.8819 (mttm) cc_final: 0.8445 (mttt) REVERT: U 125 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7733 (tp) REVERT: U 185 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: Z 26 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7473 (pt) REVERT: Z 96 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7339 (mtp) REVERT: M 27 MET cc_start: 0.8768 (ttt) cc_final: 0.8398 (ttt) REVERT: M 38 ASP cc_start: 0.7859 (t70) cc_final: 0.7355 (t70) REVERT: M 74 MET cc_start: 0.8145 (ttm) cc_final: 0.7848 (ttp) REVERT: M 93 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.4248 (pmt) REVERT: M 153 ASP cc_start: 0.7757 (m-30) cc_final: 0.7447 (m-30) REVERT: 1 26 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7403 (pt) REVERT: 1 51 ASP cc_start: 0.8300 (m-30) cc_final: 0.8050 (m-30) REVERT: 1 122 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6891 (m-30) REVERT: 1 124 TYR cc_start: 0.8817 (p90) cc_final: 0.8556 (p90) REVERT: 1 152 VAL cc_start: 0.8492 (p) cc_final: 0.8195 (t) REVERT: N 38 ASP cc_start: 0.7577 (t70) cc_final: 0.7049 (t0) REVERT: N 60 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8389 (mttp) REVERT: N 71 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7089 (mtt90) REVERT: N 122 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: N 153 ASP cc_start: 0.7923 (m-30) cc_final: 0.7631 (m-30) REVERT: 2 14 MET cc_start: 0.8687 (mtp) cc_final: 0.8414 (mtp) REVERT: 2 21 THR cc_start: 0.4094 (OUTLIER) cc_final: 0.3802 (t) REVERT: 2 26 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7274 (pt) REVERT: 2 71 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6940 (mtp180) REVERT: 2 90 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8013 (p) REVERT: 2 93 MET cc_start: 0.6607 (pmm) cc_final: 0.6210 (pmm) REVERT: H 33 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8565 (mttp) REVERT: H 38 ASP cc_start: 0.7860 (t70) cc_final: 0.7332 (t0) REVERT: H 153 ASP cc_start: 0.7891 (m-30) cc_final: 0.7495 (m-30) REVERT: V 71 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7377 (mtm110) REVERT: V 96 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7804 (mpp) REVERT: V 106 THR cc_start: 0.8588 (p) cc_final: 0.8320 (m) REVERT: V 138 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8395 (mt) REVERT: V 139 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7739 (mm-30) REVERT: V 172 MET cc_start: 0.7603 (tpt) cc_final: 0.7402 (tpp) REVERT: I 71 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7605 (mtt90) REVERT: I 79 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8342 (m) REVERT: I 153 ASP cc_start: 0.7676 (m-30) cc_final: 0.7269 (m-30) REVERT: W 26 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7460 (pt) REVERT: W 71 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7266 (mtm110) REVERT: W 90 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8075 (p) REVERT: W 93 MET cc_start: 0.6909 (pmm) cc_final: 0.6421 (pmm) REVERT: W 105 ASP cc_start: 0.8509 (p0) cc_final: 0.8102 (p0) REVERT: W 145 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8235 (mmtm) REVERT: J 77 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: J 139 GLU cc_start: 0.8115 (tp30) cc_final: 0.7904 (mm-30) REVERT: J 146 MET cc_start: 0.9008 (mtm) cc_final: 0.8762 (mtp) REVERT: J 186 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: X 26 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7387 (pt) REVERT: X 51 ASP cc_start: 0.8204 (m-30) cc_final: 0.7960 (m-30) REVERT: X 96 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7733 (mtp) REVERT: K 96 MET cc_start: 0.7731 (mpp) cc_final: 0.7497 (mtm) REVERT: K 153 ASP cc_start: 0.7730 (m-30) cc_final: 0.7405 (m-30) REVERT: Y 51 ASP cc_start: 0.8183 (m-30) cc_final: 0.7971 (m-30) REVERT: Y 122 ASP cc_start: 0.7367 (t0) cc_final: 0.7118 (m-30) REVERT: Y 165 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8187 (tpp-160) REVERT: L 22 MET cc_start: 0.1301 (OUTLIER) cc_final: 0.1021 (tmt) REVERT: L 26 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7377 (pt) REVERT: L 77 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: L 93 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4079 (mpp) REVERT: L 105 ASP cc_start: 0.8380 (p0) cc_final: 0.8032 (p0) REVERT: L 153 ASP cc_start: 0.7691 (m-30) cc_final: 0.7060 (m-30) REVERT: a 29 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: a 142 ASP cc_start: 0.8512 (p0) cc_final: 0.8280 (p0) REVERT: a 222 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.8129 (ttp-110) REVERT: b 72 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7572 (t0) REVERT: b 125 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7392 (tp-100) REVERT: b 188 GLU cc_start: 0.7441 (tp30) cc_final: 0.6990 (tp30) REVERT: b 191 THR cc_start: 0.8166 (m) cc_final: 0.7765 (p) REVERT: b 201 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7063 (mt) REVERT: b 208 LYS cc_start: 0.5459 (OUTLIER) cc_final: 0.5034 (mtmm) REVERT: c 12 ILE cc_start: 0.6333 (tp) cc_final: 0.5937 (tt) REVERT: c 90 ASP cc_start: 0.7001 (m-30) cc_final: 0.6570 (m-30) REVERT: c 125 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7993 (tp-100) REVERT: c 180 TYR cc_start: 0.7623 (t80) cc_final: 0.7301 (t80) REVERT: d 110 GLU cc_start: 0.7172 (pt0) cc_final: 0.6957 (pt0) REVERT: d 198 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7930 (tptt) REVERT: e 150 ASP cc_start: 0.7923 (t70) cc_final: 0.7699 (t0) REVERT: f 94 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9032 (mm) REVERT: f 201 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7238 (mt) REVERT: f 212 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8081 (tp) REVERT: f 228 GLU cc_start: 0.7045 (tp30) cc_final: 0.6763 (tm-30) REVERT: g 142 ASP cc_start: 0.7800 (p0) cc_final: 0.7535 (p0) REVERT: g 152 ASP cc_start: 0.7820 (t0) cc_final: 0.7363 (t0) REVERT: g 188 GLU cc_start: 0.7174 (tp30) cc_final: 0.6825 (tp30) REVERT: g 191 THR cc_start: 0.8384 (m) cc_final: 0.7979 (p) outliers start: 394 outliers final: 230 residues processed: 1456 average time/residue: 1.2310 time to fit residues: 2332.4974 Evaluate side-chains 1464 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1172 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 59 GLN Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain Q residue 223 ARG Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 96 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 71 ARG Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 29 GLU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 217 VAL Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 GLN Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 181 LYS Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 191 THR Chi-restraints excluded: chain f residue 201 LEU Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 216 THR Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 4.9990 chunk 282 optimal weight: 0.5980 chunk 423 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 450 optimal weight: 0.9990 chunk 482 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 556 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 HIS P 79 HIS Q 47 HIS Q 79 HIS R 79 HIS T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN M 89 GLN 2 109 HIS 2 141 GLN H 88 ASN H 89 GLN V 89 GLN V 141 GLN I 36 GLN I 88 ASN L 36 GLN L 88 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 59129 Z= 0.286 Angle : 0.648 14.654 79856 Z= 0.345 Chirality : 0.044 0.313 9338 Planarity : 0.004 0.054 10255 Dihedral : 5.645 55.296 8329 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 6.58 % Allowed : 25.09 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 7462 helix: 2.23 (0.09), residues: 3430 sheet: -0.51 (0.13), residues: 1421 loop : -1.39 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 28 HIS 0.013 0.002 HIS U 79 PHE 0.029 0.002 PHE d 42 TYR 0.023 0.002 TYR M 184 ARG 0.008 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1586 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 1174 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.7013 (t80) REVERT: B 94 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 187 LYS cc_start: 0.8258 (tttp) cc_final: 0.7838 (mptp) REVERT: B 221 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7232 (t80) REVERT: B 231 LYS cc_start: 0.8626 (ptmm) cc_final: 0.8150 (ptpp) REVERT: C 94 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8575 (mp) REVERT: C 177 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7808 (mm-30) REVERT: C 208 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8016 (mtmm) REVERT: D 40 MET cc_start: 0.8586 (ptp) cc_final: 0.8041 (ptp) REVERT: D 56 SER cc_start: 0.8090 (m) cc_final: 0.7859 (t) REVERT: D 94 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8535 (mp) REVERT: D 231 LYS cc_start: 0.8368 (ptpp) cc_final: 0.8120 (ptpp) REVERT: E 40 MET cc_start: 0.8327 (ptt) cc_final: 0.7942 (ptp) REVERT: E 72 ASP cc_start: 0.7598 (m-30) cc_final: 0.7123 (m-30) REVERT: E 78 THR cc_start: 0.8406 (p) cc_final: 0.8167 (p) REVERT: E 81 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8696 (mt) REVERT: E 100 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8353 (mttt) REVERT: E 221 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7329 (t80) REVERT: F 93 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8169 (mtt-85) REVERT: F 94 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8630 (mp) REVERT: F 103 TYR cc_start: 0.8966 (m-80) cc_final: 0.8441 (m-80) REVERT: F 178 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8462 (ttp-110) REVERT: G 118 ASP cc_start: 0.8490 (m-30) cc_final: 0.7990 (m-30) REVERT: G 208 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7980 (mppt) REVERT: G 231 LYS cc_start: 0.7906 (ptmm) cc_final: 0.7621 (ptpp) REVERT: O 51 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7506 (ttp-170) REVERT: O 204 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7389 (mtt) REVERT: P 77 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8934 (tp) REVERT: P 221 GLN cc_start: 0.8062 (mp10) cc_final: 0.7795 (mp10) REVERT: P 232 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6225 (ptt90) REVERT: Q 37 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: Q 125 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7434 (tp) REVERT: Q 142 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7882 (mmt) REVERT: Q 204 MET cc_start: 0.7462 (mtm) cc_final: 0.7199 (mtt) REVERT: Q 221 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: R 51 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (ttp-170) REVERT: R 101 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: R 232 ARG cc_start: 0.7226 (ptt90) cc_final: 0.6690 (mtm180) REVERT: S 34 GLN cc_start: 0.8658 (mp10) cc_final: 0.8393 (mp-120) REVERT: S 41 LYS cc_start: 0.7953 (mptt) cc_final: 0.7531 (mmtm) REVERT: S 119 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7305 (mt-10) REVERT: S 204 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7136 (mtt) REVERT: T 204 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7483 (mtt) REVERT: U 100 LYS cc_start: 0.8842 (mttm) cc_final: 0.8541 (mttp) REVERT: U 125 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7441 (mt) REVERT: U 185 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8436 (tp40) REVERT: Z 26 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7563 (pt) REVERT: Z 45 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6923 (mp) REVERT: Z 150 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: M 27 MET cc_start: 0.8827 (ttt) cc_final: 0.8460 (ttt) REVERT: M 38 ASP cc_start: 0.7883 (t70) cc_final: 0.7374 (t70) REVERT: M 77 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: M 93 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.4339 (pmt) REVERT: M 153 ASP cc_start: 0.7799 (m-30) cc_final: 0.7485 (m-30) REVERT: 1 51 ASP cc_start: 0.8392 (m-30) cc_final: 0.8124 (m-30) REVERT: 1 122 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: 1 124 TYR cc_start: 0.8872 (p90) cc_final: 0.8425 (p90) REVERT: 1 152 VAL cc_start: 0.8635 (p) cc_final: 0.8369 (t) REVERT: N 38 ASP cc_start: 0.7682 (t70) cc_final: 0.7200 (t0) REVERT: N 122 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: N 153 ASP cc_start: 0.8002 (m-30) cc_final: 0.7684 (m-30) REVERT: 2 21 THR cc_start: 0.4316 (OUTLIER) cc_final: 0.3991 (t) REVERT: 2 26 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7528 (pt) REVERT: 2 71 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6910 (mtp180) REVERT: 2 90 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8026 (p) REVERT: 2 93 MET cc_start: 0.6559 (pmm) cc_final: 0.6174 (pmm) REVERT: H 33 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8608 (mttp) REVERT: H 38 ASP cc_start: 0.7898 (t70) cc_final: 0.7374 (t0) REVERT: H 153 ASP cc_start: 0.7909 (m-30) cc_final: 0.7497 (m-30) REVERT: V 70 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8175 (mmp80) REVERT: V 71 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7432 (mtm110) REVERT: V 96 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7826 (mpp) REVERT: V 106 THR cc_start: 0.8592 (p) cc_final: 0.8354 (m) REVERT: V 138 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8431 (mt) REVERT: V 165 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7501 (mmt-90) REVERT: I 71 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7555 (mtt90) REVERT: I 79 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8475 (m) REVERT: I 93 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.3875 (mpp) REVERT: I 149 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: I 153 ASP cc_start: 0.7707 (m-30) cc_final: 0.7286 (m-30) REVERT: W 26 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7618 (pt) REVERT: W 71 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7041 (mtm-85) REVERT: W 90 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8172 (p) REVERT: W 93 MET cc_start: 0.6890 (pmm) cc_final: 0.6602 (pmm) REVERT: W 105 ASP cc_start: 0.8606 (p0) cc_final: 0.8223 (p0) REVERT: W 145 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8197 (mmtm) REVERT: J 32 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8277 (tttp) REVERT: J 77 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: J 186 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7926 (mm-40) REVERT: X 6 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8942 (pt) REVERT: X 51 ASP cc_start: 0.8413 (m-30) cc_final: 0.8159 (m-30) REVERT: X 96 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7819 (mtp) REVERT: X 122 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: K 96 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7528 (mtm) REVERT: K 153 ASP cc_start: 0.7795 (m-30) cc_final: 0.7461 (m-30) REVERT: Y 51 ASP cc_start: 0.8280 (m-30) cc_final: 0.8030 (m-30) REVERT: Y 122 ASP cc_start: 0.7503 (t0) cc_final: 0.7238 (m-30) REVERT: Y 138 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8254 (tp) REVERT: Y 165 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8253 (tpp-160) REVERT: L 22 MET cc_start: 0.1392 (OUTLIER) cc_final: 0.1054 (tmt) REVERT: L 77 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: L 93 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.4208 (mpp) REVERT: L 105 ASP cc_start: 0.8466 (p0) cc_final: 0.8172 (p0) REVERT: L 153 ASP cc_start: 0.7721 (m-30) cc_final: 0.7108 (m-30) REVERT: a 29 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: a 68 GLN cc_start: 0.7975 (mt0) cc_final: 0.7770 (mt0) REVERT: a 72 ASP cc_start: 0.8041 (t0) cc_final: 0.7817 (t70) REVERT: a 78 THR cc_start: 0.9062 (p) cc_final: 0.8841 (p) REVERT: a 142 ASP cc_start: 0.8527 (p0) cc_final: 0.8267 (p0) REVERT: b 18 ASP cc_start: 0.7836 (p0) cc_final: 0.7580 (p0) REVERT: b 72 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7674 (t0) REVERT: b 125 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7595 (tp-100) REVERT: b 144 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7994 (mp) REVERT: b 208 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.5136 (mtmm) REVERT: c 12 ILE cc_start: 0.6350 (tp) cc_final: 0.5909 (tt) REVERT: c 90 ASP cc_start: 0.7014 (m-30) cc_final: 0.6571 (m-30) REVERT: c 125 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7990 (tp-100) REVERT: c 198 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7824 (tmtm) REVERT: c 221 