Starting phenix.real_space_refine on Wed Sep 25 23:38:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/09_2024/6utj_20881.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/09_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_20881/09_2024/6utj_20881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/09_2024/6utj_20881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/09_2024/6utj_20881.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6utj_20881/09_2024/6utj_20881.cif" } 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. Time to flip 14 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 24.23, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.68 Conformation dependent library (CDL) restraints added in 5.8 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: 5.66 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: 24.04 Time building geometry restraints manager: 12.87 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: 0.00 - 4.28: 78605 4.28 - 8.56: 1123 8.56 - 12.84: 89 12.84 - 17.11: 15 17.11 - 21.39: 24 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 3.040 nonbonded pdb=" O LYS D 41 " pdb=" OH TYR D 180 " model vdw 2.212 3.040 nonbonded pdb=" O LYS F 41 " pdb=" OH TYR F 180 " model vdw 2.212 3.040 nonbonded pdb=" O LYS A 41 " pdb=" OH TYR A 180 " model vdw 2.215 3.040 nonbonded pdb=" O LYS C 41 " pdb=" OH TYR C 180 " model vdw 2.218 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.480 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: 0.060 Extract box with map and model: 1.670 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 102.650 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.560 ------------------------------------------------------------------------------- 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 : 5.020 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: 1.5407 time to fit residues: 4721.3550 Evaluate side-chains 1387 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1342 time to evaluate : 4.992 ------------------------------------------------------------------------------- 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: 8.9990 chunk 557 optimal weight: 4.9990 chunk 309 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 375 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 576 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 428 optimal weight: 2.9990 chunk 667 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN 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 72 GLN 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 111 HIS Q 185 GLN R 79 HIS R 99 HIS R 111 HIS S 99 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 84 GLN U 111 HIS U 200 HIS Z 69 GLN Z 141 GLN Z 186 GLN 1 88 ASN 1 186 GLN N 88 ASN 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 88 ASN X 141 GLN K 141 GLN Y 73 ASN L 36 GLN ** a 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 97 GLN a 98 GLN ** a 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 59129 Z= 0.267 Angle : 0.701 13.201 79856 Z= 0.379 Chirality : 0.045 0.227 9338 Planarity : 0.005 0.075 10255 Dihedral : 6.620 77.417 8355 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 6.26 % Allowed : 19.11 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.09), residues: 7462 helix: 0.59 (0.08), residues: 3430 sheet: -1.26 (0.12), residues: 1407 loop : -2.14 (0.10), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 216 HIS 0.009 0.002 HIS U 79 PHE 0.027 0.002 PHE c 42 TYR 0.028 0.002 TYR E 221 ARG 0.010 0.001 ARG U 152 *********************** 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 1843 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 392 poor density : 1451 time to evaluate : 5.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7164 (pt0) cc_final: 0.6964 (pt0) REVERT: A 90 ASP cc_start: 0.7355 (m-30) cc_final: 0.7083 (m-30) REVERT: A 231 LYS cc_start: 0.8161 (mtpm) cc_final: 0.7864 (ttpp) REVERT: B 84 ASP cc_start: 0.8574 (m-30) cc_final: 0.8232 (m-30) REVERT: B 94 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8621 (mp) REVERT: B 170 ASP cc_start: 0.7304 (m-30) cc_final: 0.7090 (m-30) REVERT: C 106 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.7922 (tp) REVERT: C 231 LYS cc_start: 0.8041 (mtpm) cc_final: 0.7477 (ttpp) REVERT: D 40 MET cc_start: 0.8302 (ptp) cc_final: 0.7703 (ptp) REVERT: E 40 MET cc_start: 0.8189 (ptt) cc_final: 0.7807 (ptp) REVERT: E 198 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8343 (mptt) REVERT: E 231 LYS cc_start: 0.7843 (mtpm) cc_final: 0.7340 (ttpp) REVERT: F 94 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8523 (mp) REVERT: F 103 TYR cc_start: 0.8825 (m-80) cc_final: 0.8453 (m-80) REVERT: F 118 ASP cc_start: 0.8677 (m-30) cc_final: 0.8377 (m-30) REVERT: F 187 LYS cc_start: 0.8132 (tttt) cc_final: 0.7892 (mptp) REVERT: F 208 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7698 (mtmt) REVERT: G 9 ASP cc_start: 0.7755 (p0) cc_final: 0.7502 (p0) REVERT: G 40 MET cc_start: 0.8268 (ptp) cc_final: 0.7888 (ptp) REVERT: G 52 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7618 (ptpp) REVERT: G 208 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7982 (mtmm) REVERT: O 37 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: O 59 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: O 142 MET cc_start: 0.8134 (mpt) cc_final: 0.7744 (mpt) REVERT: O 204 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7822 (mtt) REVERT: P 18 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7775 (tp30) REVERT: P 187 ASP cc_start: 0.8715 (m-30) cc_final: 0.8484 (m-30) REVERT: Q 34 GLN cc_start: 0.8470 (mp10) cc_final: 0.8096 (mp10) REVERT: Q 204 MET cc_start: 0.7349 (mtm) cc_final: 0.7087 (mtt) REVERT: R 142 MET cc_start: 0.7941 (mmm) cc_final: 0.7546 (mmm) REVERT: R 221 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7856 (mp10) REVERT: R 229 VAL cc_start: 0.8535 (t) cc_final: 0.8297 (p) REVERT: S 119 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7414 (mt-10) REVERT: S 204 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7168 (mtt) REVERT: T 182 GLU cc_start: 0.7692 (tt0) cc_final: 0.7443 (tp30) REVERT: T 204 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7356 (mtt) REVERT: U 191 MET cc_start: 0.8776 (mmp) cc_final: 0.8279 (mmp) REVERT: U 204 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7565 (mtt) REVERT: Z 146 MET cc_start: 0.8715 (mtt) cc_final: 0.8451 (mtm) REVERT: M 86 MET cc_start: 0.7714 (mtp) cc_final: 0.7264 (mtp) REVERT: M 131 SER cc_start: 0.8587 (t) cc_final: 0.8218 (p) REVERT: M 153 ASP cc_start: 0.7842 (m-30) cc_final: 0.7506 (m-30) REVERT: 1 51 ASP cc_start: 0.8158 (m-30) cc_final: 0.7942 (m-30) REVERT: 1 96 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: 1 177 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8535 (t) REVERT: N 153 ASP cc_start: 0.7820 (m-30) cc_final: 0.7548 (m-30) REVERT: 2 14 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8598 (mtp) REVERT: 2 21 THR cc_start: 0.4796 (OUTLIER) cc_final: 0.4440 (t) REVERT: 2 55 LEU cc_start: 0.8642 (mm) cc_final: 0.8388 (mt) REVERT: 2 90 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8021 (p) REVERT: 2 93 MET cc_start: 0.6581 (pmm) cc_final: 0.6354 (pmm) REVERT: 2 173 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8550 (mt) REVERT: H 153 ASP cc_start: 0.7851 (m-30) cc_final: 0.7494 (m-30) REVERT: V 27 MET cc_start: 0.8198 (ttt) cc_final: 0.7938 (ttt) REVERT: V 51 ASP cc_start: 0.8281 (m-30) cc_final: 0.8008 (m-30) REVERT: V 64 GLU cc_start: 0.7223 (tt0) cc_final: 0.6972 (tt0) REVERT: V 96 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: V 169 SER cc_start: 0.8360 (m) cc_final: 0.8129 (m) REVERT: V 177 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8783 (m) REVERT: I 153 ASP cc_start: 0.7658 (m-30) cc_final: 0.7235 (m-30) REVERT: W 39 THR cc_start: 0.8817 (p) cc_final: 0.8468 (m) REVERT: W 90 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8363 (p) REVERT: W 93 MET cc_start: 0.6462 (pmm) cc_final: 0.6227 (pmm) REVERT: W 96 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7096 (mmt) REVERT: W 145 LYS cc_start: 0.8494 (mppt) cc_final: 0.8237 (mmtm) REVERT: W 173 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (mt) REVERT: W 177 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8499 (p) REVERT: J 180 ARG cc_start: 0.8565 (tpp-160) cc_final: 0.8030 (tpp-160) REVERT: X 26 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7341 (pt) REVERT: X 27 MET cc_start: 0.8109 (ttt) cc_final: 0.7895 (ttt) REVERT: X 156 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8588 (mm) REVERT: X 177 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8759 (m) REVERT: K 96 MET cc_start: 0.7833 (mpp) cc_final: 0.7537 (mtm) REVERT: K 131 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8332 (p) REVERT: K 153 ASP cc_start: 0.7818 (m-30) cc_final: 0.7499 (m-30) REVERT: K 178 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8321 (tp) REVERT: Y 145 LYS cc_start: 0.8404 (mppt) cc_final: 0.8170 (mmtm) REVERT: Y 173 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (mt) REVERT: L 93 MET cc_start: 0.6068 (mpp) cc_final: 0.5799 (pmt) REVERT: L 112 SER cc_start: 0.8342 (t) cc_final: 0.8128 (t) REVERT: L 153 ASP cc_start: 0.7666 (m-30) cc_final: 0.7037 (m-30) REVERT: a 125 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8442 (tp40) REVERT: a 152 ASP cc_start: 0.8091 (t0) cc_final: 0.7760 (t0) REVERT: b 120 MET cc_start: 0.9145 (mtp) cc_final: 0.8818 (mtp) REVERT: b 161 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6624 (mmtp) REVERT: b 188 GLU cc_start: 0.7531 (tp30) cc_final: 0.7118 (tp30) REVERT: b 191 THR cc_start: 0.8294 (m) cc_final: 0.7725 (p) REVERT: c 90 ASP cc_start: 0.7013 (m-30) cc_final: 0.6679 (m-30) REVERT: c 152 ASP cc_start: 0.7862 (t0) cc_final: 0.7504 (t0) REVERT: c 184 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7091 (mm) REVERT: c 191 THR cc_start: 0.8429 (m) cc_final: 0.7844 (p) REVERT: d 120 MET cc_start: 0.9052 (mtp) cc_final: 0.8357 (mtp) REVERT: d 125 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8022 (tp40) REVERT: e 184 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7199 (mm) REVERT: f 68 GLN cc_start: 0.7750 (mp10) cc_final: 0.7470 (mp10) REVERT: f 94 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8914 (mm) REVERT: f 120 MET cc_start: 0.9020 (mtp) cc_final: 0.8694 (mtm) REVERT: f 125 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: f 191 THR cc_start: 0.8307 (m) cc_final: 0.8081 (m) REVERT: g 180 TYR cc_start: 0.7454 (t80) cc_final: 0.7173 (t80) outliers start: 392 outliers final: 129 residues processed: 1683 average time/residue: 1.3042 time to fit residues: 2827.8472 Evaluate side-chains 1372 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1206 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP 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 C residue 106 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain E residue 18 ASP 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 208 LYS Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain G residue 52 LYS 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 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 R residue 37 GLU Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain T residue 204 MET Chi-restraints excluded: chain U residue 121 GLU 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 41 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 178 ILE 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 120 VAL Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 123 ILE 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 41 THR 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 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 14 MET Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 90 VAL 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 H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR 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 41 THR Chi-restraints excluded: chain V residue 96 MET Chi-restraints excluded: chain V residue 120 VAL 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 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 90 VAL 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 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 12 