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7791 (t80) REVERT: c 222 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8303 (ttp80) REVERT: d 110 GLU cc_start: 0.7217 (pt0) cc_final: 0.6955 (pt0) REVERT: d 198 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7989 (tptt) REVERT: d 201 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7003 (mt) REVERT: e 150 ASP cc_start: 0.8000 (t70) cc_final: 0.7783 (t0) REVERT: e 221 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7497 (t80) REVERT: f 94 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9044 (mm) REVERT: f 212 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8133 (tp) REVERT: g 72 ASP cc_start: 0.8121 (m-30) cc_final: 0.7861 (m-30) REVERT: g 142 ASP cc_start: 0.7849 (p0) cc_final: 0.7603 (p0) REVERT: g 152 ASP cc_start: 0.7904 (t0) cc_final: 0.7487 (t0) REVERT: g 188 GLU cc_start: 0.7228 (tp30) cc_final: 0.6922 (tp30) REVERT: g 191 THR cc_start: 0.8408 (m) cc_final: 0.7993 (p) outliers start: 412 outliers final: 256 residues processed: 1437 average time/residue: 1.2095 time to fit residues: 2271.0021 Evaluate side-chains 1476 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1147 time to evaluate : 5.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 142 MET Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 175 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 71 ARG Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 165 ARG Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 145 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 164 GLN Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 96 MET Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 9 LYS Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 29 GLU Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 56 SER Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain b residue 221 TYR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 GLN Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 181 LYS Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain e residue 221 TYR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 200 SER Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 216 THR Chi-restraints excluded: chain g residue 217 VAL Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 7.9990 chunk 678 optimal weight: 3.9990 chunk 619 optimal weight: 9.9990 chunk 660 optimal weight: 1.9990 chunk 397 optimal weight: 0.6980 chunk 287 optimal weight: 8.9990 chunk 518 optimal weight: 0.4980 chunk 202 optimal weight: 3.9990 chunk 596 optimal weight: 2.9990 chunk 624 optimal weight: 1.9990 chunk 657 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 79 HIS R 79 HIS ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN N 88 ASN 2 141 GLN H 88 ASN H 89 GLN V 89 GLN V 141 GLN I 36 GLN I 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 GLN J 88 ASN X 89 GLN L 36 GLN L 88 ASN a 183 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 59129 Z= 0.239 Angle : 0.631 15.416 79856 Z= 0.338 Chirality : 0.043 0.305 9338 Planarity : 0.004 0.064 10255 Dihedral : 5.547 55.033 8329 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 5.91 % Allowed : 26.03 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7462 helix: 2.31 (0.09), residues: 3437 sheet: -0.61 (0.13), residues: 1470 loop : -1.37 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 28 HIS 0.014 0.001 HIS U 79 PHE 0.032 0.002 PHE g 42 TYR 0.023 0.002 TYR M 184 ARG 0.013 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1540 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1170 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 187 LYS cc_start: 0.8249 (tttp) cc_final: 0.7833 (mptp) REVERT: B 221 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.7242 (t80) REVERT: B 231 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8085 (ptpp) REVERT: C 94 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8543 (mp) REVERT: C 177 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 208 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8019 (mtmm) REVERT: C 230 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7576 (mmpt) REVERT: D 40 MET cc_start: 0.8549 (ptp) cc_final: 0.7974 (ptp) REVERT: D 56 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7691 (t) REVERT: D 94 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8464 (mp) REVERT: E 28 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7781 (mtp-110) REVERT: E 40 MET cc_start: 0.8274 (ptp) cc_final: 0.7901 (ptp) REVERT: E 78 THR cc_start: 0.8377 (p) cc_final: 0.8138 (p) REVERT: E 81 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8622 (mt) REVERT: E 100 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (mttt) REVERT: E 221 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.7386 (t80) REVERT: F 93 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8116 (mtt-85) REVERT: F 94 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (mp) REVERT: F 103 TYR cc_start: 0.8960 (m-80) cc_final: 0.8436 (m-80) REVERT: F 178 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8442 (ttp-110) REVERT: F 227 GLU cc_start: 0.7804 (pm20) cc_final: 0.7565 (pm20) REVERT: G 118 ASP cc_start: 0.8494 (m-30) cc_final: 0.7984 (m-30) REVERT: O 51 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7560 (ttp-170) REVERT: O 204 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7399 (mtt) REVERT: P 77 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8917 (tp) REVERT: P 221 GLN cc_start: 