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 104 ILE 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 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 72 VAL Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 131 SER 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 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 173 ILE 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 119 SER 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 124 THR Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER 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 59 ILE Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 125 GLN 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 d residue 217 VAL Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 184 LEU Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 18 ASP Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain f residue 124 THR 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 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 212 ILE Chi-restraints excluded: chain g residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 555 optimal weight: 5.9990 chunk 454 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 668 optimal weight: 0.9990 chunk 722 optimal weight: 3.9990 chunk 595 optimal weight: 3.9990 chunk 663 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 536 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 98 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS R 72 GLN R 79 HIS R 200 HIS S 79 HIS T 59 GLN T 79 HIS U 79 HIS M 30 ASN 1 30 ASN 1 89 GLN N 73 ASN N 88 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 K 141 GLN L 36 GLN a 23 GLN a 98 GLN a 121 GLN a 125 GLN 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 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 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 59129 Z= 0.280 Angle : 0.668 13.833 79856 Z= 0.359 Chirality : 0.045 0.252 9338 Planarity : 0.005 0.069 10255 Dihedral : 6.170 55.780 8341 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.62 % Favored : 96.15 % Rotamer: Outliers : 7.24 % Allowed : 20.82 % Favored : 71.94 % 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: -0.24 (0.09), residues: 7462 helix: 1.46 (0.09), residues: 3430 sheet: -0.89 (0.12), residues: 1421 loop : -1.95 (0.10), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 28 HIS 0.010 0.002 HIS S 79 PHE 0.027 0.002 PHE e 42 TYR 0.024 0.002 TYR S 231 ARG 0.011 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 1711 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 453 poor density : 1258 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8137 (tttp) cc_final: 0.7527 (mmmt) REVERT: A 231 LYS cc_start: 0.8140 (mtpm) cc_final: 0.7839 (tttm) REVERT: B 94 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 170 ASP cc_start: 0.7419 (m-30) cc_final: 0.7211 (m-30) REVERT: C 177 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: C 208 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7809 (mtmm) REVERT: C 231 LYS cc_start: 0.7897 (mtpm) cc_final: 0.7398 (ttpp) REVERT: D 40 MET cc_start: 0.8531 (ptp) cc_final: 0.8059 (ptp) REVERT: D 94 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8598 (mp) REVERT: E 28 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7744 (mtp-110) REVERT: E 40 MET cc_start: 0.8289 (ptt) cc_final: 0.7931 (ptp) REVERT: E 56 SER cc_start: 0.8178 (m) cc_final: 0.7955 (p) REVERT: E 78 THR cc_start: 0.8406 (p) cc_final: 0.8159 (p) REVERT: E 98 GLN cc_start: 0.7549 (mt0) cc_final: 0.7337 (mt0) REVERT: E 108 ASN cc_start: 0.8373 (t0) cc_final: 0.8130 (t0) REVERT: F 94 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (mp) REVERT: F 103 TYR cc_start: 0.8856 (m-80) cc_final: 0.8357 (m-80) REVERT: F 118 ASP cc_start: 0.8707 (m-30) cc_final: 0.8389 (m-30) REVERT: F 187 LYS cc_start: 0.8161 (tttt) cc_final: 0.7891 (mmtt) REVERT: F 208 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7701 (mtmt) REVERT: G 9 ASP cc_start: 0.8320 (p0) cc_final: 0.8091 (p0) REVERT: G 198 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8272 (mptt) REVERT: G 208 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8007 (mtmm) REVERT: O 37 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: O 51 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6550 (tpp-160) REVERT: O 142 MET cc_start: 0.8363 (mpt) cc_final: 0.8115 (mpt) REVERT: O 204 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: P 16 TYR cc_start: 0.7294 (m-10) cc_final: 0.7006 (m-10) REVERT: P 142 MET cc_start: 0.8132 (mpt) cc_final: 0.7721 (mpt) REVERT: Q 37 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: Q 61 GLU cc_start: 0.7603 (tp30) cc_final: 0.7371 (tp30) REVERT: Q 82 TYR cc_start: 0.8667 (t80) cc_final: 0.8362 (t80) REVERT: Q 204 MET cc_start: 0.7456 (mtm) cc_final: 0.7089 (mtt) REVERT: Q 221 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: R 101 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: S 119 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7498 (mt-10) REVERT: S 140 ILE cc_start: 0.7838 (pt) cc_final: 0.7613 (pt) REVERT: T 204 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7485 (mtt) REVERT: U 100 LYS cc_start: 0.8810 (mttm) cc_final: 0.8559 (mttt) REVERT: U 185 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8401 (tp40) REVERT: U 191 MET cc_start: 0.8788 (mmp) cc_final: 0.8347 (mmp) REVERT: U 204 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7529 (mtt) REVERT: Z 26 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7451 (pt) REVERT: Z 29 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: Z 146 MET cc_start: 0.8610 (mtt) cc_final: 0.8316 (mtm) REVERT: M 93 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.4713 (pmt) REVERT: M 105 ASP cc_start: 0.8451 (p0) cc_final: 0.7880 (p0) REVERT: M 153 ASP cc_start: 0.7874 (m-30) cc_final: 0.7533 (m-30) REVERT: 1 26 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7444 (pt) REVERT: 1 51 ASP cc_start: 0.8318 (m-30) cc_final: 0.7994 (m-30) REVERT: 1 122 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: N 21 THR cc_start: 0.5171 (OUTLIER) cc_final: 0.4966 (t) REVERT: N 71 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7532 (mtt90) REVERT: N 153 ASP cc_start: 0.7823 (m-30) cc_final: 0.7528 (m-30) REVERT: 2 21 THR cc_start: 0.4872 (OUTLIER) cc_final: 0.4449 (t) REVERT: 2 90 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8182 (p) REVERT: 2 93 MET cc_start: 0.6813 (pmm) cc_final: 0.6560 (pmm) REVERT: H 149 ASP cc_start: 0.7346 (p0) cc_final: 0.6844 (p0) REVERT: H 153 ASP cc_start: 0.7881 (m-30) cc_final: 0.7466 (m-30) REVERT: V 17 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6038 (pp20) REVERT: V 26 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7243 (pt) REVERT: V 51 ASP cc_start: 0.8375 (m-30) cc_final: 0.8089 (m-30) REVERT: V 96 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7886 (mtp) REVERT: I 67 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7611 (ttp-110) REVERT: I 93 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.4455 (pmt) REVERT: I 153 ASP cc_start: 0.7678 (m-30) cc_final: 0.7233 (m-30) REVERT: W 17 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: W 173 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8576 (mt) REVERT: J 62 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: J 77 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: J 172 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6918 (mtm) REVERT: J 180 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.8137 (tpp-160) REVERT: X 26 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7501 (pt) REVERT: X 30 ASN cc_start: 0.8102 (t0) cc_final: 0.7846 (t0) REVERT: K 74 MET cc_start: 0.8016 (ttp) cc_final: 0.7692 (ttp) REVERT: K 96 MET cc_start: 0.7805 (mpp) cc_final: 0.7564 (mtm) REVERT: K 131 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (p) REVERT: K 153 ASP cc_start: 0.7722 (m-30) cc_final: 0.7438 (m-30) REVERT: K 178 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8282 (tp) REVERT: Y 17 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: Y 51 ASP cc_start: 0.8369 (m-30) cc_final: 0.7971 (m-30) REVERT: Y 165 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8347 (tpp-160) REVERT: L 67 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7951 (ttp-110) REVERT: L 71 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7801 (mtm110) REVERT: L 77 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: L 153 ASP cc_start: 0.7688 (m-30) cc_final: 0.7200 (m-30) REVERT: a 152 ASP cc_start: 0.7910 (t0) cc_final: 0.7631 (t70) REVERT: a 184 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7103 (mm) REVERT: b 161 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6948 (mmtp) REVERT: b 191 THR cc_start: 0.8162 (m) cc_final: 0.7940 (m) REVERT: c 90 ASP cc_start: 0.6995 (m-30) cc_final: 0.6618 (m-30) REVERT: c 118 ASP cc_start: 0.7620 (m-30) cc_final: 0.7353 (m-30) REVERT: c 180 TYR cc_start: 0.7441 (t80) cc_final: 0.6974 (t80) REVERT: d 120 MET cc_start: 0.8937 (mtp) cc_final: 0.8381 (mtp) REVERT: d 125 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: d 198 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7929 (tptp) REVERT: e 184 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7434 (mm) REVERT: e 187 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7993 (tptt) REVERT: f 49 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7683 (mp) REVERT: f 53 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.4820 (ptmm) REVERT: f 68 GLN cc_start: 0.7748 (mp10) cc_final: 0.7522 (mp10) REVERT: f 94 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8972 (mm) REVERT: f 208 LYS cc_start: 0.4955 (OUTLIER) cc_final: 0.4568 (mtmm) REVERT: g 180 TYR cc_start: 0.7413 (t80) cc_final: 0.7130 (t80) outliers start: 453 outliers final: 184 residues processed: 1550 average time/residue: 1.2532 time to fit residues: 2509.8972 Evaluate side-chains 1364 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1133 time to evaluate : 5.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR 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 150 ASP Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 156 THR 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 156 THR Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 155 VAL 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 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 79 HIS Chi-restraints excluded: chain S residue 122 ILE 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 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 29 LYS Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE 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 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 30 ASN Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 72 VAL 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 N residue 21 THR Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 41 THR 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 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 17 GLU 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 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 144 GLU 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 72 VAL 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 6 ILE Chi-restraints excluded: chain V residue 17 GLU 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 155 VAL Chi-restraints excluded: chain V residue 178 ILE 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 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 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 ASP Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE 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 62 GLU 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 167 SER Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 26 ILE 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 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 77 GLU Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 17 GLU 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 165 ARG 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 77 GLU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 131 SER 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 47 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 13 THR Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 142 ASP 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 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 125 GLN 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 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 184 LEU Chi-restraints excluded: chain e residue 187 LYS Chi-restraints excluded: chain e residue 201 LEU Chi-restraints excluded: chain e residue 217 VAL Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 151 CYS Chi-restraints excluded: chain f residue 208 LYS 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 59 ILE Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS 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: 4.9990 chunk 502 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 449 optimal weight: 0.9980 chunk 671 optimal weight: 0.9980 chunk 710 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 636 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN C 108 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 R 79 HIS S 79 HIS T 59 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN 1 88 ASN N 36 GLN N 88 ASN 2 141 GLN H 36 GLN V 89 GLN V 141 GLN I 88 ASN W 73 ASN J 30 ASN Y 30 ASN Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN L 88 ASN L 109 HIS a 97 GLN a 98 GLN ** a 108 ASN ** 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 108 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 ASN ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4554 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= 0.305 Angle : 0.673 13.659 79856 Z= 0.360 Chirality : 0.045 0.347 9338 Planarity : 0.004 0.070 10255 Dihedral : 6.054 74.827 8332 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.73 % Favored : 96.02 % Rotamer: Outliers : 7.51 % Allowed : 21.94 % Favored : 70.55 % 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: 0.07 (0.09), residues: 7462 helix: 1.74 (0.09), residues: 3430 sheet: -0.77 (0.12), residues: 1421 loop : -1.81 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 28 HIS 0.026 0.002 HIS S 79 PHE 0.029 0.002 PHE e 42 TYR 0.021 0.002 TYR K 184 ARG 0.006 0.001 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 1706 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 470 poor density : 1236 time to evaluate : 5.026 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 56 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8063 (p) REVERT: A 231 LYS cc_start: 0.8153 (mtpm) cc_final: 0.7887 (tttm) REVERT: B 94 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8699 (mp) REVERT: B 231 LYS cc_start: 0.8588 (ptmm) cc_final: 0.8311 (ptpp) REVERT: C 94 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 208 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7918 (mtmm) REVERT: C 231 LYS cc_start: 0.7772 (mtpm) cc_final: 0.7366 (ttpp) REVERT: D 33 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: D 40 MET cc_start: 0.8588 (ptp) cc_final: 0.8119 (ptp) REVERT: D 94 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8491 (mp) REVERT: D 98 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: E 40 MET cc_start: 0.8327 (ptt) cc_final: 0.7961 (ptp) REVERT: E 55 ARG cc_start: 0.7593 (pmm-80) cc_final: 0.7345 (mtt-85) REVERT: E 98 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7326 (mt0) REVERT: E 227 GLU cc_start: 0.8050 (pm20) cc_final: 0.7678 (pm20) REVERT: F 94 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8637 (mp) REVERT: F 103 TYR cc_start: 0.8949 (m-80) cc_final: 0.8407 (m-80) REVERT: F 187 LYS cc_start: 0.8060 (tttt) cc_final: 0.7818 (mmtt) REVERT: G 9 ASP cc_start: 0.8420 (p0) cc_final: 0.8194 (p0) REVERT: G 208 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7964 (mtmm) REVERT: O 59 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: O 140 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7834 (pt) REVERT: O 142 MET cc_start: 0.8387 (mpt) cc_final: 0.7967 (mpt) REVERT: O 204 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7435 (mtt) REVERT: P 16 TYR cc_start: 0.7274 (m-10) cc_final: 0.7011 (m-10) REVERT: P 142 MET cc_start: 0.8190 (mpt) cc_final: 0.7769 (mpt) REVERT: Q 82 TYR cc_start: 0.8656 (t80) cc_final: 0.8393 (t80) REVERT: Q 100 LYS cc_start: 0.8747 (mttm) cc_final: 0.8543 (mttm) REVERT: Q 204 MET cc_start: 0.7473 (mtm) cc_final: 0.7234 (mtt) REVERT: Q 221 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: R 101 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: R 204 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7335 (mtt) REVERT: R 232 ARG cc_start: 0.7181 (ptt90) cc_final: 0.6664 (mtm180) REVERT: S 119 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7398 (mt-10) REVERT: S 125 LEU cc_start: 0.7886 (tp) cc_final: 0.7595 (tp) REVERT: S 140 ILE cc_start: 0.7909 (pt) cc_final: 0.7617 (pt) REVERT: U 100 LYS cc_start: 0.8815 (mttm) cc_final: 0.8550 (mttp) REVERT: U 119 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7524 (mt-10) REVERT: U 185 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8393 (tp40) REVERT: U 191 MET cc_start: 0.8748 (mmp) cc_final: 0.8357 (mmp) REVERT: Z 26 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7480 (pt) REVERT: Z 29 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: Z 39 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8583 (p) REVERT: Z 96 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7724 (mtt) REVERT: Z 146 MET cc_start: 0.8556 (mtt) cc_final: 0.8331 (mtm) REVERT: Z 150 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: M 27 MET cc_start: 0.8862 (ttt) cc_final: 0.8654 (ttt) REVERT: M 74 MET cc_start: 0.7980 (ttm) cc_final: 0.7685 (ttp) REVERT: M 89 GLN cc_start: 0.7991 (mt0) cc_final: 0.7772 (mt0) REVERT: M 93 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.4791 (pmt) REVERT: M 153 ASP cc_start: 0.7820 (m-30) cc_final: 0.7533 (m-30) REVERT: 1 51 ASP cc_start: 0.8388 (m-30) cc_final: 0.8053 (m-30) REVERT: 1 55 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (mt) REVERT: 1 96 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7870 (mtt) REVERT: 1 122 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6729 (m-30) REVERT: 1 152 VAL cc_start: 0.8528 (p) cc_final: 0.8207 (t) REVERT: N 21 THR cc_start: 0.5129 (OUTLIER) cc_final: 0.4896 (t) REVERT: N 38 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7791 (t0) REVERT: N 153 ASP cc_start: 0.7897 (m-30) cc_final: 0.7597 (m-30) REVERT: 2 21 THR cc_start: 0.4816 (OUTLIER) cc_final: 0.4451 (t) REVERT: 2 90 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8129 (p) REVERT: 2 93 MET cc_start: 0.6516 (pmm) cc_final: 0.6302 (pmm) REVERT: 2 177 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8805 (t) REVERT: H 33 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8657 (mttp) REVERT: H 149 ASP cc_start: 0.7288 (p0) cc_final: 0.6764 (p0) REVERT: H 153 ASP cc_start: 0.7886 (m-30) cc_final: 0.7482 (m-30) REVERT: V 26 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7353 (pt) REVERT: V 51 ASP cc_start: 0.8442 (m-30) cc_final: 0.8143 (m-30) REVERT: V 96 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: I 21 THR cc_start: 0.4927 (OUTLIER) cc_final: 0.4680 (t) REVERT: I 67 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7600 (ttp-110) REVERT: I 88 ASN cc_start: 0.8947 (t0) cc_final: 0.8703 (t0) REVERT: I 93 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.4173 (pmt) REVERT: I 153 ASP cc_start: 0.7706 (m-30) cc_final: 0.7279 (m-30) REVERT: W 17 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: W 26 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7372 (pt) REVERT: W 93 MET cc_start: 0.6754 (pmm) cc_final: 0.6460 (pmm) REVERT: W 96 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: W 173 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8573 (mt) REVERT: J 77 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: J 93 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.4227 (mpp) REVERT: X 6 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8903 (pt) REVERT: X 30 ASN cc_start: 0.8182 (t0) cc_final: 0.7939 (t0) REVERT: X 122 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: X 177 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8675 (m) REVERT: K 74 MET cc_start: 0.8081 (ttp) cc_final: 0.7550 (ttm) REVERT: K 93 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5728 (pmt) REVERT: K 122 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7372 (t0) REVERT: K 131 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8498 (p) REVERT: K 149 ASP cc_start: 0.7462 (p0) cc_final: 0.7152 (p0) REVERT: K 153 ASP cc_start: 0.7825 (m-30) cc_final: 0.7495 (m-30) REVERT: Y 17 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6948 (pp20) REVERT: Y 51 ASP cc_start: 0.8434 (m-30) cc_final: 0.8044 (m-30) REVERT: Y 165 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8392 (tpp-160) REVERT: L 67 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7945 (ttp-110) REVERT: L 77 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: L 153 ASP cc_start: 0.7691 (m-30) cc_final: 0.7232 (m-30) REVERT: a 184 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7336 (mm) REVERT: b 126 TYR cc_start: 0.7450 (m-80) cc_final: 0.7160 (m-80) REVERT: b 147 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8040 (mmm-85) REVERT: b 161 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7440 (mmtp) REVERT: b 182 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6955 (tp30) REVERT: b 187 LYS cc_start: 0.8236 (tptt) cc_final: 0.7793 (tptm) REVERT: b 208 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4636 (mmmm) REVERT: c 16 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8798 (p) REVERT: c 49 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7434 (pp) REVERT: c 90 ASP cc_start: 0.7011 (m-30) cc_final: 0.6606 (m-30) REVERT: c 118 ASP cc_start: 0.7629 (m-30) cc_final: 0.7372 (m-30) REVERT: c 197 LEU cc_start: 0.8238 (tp) cc_final: 0.8016 (tt) REVERT: d 120 MET cc_start: 0.8907 (mtp) cc_final: 0.8521 (mtp) REVERT: d 142 ASP cc_start: 0.7898 (p0) cc_final: 0.7527 (p0) REVERT: d 228 GLU cc_start: 0.6818 (tp30) cc_final: 0.6275 (mp0) REVERT: e 187 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.6997 (tmtt) REVERT: e 197 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (tp) REVERT: f 94 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9015 (mm) REVERT: f 208 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.4622 (mtmm) REVERT: f 221 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7819 (t80) REVERT: g 152 ASP cc_start: 0.8031 (t0) cc_final: 0.7684 (t0) REVERT: g 188 GLU cc_start: 0.7153 (tp30) cc_final: 0.6929 (tp30) REVERT: g 191 THR cc_start: 0.8244 (m) cc_final: 0.7807 (p) outliers start: 470 outliers final: 227 residues processed: 1538 average time/residue: 1.2420 time to fit residues: 2485.7285 Evaluate side-chains 1454 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1167 time to evaluate : 4.