0.8077 (mp10) cc_final: 0.7821 (mp10) REVERT: P 232 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6167 (ptt90) REVERT: Q 125 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7240 (tp) REVERT: Q 204 MET cc_start: 0.7445 (mtm) cc_final: 0.7186 (mtt) REVERT: Q 221 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: R 51 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7542 (ttp-170) REVERT: R 101 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: R 232 ARG cc_start: 0.7186 (ptt90) cc_final: 0.6674 (mtm180) REVERT: S 41 LYS cc_start: 0.7920 (mptt) cc_final: 0.7572 (mmtm) REVERT: S 119 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7277 (mt-10) REVERT: S 204 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7140 (mtt) REVERT: T 204 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7469 (mtt) REVERT: U 100 LYS cc_start: 0.8824 (mttm) cc_final: 0.8433 (mttt) REVERT: U 185 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (tp40) REVERT: Z 26 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7503 (pt) REVERT: Z 45 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6738 (mp) REVERT: Z 150 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: M 27 MET cc_start: 0.8817 (ttt) cc_final: 0.8425 (ttt) REVERT: M 38 ASP cc_start: 0.7806 (t70) cc_final: 0.7305 (t0) REVERT: M 74 MET cc_start: 0.8122 (ttp) cc_final: 0.7784 (ttp) REVERT: M 93 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.4691 (pmt) REVERT: M 153 ASP cc_start: 0.7781 (m-30) cc_final: 0.7464 (m-30) REVERT: 1 26 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7421 (pt) REVERT: 1 51 ASP cc_start: 0.8324 (m-30) cc_final: 0.8064 (m-30) REVERT: 1 122 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: 1 124 TYR cc_start: 0.8879 (p90) cc_final: 0.8426 (p90) REVERT: 1 152 VAL cc_start: 0.8598 (p) cc_final: 0.8325 (t) REVERT: N 38 ASP cc_start: 0.7650 (t70) cc_final: 0.7167 (t0) REVERT: N 122 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: N 153 ASP cc_start: 0.7987 (m-30) cc_final: 0.7665 (m-30) REVERT: 2 21 THR cc_start: 0.4102 (OUTLIER) cc_final: 0.3770 (t) REVERT: 2 26 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7340 (pt) REVERT: 2 29 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8220 (mtmm) REVERT: 2 71 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6868 (mtp180) REVERT: 2 90 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8026 (p) REVERT: H 33 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8575 (mttp) REVERT: H 38 ASP cc_start: 0.7856 (t70) cc_final: 0.7353 (t0) REVERT: H 153 ASP cc_start: 0.7902 (m-30) cc_final: 0.7505 (m-30) REVERT: V 71 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7393 (mtm110) REVERT: V 96 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7858 (mpp) REVERT: V 138 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8398 (mt) REVERT: I 26 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7390 (pp) REVERT: I 71 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7573 (mtt90) REVERT: I 79 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (m) REVERT: I 153 ASP cc_start: 0.7684 (m-30) cc_final: 0.7275 (m-30) REVERT: W 14 MET cc_start: 0.8534 (mtp) cc_final: 0.8271 (mtt) REVERT: W 26 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7532 (pt) REVERT: W 71 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7123 (mtm-85) REVERT: W 90 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8012 (p) REVERT: W 93 MET cc_start: 0.6780 (pmm) cc_final: 0.6412 (pmm) REVERT: W 105 ASP cc_start: 0.8573 (p0) cc_final: 0.8185 (p0) REVERT: W 145 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8238 (mmtm) REVERT: J 77 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: J 93 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4111 (mpp) REVERT: J 186 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: X 6 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8917 (pt) REVERT: X 26 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7397 (pt) REVERT: X 51 ASP cc_start: 0.8252 (m-30) cc_final: 0.8002 (m-30) REVERT: X 122 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: K 96 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7498 (mtm) REVERT: K 153 ASP cc_start: 0.7746 (m-30) cc_final: 0.7414 (m-30) REVERT: Y 51 ASP cc_start: 0.8225 (m-30) cc_final: 0.7988 (m-30) REVERT: Y 122 ASP cc_start: 0.7407 (t0) cc_final: 0.7157 (m-30) REVERT: Y 165 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8305 (tpp-160) REVERT: L 22 MET cc_start: 0.1478 (OUTLIER) cc_final: 0.1097 (tmt) REVERT: L 71 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7236 (mpp80) REVERT: L 77 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: L 93 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.4141 (mpp) REVERT: L 105 ASP cc_start: 0.8441 (p0) cc_final: 0.8098 (p0) REVERT: L 153 ASP cc_start: 0.7702 (m-30) cc_final: 0.7085 (m-30) REVERT: a 72 ASP cc_start: 0.8039 (t0) cc_final: 0.7828 (t70) REVERT: a 78 THR cc_start: 0.9082 (p) cc_final: 0.8867 (p) REVERT: a 142 ASP cc_start: 0.8517 (p0) cc_final: 0.8258 (p0) REVERT: b 72 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7633 (t0) REVERT: b 125 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7465 (tp-100) REVERT: b 144 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8004 (mp) REVERT: b 188 GLU cc_start: 0.7432 (tp30) cc_final: 0.7022 (tp30) REVERT: b 191 THR cc_start: 0.8166 (m) cc_final: 0.7784 (p) REVERT: b 208 