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP 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 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 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 33 LYS 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 156 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 98 GLN 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 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 156 THR Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain O residue 59 GLN 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 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 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 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 29 LYS Chi-restraints excluded: chain Z residue 39 THR 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 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 178 ILE 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 140 SER 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 30 ASN Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 72 VAL 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 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 17 GLU 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 84 SER Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 145 LYS Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 177 VAL Chi-restraints excluded: chain 2 residue 178 ILE 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 110 VAL 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 6 ILE Chi-restraints excluded: chain V residue 26 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER 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 178 ILE 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 72 VAL 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 122 ASP 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 185 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR 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 134 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE 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 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 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 177 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 203 LEU Chi-restraints excluded: chain Y residue 17 GLU 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 84 SER 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 6 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 72 VAL Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 134 VAL 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 124 THR Chi-restraints excluded: chain a residue 184 LEU 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 147 ARG 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 b residue 217 VAL 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 49 ILE 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 201 LEU Chi-restraints excluded: chain c residue 216 THR 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 38 LEU Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 184 LEU 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 124 THR Chi-restraints excluded: chain e residue 144 ILE Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 187 LYS Chi-restraints excluded: chain e residue 197 LEU 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 47 LEU Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 124 THR Chi-restraints excluded: chain f residue 208 LYS 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 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 0.9990 chunk 403 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 528 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 606 optimal weight: 4.9990 chunk 491 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 chunk 637 optimal weight: 0.0470 chunk 179 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 158 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN G 122 GLN P 59 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 ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 HIS T 59 GLN T 75 GLN T 79 HIS U 79 HIS Z 141 GLN M 30 ASN M 88 ASN 1 89 GLN N 36 GLN N 88 ASN 2 73 ASN 2 141 GLN H 36 GLN H 88 ASN V 30 ASN V 89 GLN V 141 GLN W 141 GLN J 88 ASN J 141 GLN X 141 GLN K 85 ASN Y 30 ASN Y 141 GLN L 36 GLN L 88 ASN a 97 GLN ** a 108 ASN ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 121 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 121 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59129 Z= 0.179 Angle : 0.612 13.382 79856 Z= 0.328 Chirality : 0.042 0.296 9338 Planarity : 0.004 0.072 10255 Dihedral : 5.652 67.870 8331 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.31 % Favored : 96.53 % Rotamer: Outliers : 6.10 % Allowed : 23.62 % Favored : 70.28 % 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: 0.41 (0.09), residues: 7462 helix: 2.09 (0.09), residues: 3437 sheet: -0.64 (0.12), residues: 1421 loop : -1.72 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 28 HIS 0.011 0.001 HIS R 79 PHE 0.027 0.001 PHE g 42 TYR 0.022 0.001 TYR K 184 ARG 0.012 0.000 ARG C 28 *********************** 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 1674 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1292 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 94 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8676 (mp) REVERT: B 101 VAL cc_start: 0.8698 (m) cc_final: 0.8372 (m) REVERT: B 221 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7465 (t80) REVERT: B 231 LYS cc_start: 0.8540 (ptmm) cc_final: 0.8138 (ptpp) REVERT: C 94 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8549 (mp) REVERT: C 208 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7964 (mtmm) REVERT: C 227 GLU cc_start: 0.7695 (pm20) cc_final: 0.7343 (pm20) REVERT: D 33 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8609 (mtmm) REVERT: D 40 MET cc_start: 0.8501 (ptp) cc_final: 0.8082 (ptp) REVERT: D 52 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7794 (ptpt) REVERT: D 94 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8440 (mp) REVERT: D 98 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: E 28 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7694 (mtp-110) REVERT: E 40 MET cc_start: 0.8151 (ptt) cc_final: 0.7833 (ptp) REVERT: E 55 ARG cc_start: 0.7580 (pmm-80) cc_final: 0.7240 (ptp-170) REVERT: E 98 GLN cc_start: 0.7604 (mt0) cc_final: 0.7395 (mt0) REVERT: E 221 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7530 (t80) REVERT: F 35 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8712 (m) REVERT: F 94 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8587 (mp) REVERT: F 103 TYR cc_start: 0.8930 (m-80) cc_final: 0.8412 (m-80) REVERT: F 118 ASP cc_start: 0.8678 (m-30) cc_final: 0.8419 (m-30) REVERT: F 225 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6059 (OUTLIER) REVERT: F 227 GLU cc_start: 0.7814 (pm20) cc_final: 0.7606 (pm20) REVERT: F 231 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7999 (ptpp) REVERT: G 9 ASP cc_start: 0.8390 (p0) cc_final: 0.8146 (p0) REVERT: G 208 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7914 (mtmm) REVERT: G 221 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7259 (t80) REVERT: O 51 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: O 140 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7555 (pt) REVERT: O 142 MET cc_start: 0.8355 (mpt) cc_final: 0.8045 (mpt) REVERT: O 204 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: P 16 TYR cc_start: 0.7077 (m-10) cc_final: 0.6821 (m-10) REVERT: P 77 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8887 (tp) REVERT: P 142 MET cc_start: 0.8179 (mpt) cc_final: 0.7750 (mpt) REVERT: Q 18 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: Q 82 TYR cc_start: 0.8611 (t80) cc_final: 0.8401 (t80) REVERT: R 51 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7118 (ttp-170) REVERT: R 232 ARG cc_start: 0.7138 (ptt90) cc_final: 0.6617 (mtm180) REVERT: S 119 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7351 (mt-10) REVERT: S 191 MET cc_start: 0.9028 (mmm) cc_final: 0.8772 (mmp) REVERT: U 100 LYS cc_start: 0.8793 (mttm) cc_final: 0.8466 (mttt) REVERT: U 119 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7465 (mt-10) REVERT: U 125 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7786 (tp) REVERT: U 191 MET cc_start: 0.8661 (mmp) cc_final: 0.8346 (mmp) REVERT: U 204 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: Z 150 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: M 27 MET cc_start: 0.8735 (ttt) cc_final: 0.8500 (ttt) REVERT: M 38 ASP cc_start: 0.7976 (t70) cc_final: 0.7413 (t70) REVERT: M 74 MET cc_start: 0.8190 (ttm) cc_final: 0.7958 (ttp) REVERT: M 89 GLN cc_start: 0.7998 (mt0) cc_final: 0.7753 (mt0) REVERT: M 93 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.4187 (pmt) REVERT: M 120 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8805 (t) REVERT: M 153 ASP cc_start: 0.7738 (m-30) cc_final: 0.7444 (m-30) REVERT: 1 122 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6573 (m-30) REVERT: N 38 ASP cc_start: 0.7987 (t70) cc_final: 0.7328 (t0) REVERT: N 60 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8359 (mttp) REVERT: N 153 ASP cc_start: 0.7812 (m-30) cc_final: 0.7535 (m-30) REVERT: 2 21 THR cc_start: 0.4390 (OUTLIER) cc_final: 0.4107 (t) REVERT: 2 90 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.7945 (p) REVERT: 2 93 MET cc_start: 0.6495 (pmm) cc_final: 0.6196 (pmm) REVERT: H 149 ASP cc_start: 0.7309 (p0) cc_final: 0.6776 (p0) REVERT: H 153 ASP cc_start: 0.7824 (m-30) cc_final: 0.7458 (m-30) REVERT: V 51 ASP cc_start: 0.8363 (m-30) cc_final: 0.8062 (m-30) REVERT: V 96 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7898 (mtp) REVERT: I 93 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4117 (pmt) REVERT: I 105 ASP cc_start: 0.8293 (p0) cc_final: 0.8068 (p0) REVERT: I 139 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7905 (mm-30) REVERT: I 153 ASP cc_start: 0.7616 (m-30) cc_final: 0.7209 (m-30) REVERT: W 17 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6821 (pp20) REVERT: W 71 ARG cc_start: 0.7344 (mtm110) cc_final: 0.7052 (mtm-85) REVERT: W 93 MET cc_start: 0.6832 (pmm) cc_final: 0.6565 (pmm) REVERT: J 77 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: J 146 MET cc_start: 0.9067 (mtm) cc_final: 0.8828 (mtp) REVERT: J 180 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: X 26 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (pt) REVERT: X 141 GLN cc_start: 0.8321 (mt0) cc_final: 0.8005 (mt0) REVERT: X 165 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8339 (tpp-160) REVERT: K 71 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (mtt90) REVERT: K 153 ASP cc_start: 0.7776 (m-30) cc_final: 0.7465 (m-30) REVERT: Y 26 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7193 (pt) REVERT: Y 51 ASP cc_start: 0.8329 (m-30) cc_final: 0.7907 (m-30) REVERT: Y 165 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8337 (tpp-160) REVERT: L 26 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7480 (pt) REVERT: L 27 MET cc_start: 0.8501 (ttt) cc_final: 0.8265 (ttt) REVERT: L 74 MET cc_start: 0.8192 (ttp) cc_final: 0.7927 (ttp) REVERT: L 77 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: L 153 ASP cc_start: 0.7666 (m-30) cc_final: 0.7081 (m-30) REVERT: a 68 GLN cc_start: 0.7938 (mt0) cc_final: 0.7590 (mp10) REVERT: a 72 ASP cc_start: 0.7833 (t0) cc_final: 0.7597 (t70) REVERT: a 184 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7291 (mm) REVERT: b 53 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5372 (ptpp) REVERT: b 72 ASP cc_start: 0.7710 (t0) cc_final: 0.7418 (t70) REVERT: b 126 TYR cc_start: 0.7458 (m-80) cc_final: 0.7228 (m-80) REVERT: b 142 ASP cc_start: 0.7734 (p0) cc_final: 0.7451 (p0) REVERT: b 144 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7829 (mp) REVERT: b 161 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7397 (mttp) REVERT: b 208 LYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4449 (mmmm) REVERT: b 228 GLU cc_start: 0.6863 (tp30) cc_final: 0.6468 (mt-10) REVERT: c 90 ASP cc_start: 0.7006 (m-30) cc_final: 0.6597 (m-30) REVERT: c 118 ASP cc_start: 0.7488 (m-30) cc_final: 0.7256 (m-30) REVERT: c 180 TYR cc_start: 0.7387 (t80) cc_final: 0.6977 (t80) REVERT: c 197 LEU cc_start: 0.8227 (tp) cc_final: 0.7962 (tt) REVERT: d 120 MET cc_start: 0.8785 (mtp) cc_final: 0.8456 (mtp) REVERT: d 142 ASP cc_start: 0.7807 (p0) cc_final: 0.7468 (p0) REVERT: d 195 LYS cc_start: 0.7685 (tppt) cc_final: 0.7450 (ptmt) REVERT: d 198 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (tptt) REVERT: e 28 ARG cc_start: 0.7889 (mmt90) cc_final: 0.7492 (mtt-85) REVERT: e 208 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.5338 (mtmm) REVERT: e 228 GLU cc_start: 0.7020 (tp30) cc_final: 0.6554 (mp0) REVERT: f 53 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.4518 (ptmm) REVERT: f 94 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9010 (mm) REVERT: f 142 ASP cc_start: 0.8003 (p0) cc_final: 0.7783 (p0) REVERT: f 191 THR cc_start: 0.8447 (m) cc_final: 0.8187 (m) REVERT: f 228 GLU cc_start: 0.7001 (tp30) cc_final: 0.6730 (tp30) REVERT: g 152 ASP cc_start: 0.7947 (t0) cc_final: 0.7640 (t0) REVERT: g 188 GLU cc_start: 0.7350 (tp30) cc_final: 0.7058 (tp30) REVERT: g 191 THR cc_start: 0.8228 (m) cc_final: 0.7782 (p) outliers start: 382 outliers final: 150 residues processed: 1537 average time/residue: 1.2430 time to fit residues: 2482.7644 Evaluate side-chains 1356 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1159 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP 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 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 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 52 LYS 