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5240 (mtmm) REVERT: c 12 ILE cc_start: 0.6369 (tp) cc_final: 0.5977 (tt) REVERT: c 90 ASP cc_start: 0.7013 (m-30) cc_final: 0.6578 (m-30) REVERT: c 125 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8033 (tp-100) REVERT: c 198 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7701 (tmtm) REVERT: c 221 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7692 (t80) REVERT: d 51 ASP cc_start: 0.7386 (t0) cc_final: 0.7183 (t0) REVERT: d 110 GLU cc_start: 0.7127 (pt0) cc_final: 0.6868 (pt0) REVERT: d 198 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7950 (tptt) REVERT: d 201 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7280 (mt) REVERT: e 125 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (tp-100) REVERT: e 150 ASP cc_start: 0.8005 (t70) cc_final: 0.7787 (t0) REVERT: e 221 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.7316 (t80) REVERT: f 94 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9037 (mm) REVERT: f 212 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8103 (tp) REVERT: g 72 ASP cc_start: 0.8065 (m-30) cc_final: 0.7758 (m-30) REVERT: g 142 ASP cc_start: 0.7803 (p0) cc_final: 0.7561 (p0) REVERT: g 161 LYS cc_start: 0.7844 (mtpt) cc_final: 0.7555 (mttp) REVERT: g 188 GLU cc_start: 0.7406 (tp30) cc_final: 0.7114 (tp30) REVERT: g 191 THR cc_start: 0.8327 (m) cc_final: 0.7924 (p) outliers start: 370 outliers final: 247 residues processed: 1406 average time/residue: 1.2354 time to fit residues: 2258.9942 Evaluate side-chains 1461 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1146 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 100 LYS Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 175 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 77 GLU Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 29 LYS Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 71 ARG Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 203 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 145 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 9 LYS Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 221 TYR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 GLN Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 125 GLN Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain e residue 221 TYR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 216 THR Chi-restraints excluded: chain g residue 217 VAL Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 2.9990 chunk 698 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 331 optimal weight: 0.6980 chunk 485 optimal weight: 6.9990 chunk 732 optimal weight: 8.9990 chunk 673 optimal weight: 8.9990 chunk 583 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 450 optimal weight: 0.3980 chunk 357 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN D 23 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 HIS P 79 HIS Q 47 HIS Q 79 HIS ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN M 89 GLN N 88 ASN 2 141 GLN H 89 GLN V 89 GLN I 36 GLN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN X 73 ASN L 36 GLN L 88 ASN a 62 ASN a 226 GLN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 ASN d 108 ASN d 183 ASN e 108 ASN ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 183 ASN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 59129 Z= 0.374 Angle : 0.703 16.467 79856 Z= 0.373 Chirality : 0.047 0.341 9338 Planarity : 0.005 0.059 10255 Dihedral : 5.842 56.362 8329 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.19 % Rotamer: Outliers : 6.04 % Allowed : 26.05 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 7462 helix: 2.10 (0.09), residues: 3423 sheet: -0.55 (0.13), residues: 1421 loop : -1.28 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 28 HIS 0.015 0.002 HIS U 79 PHE 0.030 0.002 PHE g 42 TYR 0.027 0.002 TYR L 58 ARG 0.014 0.001 ARG E 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1165 time to evaluate : 5.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8428 (mtmm) REVERT: B 94 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 123 TYR cc_start: 0.8756 (m-80) cc_final: 0.8535 (m-80) REVERT: B 231 LYS cc_start: 0.8567 (ptmm) cc_final: 0.8303 (ptpp) REVERT: C 68 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: C 94 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 177 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 208 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (mtmm) REVERT: D 40 MET cc_start: 0.8608 (ptp) cc_final: 0.8193 (ptm) REVERT: D 56 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7813 (t) REVERT: D 94 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8581 (mp) REVERT: D 170 ASP cc_start: 0.7891 (m-30) cc_final: 0.7682 (m-30) REVERT: D 231 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7976 (pttp) REVERT: E 28 ARG cc_start: 0.8294 (ttm110) cc_final: 0.7849 (mtp-110) REVERT: E 72 ASP cc_start: 0.7614 (m-30) cc_final: 0.7199 (m-30) REVERT: E 78 THR cc_start: 0.8486 (p) cc_final: 0.8243 (p) REVERT: E 221 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7438 (t80) REVERT: E 231 LYS cc_start: 0.8260 (ttpm) cc_final: 0.7979 (ptpp) REVERT: F 93 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8200 (mtt-85) REVERT: F 94 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8639 (mp) REVERT: F 103 TYR cc_start: 0.8982 (m-80) cc_final: 0.8519 (m-80) REVERT: F 178 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8492 (ttp-110) REVERT: G 118 ASP cc_start: 0.8447 (m-30) cc_final: 0.7975 (m-30) REVERT: O 51 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7610 (ttp-170) REVERT: O 204 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: O 221 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: P 221 GLN cc_start: 0.8166 (mp10) cc_final: 0.7887 (mp10) REVERT: P 232 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6263 (ptt90) REVERT: Q 125 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7264 (tp) REVERT: Q 204 MET cc_start: 0.7552 (mtm) cc_final: 0.7269 (mtt) REVERT: Q 221 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: R 101 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: R 232 ARG cc_start: 0.7179 (ptt90) cc_final: 0.6656 (mtm180) REVERT: S 41 LYS cc_start: 0.7945 (mptt) cc_final: 0.7587 (mmtm) REVERT: S 119 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7425 (mt-10) REVERT: T 142 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.6372 (mpt) REVERT: T 204 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: U 185 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8514 (tp40) REVERT: Z 37 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7840 (tp) REVERT: Z 150 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: M 27 MET cc_start: 0.8876 (ttt) cc_final: 0.8655 (ttt) REVERT: M 38 ASP cc_start: 0.7881 (t70) cc_final: 0.7375 (t70) REVERT: M 93 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.4569 (pmt) REVERT: M 153 ASP cc_start: 0.7834 (m-30) cc_final: 0.7519 (m-30) REVERT: 1 51 ASP cc_start: 0.8460 (m-30) cc_final: 0.8174 (m-30) REVERT: 1 122 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: 1 124 TYR cc_start: 0.8954 (p90) cc_final: 0.8531 (p90) REVERT: 1 152 VAL cc_start: 0.8653 (p) cc_final: 0.8383 (t) REVERT: N 38 ASP cc_start: 0.7916 (t70) cc_final: 0.7416 (t0) REVERT: N 93 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5003 (pmt) REVERT: N 122 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: N 153 ASP cc_start: 0.7997 (m-30) cc_final: 0.7699 (m-30) REVERT: 2 21 THR cc_start: 0.4463 (OUTLIER) cc_final: 0.4140 (t) REVERT: 2 29 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8277 (mtmm) REVERT: 2 71 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6919 (mtp180) REVERT: 2 90 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8111 (p) REVERT: 2 93 MET cc_start: 0.6285 (pmm) cc_final: 0.6062 (pmm) REVERT: H 33 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: H 38 ASP cc_start: 0.7833 (t70) cc_final: 0.7381 (t0) REVERT: H 93 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5072 (pmt) REVERT: H 153 ASP cc_start: 0.7918 (m-30) cc_final: 0.7506 (m-30) REVERT: V 70 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8116 (mmp80) REVERT: V 71 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7434 (mtm110) REVERT: V 96 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7969 (mtp) REVERT: V 138 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8452 (mt) REVERT: V 152 VAL cc_start: 0.8818 (p) cc_final: 0.8428 (t) REVERT: I 153 ASP cc_start: 0.7745 (m-30) cc_final: 0.7310 (m-30) REVERT: W 14 MET cc_start: 0.8582 (mtp) cc_final: 0.8361 (mtt) REVERT: W 90 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8086 (p) REVERT: W 93 MET cc_start: 0.6914 (pmm) cc_final: 0.6490 (pmm) REVERT: W 105 ASP cc_start: 0.8646 (p0) cc_final: 0.8310 (p0) REVERT: W 145 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8173 (mmtm) REVERT: J 77 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: J 186 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: X 6 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8956 (pt) REVERT: X 51 ASP cc_start: 0.8503 (m-30) cc_final: 0.8279 (m-30) REVERT: X 122 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: K 96 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: K 153 ASP cc_start: 0.7774 (m-30) cc_final: 0.7442 (m-30) REVERT: Y 51 ASP cc_start: 0.8354 (m-30) cc_final: 0.8089 (m-30) REVERT: Y 122 ASP cc_start: 0.7508 (t0) cc_final: 0.7281 (m-30) REVERT: Y 138 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8306 (tp) REVERT: Y 165 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8296 (tpp-160) REVERT: L 71 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7223 (mpp80) REVERT: L 77 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: L 93 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.4305 (mpp) REVERT: L 153 ASP cc_start: 0.7746 (m-30) cc_final: 0.7279 (m-30) REVERT: a 72 ASP cc_start: 0.8091 (t0) cc_final: 0.7879 (t70) REVERT: a 142 ASP cc_start: 0.8558 (p0) cc_final: 0.8318 (p0) REVERT: a 228 GLU cc_start: 0.6584 (tm-30) cc_final: 0.6288 (tt0) REVERT: b 72 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7747 (t0) REVERT: b 125 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: b 144 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8110 (mp) REVERT: b 179 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: b 208 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5314 (mtmm) REVERT: c 12 ILE cc_start: 0.6403 (tp) cc_final: 0.6086 (tt) REVERT: c 125 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7958 (tp-100) REVERT: c 221 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7541 (t80) REVERT: d 110 GLU cc_start: 0.7220 (pt0) cc_final: 0.6973 (pt0) REVERT: d 201 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7283 (mt) REVERT: e 221 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.6887 (t80) REVERT: f 94 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9008 (mm) REVERT: f 212 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8171 (tp) REVERT: g 72 ASP cc_start: 0.8138 (m-30) cc_final: 0.7838 (m-30) REVERT: g 152 ASP cc_start: 0.8021 (t0) cc_final: 0.7611 (t0) REVERT: g 161 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7617 (mttp) REVERT: g 188 GLU cc_start: 0.7256 (tp30) cc_final: 0.6967 (tp30) REVERT: g 191 THR cc_start: 0.8402 (m) cc_final: 0.7988 (p) outliers start: 378 outliers final: 267 residues processed: 1406 average time/residue: 1.1986 time to fit residues: 2204.6092 Evaluate side-chains 1470 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1145 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 204 MET Chi-restraints excluded: chain O residue 221 GLN Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 204 MET Chi-restraints excluded: chain P residue 229 VAL Chi-restraints excluded: chain P residue 232 ARG Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain Q residue 140 ILE Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 20 SER Chi-restraints excluded: chain T residue 142 MET Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 185 GLN Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 37 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 45 ILE Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 VAL Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 93 MET Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 122 ASP Chi-restraints excluded: chain 1 residue 155 VAL Chi-restraints excluded: chain 1 residue 175 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 131 SER Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 26 ILE Chi-restraints excluded: chain 2 residue 29 LYS Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 71 ARG Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 175 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 112 SER Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 145 LYS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 165 ARG Chi-restraints excluded: chain W residue 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 186 GLN Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 6 ILE Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 123 ILE Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 175 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 9 LYS Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 175 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 56 SER Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 216 THR Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 221 TYR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 36 THR Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 179 GLU Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 208 LYS Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 221 TYR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 31 VAL Chi-restraints excluded: chain c residue 36 THR Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 GLN Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 163 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 201 LEU Chi-restraints excluded: chain d residue 216 THR Chi-restraints excluded: chain d residue 221 TYR Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 31 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain e residue 221 TYR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 212 ILE Chi-restraints excluded: chain f residue 216 THR Chi-restraints excluded: chain f residue 217 VAL Chi-restraints excluded: chain f residue 221 TYR Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 163 THR Chi-restraints excluded: chain g residue 216 THR Chi-restraints excluded: chain g residue 217 VAL Chi-restraints excluded: chain g residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 0.0050 chunk 621 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 537 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 584 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 599 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN G 122 GLN ** O 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 HIS P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 79 HIS R 59 GLN R 79 HIS ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN N 88 ASN H 36 GLN H 88 ASN H 89 GLN V 89 GLN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN J 36 GLN J 88 ASN L 36 GLN L 88 ASN a 122 GLN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN ** e 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116284 restraints weight = 65063.802| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.03 r_work: 0.3167 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 59129 Z= 0.250 Angle : 0.649 16.445 79856 Z= 0.347 Chirality : 0.044 0.302 9338 Planarity : 0.004 0.062 10255 Dihedral : 5.642 55.376 8329 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.58 % Favored : 96.29 % Rotamer: Outliers : 5.61 % Allowed : 26.56 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.10), residues: 7462 helix: 2.26 (0.09), residues: 3430 sheet: -0.47 (0.13), residues: 1379 loop : -1.31 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 28 HIS 0.015 0.002 HIS U 79 PHE 0.030 0.002 PHE g 42 TYR 0.026 0.002 TYR L 58 ARG 0.013 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31606.61 seconds wall clock time: 544 minutes 16.22 seconds (32656.22 seconds total)