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 156 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 35 SER 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 G residue 221 TYR Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 77 LEU 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 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 18 GLU Chi-restraints excluded: chain Q residue 125 LEU Chi-restraints excluded: chain R residue 51 ARG Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 204 MET 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 125 LEU Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 84 SER Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 138 LEU Chi-restraints excluded: chain Z residue 150 GLU Chi-restraints excluded: chain Z residue 203 LEU Chi-restraints excluded: chain M residue 26 ILE 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 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 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 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 77 GLU 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 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 41 THR Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER 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 41 THR Chi-restraints excluded: chain H residue 77 GLU 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 203 LEU Chi-restraints excluded: chain V residue 30 ASN 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 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 26 ILE 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 178 ILE Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 ASP 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 203 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 165 ARG Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL 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 84 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 167 SER 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 16 SER Chi-restraints excluded: chain a residue 53 LYS 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 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 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 53 LYS Chi-restraints excluded: chain c residue 124 THR 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 38 LEU Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain e residue 31 VAL 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 200 SER Chi-restraints excluded: chain e residue 208 LYS Chi-restraints excluded: chain e residue 217 VAL 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 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 53 LYS Chi-restraints excluded: chain g residue 151 CYS 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: 8.9990 chunk 639 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 417 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 711 optimal weight: 10.0000 chunk 590 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 HIS R 79 HIS T 47 HIS T 59 GLN T 79 HIS U 79 HIS Z 141 GLN Z 164 GLN M 30 ASN 1 88 ASN N 36 GLN N 88 ASN 2 141 GLN H 88 ASN H 89 GLN V 89 GLN V 141 GLN I 88 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN K 88 ASN Y 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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 ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5000 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= 0.229 Angle : 0.628 14.525 79856 Z= 0.335 Chirality : 0.043 0.319 9338 Planarity : 0.004 0.049 10255 Dihedral : 5.557 54.330 8323 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Rotamer: Outliers : 6.07 % Allowed : 24.10 % Favored : 69.83 % 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 (0.09), residues: 7462 helix: 2.18 (0.09), residues: 3430 sheet: -0.56 (0.13), residues: 1421 loop : -1.61 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 28 HIS 0.012 0.002 HIS R 79 PHE 0.030 0.002 PHE g 42 TYR 0.023 0.002 TYR K 184 ARG 0.009 0.000 ARG C 28 *********************** 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 1609 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 1229 time to evaluate : 5.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 142 ASP cc_start: 0.7746 (p0) cc_final: 0.7500 (p0) REVERT: A 187 LYS cc_start: 0.8070 (tttp) cc_final: 0.7546 (mmmt) REVERT: A 188 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: A 221 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.6849 (t80) REVERT: B 94 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8702 (mp) REVERT: B 187 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7912 (mptp) REVERT: B 221 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7346 (t80) REVERT: B 231 LYS cc_start: 0.8469 (ptmm) cc_final: 0.8130 (ptpp) REVERT: C 94 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8589 (mp) REVERT: C 208 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7970 (mtmm) REVERT: C 227 GLU cc_start: 0.7684 (pm20) cc_final: 0.7480 (pm20) REVERT: D 33 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (mtmm) REVERT: D 40 MET cc_start: 0.8543 (ptp) cc_final: 0.8051 (ptp) REVERT: D 52 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7840 (ptpt) REVERT: D 94 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8609 (mp) REVERT: E 28 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7728 (mtp-110) REVERT: E 40 MET cc_start: 0.8275 (ptt) cc_final: 0.7892 (ptp) REVERT: E 55 ARG cc_start: 0.7636 (pmm-80) cc_final: 0.7337 (ptp-170) REVERT: E 98 GLN cc_start: 0.7523 (mt0) cc_final: 0.7310 (mt0) REVERT: E 221 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7368 (t80) REVERT: F 94 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8582 (mp) REVERT: F 103 TYR cc_start: 0.8998 (m-80) cc_final: 0.8499 (m-80) REVERT: F 178 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8314 (ttp-110) REVERT: F 231 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8070 (ptpp) REVERT: G 9 ASP cc_start: 0.8482 (p0) cc_final: 0.8241 (p0) REVERT: G 177 GLU cc_start: 0.8147 (tp30) cc_final: 0.7843 (mm-30) REVERT: G 221 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7139 (t80) REVERT: O 204 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7449 (mtt) REVERT: P 16 TYR cc_start: 0.7226 (m-10) cc_final: 0.6901 (m-10) REVERT: P 77 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8913 (tp) REVERT: Q 82 TYR cc_start: 0.8642 (t80) cc_final: 0.8387 (t80) REVERT: Q 100 LYS cc_start: 0.8762 (mttm) cc_final: 0.8423 (mtmm) REVERT: Q 221 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: R 55 TYR cc_start: 0.8167 (m-10) cc_final: 0.7655 (m-10) REVERT: R 101 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: R 232 ARG cc_start: 0.7295 (ptt90) cc_final: 0.6755 (mtm180) REVERT: S 34 GLN cc_start: 0.8678 (mp10) cc_final: 0.8344 (mp-120) REVERT: S 119 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7322 (mt-10) REVERT: S 125 LEU cc_start: 0.7903 (tp) cc_final: 0.7681 (tp) REVERT: S 140 ILE cc_start: 0.7864 (pt) cc_final: 0.7629 (pt) REVERT: S 191 MET cc_start: 0.8970 (mmm) cc_final: 0.8710 (mmp) REVERT: S 204 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7157 (mtt) REVERT: T 221 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: U 119 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7507 (mt-10) REVERT: U 125 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7799 (tp) REVERT: U 204 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7637 (mtt) REVERT: Z 96 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: Z 146 MET cc_start: 0.8603 (mtt) cc_final: 0.8339 (mtm) REVERT: Z 150 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: M 27 MET cc_start: 0.8768 (ttt) cc_final: 0.8338 (ttt) REVERT: M 38 ASP cc_start: 0.7940 (t70) cc_final: 0.7364 (t70) REVERT: M 89 GLN cc_start: 0.7999 (mt0) cc_final: 0.7747 (mt0) REVERT: M 93 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.4358 (pmt) REVERT: M 153 ASP cc_start: 0.7767 (m-30) cc_final: 0.7469 (m-30) REVERT: 1 26 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7402 (pt) REVERT: 1 51 ASP cc_start: 0.8354 (m-30) cc_final: 0.8096 (m-30) REVERT: 1 122 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6729 (m-30) REVERT: 1 152 VAL cc_start: 0.8567 (p) cc_final: 0.8287 (t) REVERT: N 38 ASP cc_start: 0.7922 (t70) cc_final: 0.7280 (t0) REVERT: N 60 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8390 (mttm) REVERT: N 153 ASP cc_start: 0.7850 (m-30) cc_final: 0.7566 (m-30) REVERT: 2 21 THR cc_start: 0.4541 (OUTLIER) cc_final: 0.4214 (t) REVERT: 2 90 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7959 (p) REVERT: 2 93 MET cc_start: 0.6507 (pmm) cc_final: 0.6216 (pmm) REVERT: 2 138 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8235 (mt) REVERT: 2 150 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: H 33 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8525 (mttp) REVERT: H 149 ASP cc_start: 0.7333 (p0) cc_final: 0.6827 (p0) REVERT: H 153 ASP cc_start: 0.7875 (m-30) cc_final: 0.7477 (m-30) REVERT: V 51 ASP cc_start: 0.8350 (m-30) cc_final: 0.8121 (m-30) REVERT: V 70 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8112 (mmp80) REVERT: V 138 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8392 (mt) REVERT: I 93 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.4185 (pmt) REVERT: I 112 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.7954 (p) REVERT: I 153 ASP cc_start: 0.7648 (m-30) cc_final: 0.7230 (m-30) REVERT: W 21 THR cc_start: 0.4692 (OUTLIER) cc_final: 0.4281 (t) REVERT: W 26 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7387 (pt) REVERT: W 71 ARG cc_start: 0.7410 (mtm110) cc_final: 0.7092 (mtm-85) REVERT: W 93 MET cc_start: 0.6667 (pmm) cc_final: 0.6420 (pmm) REVERT: W 122 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: J 17 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: J 77 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: J 146 MET cc_start: 0.9110 (mtm) cc_final: 0.8845 (mtp) REVERT: K 21 THR cc_start: 0.4788 (OUTLIER) cc_final: 0.4543 (t) REVERT: K 153 ASP cc_start: 0.7819 (m-30) cc_final: 0.7485 (m-30) REVERT: Y 51 ASP cc_start: 0.8327 (m-30) cc_final: 0.7958 (m-30) REVERT: Y 122 ASP cc_start: 0.7418 (t0) cc_final: 0.7214 (m-30) REVERT: Y 165 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8353 (tpp-160) REVERT: L 26 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7598 (pt) REVERT: L 27 MET cc_start: 0.8582 (ttt) cc_final: 0.8338 (ttt) REVERT: L 77 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: L 153 ASP cc_start: 0.7705 (m-30) cc_final: 0.7104 (m-30) REVERT: a 72 ASP cc_start: 0.7878 (t0) cc_final: 0.7604 (t70) REVERT: a 184 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7356 (mm) REVERT: b 53 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5523 (ptpp) REVERT: b 72 ASP cc_start: 0.7807 (t0) cc_final: 0.7486 (t70) REVERT: b 126 TYR cc_start: 0.7473 (m-80) cc_final: 0.7270 (m-80) REVERT: b 142 ASP cc_start: 0.7671 (p0) cc_final: 0.7447 (p0) REVERT: b 161 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7556 (mppt) REVERT: b 208 LYS cc_start: 0.5050 (OUTLIER) cc_final: 0.4621 (mmmm) REVERT: b 228 GLU cc_start: 0.6877 (tp30) cc_final: 0.6570 (mt-10) REVERT: c 12 ILE cc_start: 0.6498 (tp) cc_final: 0.6113 (tt) REVERT: c 16 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8826 (p) REVERT: c 90 ASP cc_start: 0.6905 (m-30) cc_final: 0.6482 (m-30) REVERT: d 120 MET cc_start: 0.8805 (mtp) cc_final: 0.8535 (mtp) REVERT: d 182 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6376 (tt0) REVERT: d 195 LYS cc_start: 0.7713 (tppt) cc_final: 0.7481 (ptmt) REVERT: d 198 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7794 (tptt) REVERT: d 221 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8156 (t80) REVERT: e 150 ASP cc_start: 0.7981 (t70) cc_final: 0.7757 (t0) REVERT: e 221 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7609 (t80) REVERT: f 53 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.4858 (ptmm) REVERT: f 94 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9008 (mm) REVERT: f 201 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7071 (mt) REVERT: f 228 GLU cc_start: 0.7041 (tp30) cc_final: 0.6752 (tp30) REVERT: g 71 ASP cc_start: 0.7871 (t70) cc_final: 0.7667 (t70) REVERT: g 152 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7624 (t0) REVERT: g 179 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: g 188 GLU cc_start: 0.7417 (tp30) cc_final: 0.7200 (tp30) REVERT: g 191 THR cc_start: 0.8392 (m) cc_final: 0.7953 (p) outliers start: 380 outliers final: 191 residues processed: 1475 average time/residue: 1.2597 time to fit residues: 2409.3633 Evaluate side-chains 1422 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1173 time to evaluate : 4.979 ------------------------------------------------------------------------------- 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 188 GLU Chi-restraints excluded: chain A residue 221 TYR 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 94 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 134 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 33 LYS Chi-restraints excluded: chain D residue 52 LYS 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 156 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 182 GLU 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 F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 178 ARG 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 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 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 77 LEU Chi-restraints excluded: chain S residue 155 VAL 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 T residue 221 GLN Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 84 SER 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 138 LEU Chi-restraints excluded: chain Z residue 150 GLU 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 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 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 41 THR Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 77 GLU 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 139 GLU 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 84 SER Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 LEU Chi-restraints excluded: chain 2 residue 150 GLU 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 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 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 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER 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 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER 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 41 THR 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 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR 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 167 SER Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 77 GLU 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 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 21 THR 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 134 VAL 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 84 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 165 ARG Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 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 203 LEU 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 53 LYS 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 a residue 221 TYR Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 152 ASP 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 b residue 216 THR Chi-restraints excluded: chain b residue 217 VAL 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 124 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 51 ASP Chi-restraints excluded: chain d residue 72 ASP Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 216 THR Chi-restraints excluded: chain d residue 221 TYR 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 124 THR Chi-restraints excluded: chain e residue 144 ILE 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 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 201 LEU 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 53 LYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 152 ASP Chi-restraints excluded: chain g residue 179 GLU 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: 0.9980 chunk 80 optimal weight: 0.9990 chunk 405 optimal weight: 6.9990 chunk 519 optimal weight: 3.9990 chunk 402 optimal weight: 1.9990 chunk 598 optimal weight: 10.0000 chunk 397 optimal weight: 2.9990 chunk 708 optimal weight: 9.9990 chunk 443 optimal weight: 0.9980 chunk 431 optimal weight: 0.5980 chunk 327 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 108 ASN ** D 111 ASN ** 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 72 GLN Q 79 HIS ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS S 79 HIS T 47 HIS T 79 HIS U 79 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN Z 164 GLN M 30 ASN N 88 ASN 2 141 GLN H 88 ASN H 89 GLN V 88 ASN V 89 GLN I 88 ASN W 109 HIS J 30 ASN J 36 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 ASN ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5133 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= 0.229 Angle : 0.630 14.666 79856 Z= 0.336 Chirality : 0.043 0.319 9338 Planarity : 0.004 0.052 10255 Dihedral : 5.461 54.129 8321 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.43 % Favored : 96.42 % Rotamer: Outliers : 5.96 % Allowed : 25.07 % Favored : 68.97 % 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: 0.63 (0.10), residues: 7462 helix: 2.22 (0.09), residues: 3430 sheet: -0.52 (0.13), residues: 1421 loop : -1.54 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 28 HIS 0.014 0.002 HIS U 79 PHE 0.031 0.002 PHE g 42 TYR 0.024 0.002 TYR K 184 ARG 0.013 0.000 ARG S 89 *********************** 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 1587 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1214 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8113 (tttp) cc_final: 0.7546 (mmmt) REVERT: A 188 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: A 221 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.6824 (t80) REVERT: B 93 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8321 (mtt-85) REVERT: B 94 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (mp) REVERT: B 187 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7891 (mptp) REVERT: B 221 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7177 (t80) REVERT: B 231 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8003 (ptpp) REVERT: C 68 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: C 72 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: C 94 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8597 (mp) REVERT: C 208 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mtmm) REVERT: C 227 GLU cc_start: 0.7580 (pm20) cc_final: 0.7346 (pm20) REVERT: D 23 GLN cc_start: 0.8312 (tp40) cc_final: 0.7983 (mm110) REVERT: D 33 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8600 (mtmm) REVERT: D 40 MET cc_start: 0.8544 (ptp) cc_final: 0.8053 (ptp) REVERT: D 52 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7843 (ptpt) REVERT: D 94 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 226 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: E 40 MET cc_start: 0.8260 (ptp) cc_final: 0.7894 (ptp) REVERT: E 55 ARG cc_start: 0.7656 (pmm-80) cc_final: 0.7302 (ptp-170) REVERT: E 98 GLN cc_start: 0.7592 (mt0) cc_final: 0.7380 (mt0) REVERT: E 108 ASN cc_start: 0.8308 (t0) cc_final: 0.8081 (t160) REVERT: E 221 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7380 (t80) REVERT: F 94 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8587 (mp) REVERT: F 103 TYR cc_start: 0.8980 (m-80) cc_final: 0.8465 (m-80) REVERT: F 178 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (ttp-110) REVERT: F 221 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7443 (t80) REVERT: F 231 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8200 (ptpp) REVERT: G 9 ASP cc_start: 0.8497 (p0) cc_final: 0.8253 (p0) REVERT: P 77 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8909 (tp) REVERT: Q 82 TYR cc_start: 0.8656 (t80) cc_final: 0.8396 (t80) REVERT: Q 100 LYS cc_start: 0.8782 (mttm) cc_final: 0.8430 (mtmm) REVERT: Q 204 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6741 (mtt) REVERT: Q 221 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: Q 232 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6930 (mtm110) REVERT: R 55 TYR cc_start: 0.8172 (m-10) cc_final: 0.7797 (m-10) REVERT: R 204 MET cc_start: 0.7173 (mtt) cc_final: 0.6944 (mtt) REVERT: R 232 ARG cc_start: 0.7253 (ptt90) cc_final: 0.6726 (mtm180) REVERT: S 41 LYS cc_start: 0.7935 (mptt) cc_final: 0.7403 (mmtm) REVERT: S 119 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7313 (mt-10) REVERT: S 140 ILE cc_start: 0.7733 (pt) cc_final: 0.7485 (pt) REVERT: S 204 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7133 (mtt) REVERT: T 160 LEU cc_start: 0.7579 (mt) cc_final: 0.7326 (mt) REVERT: T 204 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7476 (mtt) REVERT: U 51 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7190 (ttp-170) REVERT: U 119 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7419 (mt-10) REVERT: U 125 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7480 (tp) REVERT: U 204 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7640 (mtt) REVERT: Z 96 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: Z 150 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: M 27 MET cc_start: 0.8765 (ttt) cc_final: 0.8304 (ttt) REVERT: M 38 ASP cc_start: 0.7959 (t70) cc_final: 0.7338 (t70) REVERT: M 89 GLN cc_start: 0.8087 (mt0) cc_final: 0.7669 (mt0) REVERT: M 93 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.4348 (pmt) REVERT: M 153 ASP cc_start: 0.7768 (m-30) cc_final: 0.7483 (m-30) REVERT: 1 26 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7400 (pt) REVERT: 1 51 ASP cc_start: 0.8346 (m-30) cc_final: 0.8084 (m-30) REVERT: 1 122 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: 1 152 VAL cc_start: 0.8574 (p) cc_final: 0.8298 (t) REVERT: N 38 ASP cc_start: 0.7870 (t70) cc_final: 0.7250 (t0) REVERT: N 60 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8370 (mttm) REVERT: N 153 ASP cc_start: 0.7853 (m-30) cc_final: 0.7573 (m-30) REVERT: 2 21 THR cc_start: 0.4532 (OUTLIER) cc_final: 0.4226 (t) REVERT: 2 26 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7292 (pt) REVERT: 2 90 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.7989 (p) REVERT: 2 93 MET cc_start: 0.6379 (pmm) cc_final: 0.6128 (pmm) REVERT: 2 138 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8234 (mt) REVERT: 2 150 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: H 33 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8523 (mttp) REVERT: H 149 ASP cc_start: 0.7336 (p0) cc_final: 0.6808 (p0) REVERT: H 153 ASP cc_start: 0.7878 (m-30) cc_final: 0.7475 (m-30) REVERT: V 51 ASP cc_start: 0.8332 (m-30) cc_final: 0.8118 (m-30) REVERT: V 70 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8049 (mmp80) REVERT: V 138 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mt) REVERT: I 71 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7603 (mtt90) REVERT: I 79 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (m) REVERT: I 93 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.4171 (pmt) REVERT: I 112 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.7985 (p) REVERT: I 153 ASP cc_start: 0.7645 (m-30) cc_final: 0.7233 (m-30) REVERT: W 14 MET cc_start: 0.8551 (mtp) cc_final: 0.8301 (mtm) REVERT: W 21 THR cc_start: 0.4635 (OUTLIER) cc_final: 0.4276 (t) REVERT: W 26 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7400 (pt) REVERT: W 93 MET cc_start: 0.6770 (pmm) cc_final: 0.6450 (pmm) REVERT: W 122 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: J 17 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: J 77 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: J 146 MET cc_start: 0.9101 (mtm) cc_final: 0.8852 (mtp) REVERT: J 186 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: X 86 MET cc_start: 0.7937 (ttm) cc_final: 0.7667 (ttm) REVERT: K 21 THR cc_start: 0.5034 (OUTLIER) cc_final: 0.4761 (t) REVERT: K 71 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7869 (mtt90) REVERT: K 153 ASP cc_start: 0.7821 (m-30) cc_final: 0.7479 (m-30) REVERT: Y 51 ASP cc_start: 0.8298 (m-30) cc_final: 0.7923 (m-30) REVERT: Y 122 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: Y 165 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8480 (tpp-160) REVERT: L 26 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7662 (pt) REVERT: L 27 MET cc_start: 0.8619 (ttt) cc_final: 0.8364 (ttt) REVERT: L 77 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: L 153 ASP cc_start: 0.7711 (m-30) cc_final: 0.7121 (m-30) REVERT: a 68 GLN cc_start: 0.7962 (mt0) cc_final: 0.7610 (mp10) REVERT: a 72 ASP cc_start: 0.7855 (t0) cc_final: 0.7594 (t70) REVERT: a 184 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7351 (mm) REVERT: b 51 ASP cc_start: 0.7076 (t0) cc_final: 0.6661 (t0) REVERT: b 72 ASP cc_start: 0.7852 (t0) cc_final: 0.7512 (t70) REVERT: b 125 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7394 (tp-100) REVERT: b 161 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7543 (mppt) REVERT: b 201 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6681 (mt) REVERT: b 208 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4640 (mmmm) REVERT: b 228 GLU cc_start: 0.6847 (tp30) cc_final: 0.6622 (mt-10) REVERT: c 12 ILE cc_start: 0.6450 (tp) cc_final: 0.6082 (tt) REVERT: c 16 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (p) REVERT: c 90 ASP cc_start: 0.6978 (m-30) cc_final: 0.6552 (m-30) REVERT: c 221 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7890 (t80) REVERT: d 182 GLU cc_start: 0.6457 (mm-30) cc_final: 0.6217 (tp30) REVERT: d 195 LYS cc_start: 0.7699 (tppt) cc_final: 0.7476 (ptmt) REVERT: d 198 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7851 (tptt) REVERT: e 84 ASP cc_start: 0.8888 (m-30) cc_final: 0.8687 (m-30) REVERT: e 150 ASP cc_start: 0.7997 (t70) cc_final: 0.7794 (t0) REVERT: e 161 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (mttp) REVERT: e 221 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.7334 (t80) REVERT: e 228 GLU cc_start: 0.7058 (tp30) cc_final: 0.6766 (mp0) REVERT: f 94 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9014 (mm) REVERT: f 201 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7105 (mt) REVERT: f 228 GLU cc_start: 0.6919 (tp30) cc_final: 0.6649 (tp30) REVERT: g 142 ASP cc_start: 0.7870 (p0) cc_final: 0.7597 (p0) REVERT: g 152 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (t0) REVERT: g 179 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: g 188 GLU cc_start: 0.7377 (tp30) cc_final: 0.7176 (tp30) REVERT: g 191 THR cc_start: 0.8364 (m) cc_final: 0.7931 (p) outliers start: 373 outliers final: 210 residues processed: 1456 average time/residue: 1.2366 time to fit residues: 2342.7727 Evaluate side-chains 1433 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1157 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 VAL 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 93 ARG 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 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 134 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 33 LYS Chi-restraints excluded: chain D residue 52 LYS 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 156 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 182 GLU 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 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 156 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 77 LEU 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 Q residue 125 LEU Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 221 GLN Chi-restraints excluded: chain R residue 155 VAL 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 51 ARG Chi-restraints excluded: chain U residue 125 LEU Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 74 MET Chi-restraints excluded: chain Z residue 84 SER 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 150 GLU 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 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 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 30 ASN Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 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 77 GLU 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 139 GLU 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 84 SER Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 LEU Chi-restraints excluded: chain 2 residue 150 GLU 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 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 77 GLU 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 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER 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 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER 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 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 175 VAL Chi-restraints excluded: chain W residue 203 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR 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 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 26 ILE Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL 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 21 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 134 VAL 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 84 SER 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 203 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 26 ILE 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 131 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 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 53 LYS Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 184 LEU 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 38 LEU Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 152 ASP 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 b residue 217 VAL 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 53 LYS Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR 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 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 216 THR 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 53 LYS 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 161 LYS Chi-restraints excluded: chain e residue 200 SER 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 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 201 LEU 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 38 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 152 ASP Chi-restraints excluded: chain g residue 179 GLU 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: 0.9980 chunk 282 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 450 optimal weight: 0.4980 chunk 482 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 556 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 108 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN 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 ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS U 79 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 GLN Z 164 GLN M 30 ASN M 88 ASN N 88 ASN 2 141 GLN H 88 ASN H 89 GLN V 88 ASN V 89 GLN V 141 GLN I 88 ASN ** W 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 88 ASN K 88 ASN Y 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** ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 ASN ** 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: 0.7948 moved from start: 0.5248 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= 0.228 Angle : 0.629 14.910 79856 Z= 0.336 Chirality : 0.043 0.315 9338 Planarity : 0.004 0.054 10255 Dihedral : 5.434 54.470 8321 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.59 % Favored : 96.26 % Rotamer: Outliers : 5.91 % Allowed : 25.31 % Favored : 68.78 % 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: 0.68 (0.10), residues: 7462 helix: 2.25 (0.09), residues: 3437 sheet: -0.50 (0.13), residues: 1421 loop : -1.50 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 28 HIS 0.014 0.002 HIS U 79 PHE 0.032 0.002 PHE g 42 TYR 0.024 0.002 TYR K 184 ARG 0.012 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 1568 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1198 time to evaluate : 5.012 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 188 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: A 221 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.6821 (t80) REVERT: B 93 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8314 (mtt-85) REVERT: B 94 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 221 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.7166 (t80) REVERT: B 231 LYS cc_start: 0.8334 (ptmm) cc_final: 0.8004 (pttp) REVERT: C 13 THR cc_start: 0.9184 (p) cc_final: 0.8944 (p) REVERT: C 68 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: C 72 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 94 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 208 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: C 227 GLU cc_start: 0.7539 (pm20) cc_final: 0.7320 (pm20) REVERT: D 33 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8593 (mtmm) REVERT: D 40 MET cc_start: 0.8525 (ptp) cc_final: 0.7999 (ptp) REVERT: D 94 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8534 (mp) REVERT: E 40 MET cc_start: 0.8244 (ptp) cc_final: 0.7865 (ptp) REVERT: E 55 ARG cc_start: 0.7550 (pmm-80) cc_final: 0.7208 (ptp-170) REVERT: E 81 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8605 (mt) REVERT: E 98 GLN cc_start: 0.7457 (mt0) cc_final: 0.7254 (mt0) REVERT: E 221 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7412 (t80) REVERT: F 94 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8592 (mp) REVERT: F 103 TYR cc_start: 0.8981 (m-80) cc_final: 0.8464 (m-80) REVERT: F 178 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8351 (ttp-110) REVERT: F 227 GLU cc_start: 0.7648 (pm20) cc_final: 0.7415 (pm20) REVERT: F 231 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8214 (ptpp) REVERT: G 9 ASP cc_start: 0.8518 (p0) cc_final: 0.8275 (p0) REVERT: G 208 LYS cc_start: 0.8225 (mtmm) cc_final: 0.8023 (mppt) REVERT: G 231 LYS cc_start: 0.7836 (ptmm) cc_final: 0.7556 (ptpp) REVERT: O 59 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: P 77 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8911 (tp) REVERT: Q 82 TYR cc_start: 0.8651 (t80) cc_final: 0.8423 (t80) REVERT: Q 100 LYS cc_start: 0.8799 (mttm) cc_final: 0.8436 (mtmm) REVERT: Q 204 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7027 (mtp) REVERT: Q 221 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7556 (mp10) REVERT: Q 232 ARG cc_start: 0.7262 (mtm180) cc_final: 0.7046 (mtm110) REVERT: R 51 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7378 (ttp-170) REVERT: R 55 TYR cc_start: 0.8217 (m-10) cc_final: 0.7964 (m-10) REVERT: R 101 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: R 204 MET cc_start: 0.7304 (mtt) cc_final: 0.7101 (mtt) REVERT: R 232 ARG cc_start: 0.7245 (ptt90) cc_final: 0.6729 (mtm180) REVERT: S 41 LYS cc_start: 0.7957 (mptt) cc_final: 0.7454 (mmtm) REVERT: S 119 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7311 (mt-10) REVERT: S 140 ILE cc_start: 0.7608 (pt) cc_final: 0.7377 (pt) REVERT: S 204 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7141 (mtt) REVERT: Z 96 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: Z 150 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: M 27 MET cc_start: 0.8775 (ttt) cc_final: 0.8435 (ttt) REVERT: M 38 ASP cc_start: 0.7847 (t70) cc_final: 0.7211 (t70) REVERT: M 93 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.4387 (pmt) REVERT: M 131 SER cc_start: 0.8685 (t) cc_final: 0.8409 (p) REVERT: M 153 ASP cc_start: 0.7772 (m-30) cc_final: 0.7479 (m-30) REVERT: 1 26 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7459 (pt) REVERT: 1 51 ASP cc_start: 0.8354 (m-30) cc_final: 0.8097 (m-30) REVERT: 1 122 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6888 (m-30) REVERT: 1 152 VAL cc_start: 0.8564 (p) cc_final: 0.8312 (t) REVERT: N 38 ASP cc_start: 0.7737 (t70) cc_final: 0.7127 (t0) REVERT: N 60 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8375 (mttm) REVERT: N 71 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7074 (mtt90) REVERT: N 153 ASP cc_start: 0.7855 (m-30) cc_final: 0.7472 (m-30) REVERT: 2 21 THR cc_start: 0.4466 (OUTLIER) cc_final: 0.4171 (t) REVERT: 2 26 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7303 (pt) REVERT: 2 90 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8011 (p) REVERT: 2 93 MET cc_start: 0.6470 (pmm) cc_final: 0.6201 (pmm) REVERT: 2 138 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (mt) REVERT: 2 150 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: H 149 ASP cc_start: 0.7327 (p0) cc_final: 0.6816 (p0) REVERT: H 153 ASP cc_start: 0.7873 (m-30) cc_final: 0.7483 (m-30) REVERT: V 51 ASP cc_start: 0.8310 (m-30) cc_final: 0.8103 (m-30) REVERT: V 70 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8015 (mmp80) REVERT: V 138 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8358 (mt) REVERT: V 172 MET cc_start: 0.7644 (tpt) cc_final: 0.7443 (tpp) REVERT: I 71 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7602 (mtt90) REVERT: I 79 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (m) REVERT: I 93 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.4164 (pmt) REVERT: I 112 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7961 (p) REVERT: I 153 ASP cc_start: 0.7646 (m-30) cc_final: 0.7220 (m-30) REVERT: W 14 MET cc_start: 0.8538 (mtp) cc_final: 0.8283 (mtm) REVERT: W 21 THR cc_start: 0.4615 (OUTLIER) cc_final: 0.4264 (t) REVERT: W 26 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7418 (pt) REVERT: J 17 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: J 77 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: J 146 MET cc_start: 0.9082 (mtm) cc_final: 0.8853 (mtp) REVERT: J 186 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: X 45 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6463 (mp) REVERT: X 86 MET cc_start: 0.7948 (ttm) cc_final: 0.7714 (ttm) REVERT: K 21 THR cc_start: 0.5057 (OUTLIER) cc_final: 0.4794 (t) REVERT: K 71 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (mtt90) REVERT: K 153 ASP cc_start: 0.7822 (m-30) cc_final: 0.7487 (m-30) REVERT: Y 51 ASP cc_start: 0.8302 (m-30) cc_final: 0.7914 (m-30) REVERT: Y 122 ASP cc_start: 0.7326 (t0) cc_final: 0.6855 (m-30) REVERT: L 22 MET cc_start: 0.1577 (OUTLIER) cc_final: 0.0660 (ppp) REVERT: L 26 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7671 (pt) REVERT: L 27 MET cc_start: 0.8621 (ttt) cc_final: 0.8360 (ttt) REVERT: L 77 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: L 93 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5434 (pmm) REVERT: L 153 ASP cc_start: 0.7720 (m-30) cc_final: 0.7126 (m-30) REVERT: a 72 ASP cc_start: 0.7915 (t0) cc_final: 0.7651 (t70) REVERT: a 184 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7371 (mm) REVERT: b 72 ASP cc_start: 0.7890 (t0) cc_final: 0.7582 (t70) REVERT: b 125 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7374 (tp-100) REVERT: b 142 ASP cc_start: 0.7885 (p0) cc_final: 0.7674 (p0) REVERT: b 161 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7519 (mppt) REVERT: b 201 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.7013 (mm) REVERT: b 228 GLU cc_start: 0.6899 (tp30) cc_final: 0.6679 (mt-10) REVERT: c 12 ILE cc_start: 0.6510 (tp) cc_final: 0.6177 (tt) REVERT: c 16 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8947 (p) REVERT: c 72 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7643 (t70) REVERT: c 221 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.7789 (t80) REVERT: d 195 LYS cc_start: 0.7683 (tppt) cc_final: 0.7479 (ptmt) REVERT: d 198 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7807 (tptt) REVERT: e 84 ASP cc_start: 0.8892 (m-30) cc_final: 0.8678 (m-30) REVERT: e 150 ASP cc_start: 0.8003 (t70) cc_final: 0.7794 (t0) REVERT: e 161 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7640 (mttp) REVERT: e 221 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7016 (t80) REVERT: f 51 ASP cc_start: 0.6682 (t0) cc_final: 0.6411 (t0) REVERT: f 94 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9024 (mm) REVERT: f 201 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6965 (mt) REVERT: f 228 GLU cc_start: 0.6925 (tp30) cc_final: 0.6640 (tp30) REVERT: g 120 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: g 142 ASP cc_start: 0.7889 (p0) cc_final: 0.7618 (p0) REVERT: g 152 ASP cc_start: 0.7695 (t0) cc_final: 0.7312 (t0) REVERT: g 191 THR cc_start: 0.8292 (m) cc_final: 0.7922 (p) outliers start: 370 outliers final: 223 residues processed: 1439 average time/residue: 1.2323 time to fit residues: 2315.7500 Evaluate side-chains 1442 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1156 time to evaluate : 4.953 ------------------------------------------------------------------------------- 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 188 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP 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 134 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 33 LYS 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 156 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 182 GLU 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 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 156 THR Chi-restraints excluded: chain F residue 178 ARG Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 59 GLN Chi-restraints excluded: chain O residue 77 LEU 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 Q residue 125 LEU Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 221 GLN 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 S residue 155 VAL 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 155 VAL Chi-restraints excluded: chain U residue 204 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 84 SER 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 150 GLU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 175 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 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 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 30 ASN Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 1 residue 203 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 77 GLU 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 139 GLU 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 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 LEU Chi-restraints excluded: chain 2 residue 150 GLU 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 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 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 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER 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 79 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER 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 2 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 120 VAL 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 12 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR 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 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 45 ILE Chi-restraints excluded: chain X residue 74 MET Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 155 VAL 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 21 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 71 ARG 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 134 VAL 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 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 84 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE 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 120 VAL Chi-restraints excluded: chain L residue 131 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 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 53 LYS Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 184 LEU 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 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 201 LEU Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 217 VAL 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 53 LYS 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 216 THR Chi-restraints excluded: chain c residue 221 TYR 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 184 LEU Chi-restraints excluded: chain d residue 194 ILE 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 53 LYS Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 161 LYS Chi-restraints excluded: chain e residue 200 SER 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 201 LEU 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 18 ASP 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 120 MET 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 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: 9.9990 chunk 678 optimal weight: 2.9990 chunk 619 optimal weight: 5.9990 chunk 660 optimal weight: 5.9990 chunk 397 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 518 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 596 optimal weight: 5.9990 chunk 624 optimal weight: 3.9990 chunk 657 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 44 ASN C 158 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 108 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN G 122 GLN O 79 HIS P 79 HIS Q 47 HIS Q 79 HIS R 47 HIS R 79 HIS T 47 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS U 79 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 109 HIS Z 164 GLN M 30 ASN M 109 HIS N 88 ASN 2 109 HIS 2 141 GLN H 36 GLN H 88 ASN H 89 GLN V 88 ASN V 89 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** X 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN L 88 ASN a 108 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 183 ASN ** 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** e 183 ASN ** f 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 ASN ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 59129 Z= 0.376 Angle : 0.708 15.230 79856 Z= 0.375 Chirality : 0.047 0.364 9338 Planarity : 0.005 0.056 10255 Dihedral : 5.773 55.595 8320 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.66 % Favored : 96.14 % Rotamer: Outliers : 6.33 % Allowed : 25.36 % Favored : 68.31 % 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: 0.52 (0.09), residues: 7462 helix: 2.02 (0.09), residues: 3444 sheet: -0.64 (0.13), residues: 1463 loop : -1.39 (0.11), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 28 HIS 0.015 0.002 HIS U 79 PHE 0.030 0.002 PHE g 42 TYR 0.025 0.002 TYR K 184 ARG 0.013 0.001 ARG X 70 *********************** 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 1571 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 1175 time to evaluate : 5.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: B 93 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8294 (mtt-85) REVERT: B 94 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8720 (mp) REVERT: B 221 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.7377 (t80) REVERT: B 231 LYS cc_start: 0.8367 (ptmm) cc_final: 0.8039 (ptpp) REVERT: C 13 THR cc_start: 0.9292 (p) cc_final: 0.9070 (p) REVERT: C 68 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: C 72 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: C 94 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 208 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7961 (mtmm) REVERT: D 33 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8551 (mtmm) REVERT: D 40 MET cc_start: 0.8643 (ptp) cc_final: 0.8211 (ptm) REVERT: D 94 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8508 (mp) REVERT: D 231 LYS cc_start: 0.8123 (ptpt) cc_final: 0.7810 (pttm) REVERT: E 40 MET cc_start: 0.8285 (ptp) cc_final: 0.7933 (ptp) REVERT: E 78 THR cc_start: 0.8466 (p) cc_final: 0.8203 (p) REVERT: E 81 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8710 (mt) REVERT: E 98 GLN cc_start: 0.7495 (mt0) cc_final: 0.7289 (mt0) REVERT: E 221 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7507 (t80) REVERT: F 94 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8640 (mp) REVERT: F 103 TYR cc_start: 0.8988 (m-80) cc_final: 0.8523 (m-80) REVERT: F 231 LYS cc_start: 0.8329 (ptpp) cc_final: 0.7996 (ptpp) REVERT: G 70 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8361 (mp) REVERT: G 231 LYS cc_start: 0.7905 (ptmm) cc_final: 0.7614 (ptpp) REVERT: O 37 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: O 79 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.5560 (t-90) REVERT: Q 82 TYR cc_start: 0.8721 (t80) cc_final: 0.8462 (t80) REVERT: Q 204 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: Q 221 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: R 51 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7452 (ttp-170) REVERT: R 101 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: R 204 MET cc_start: 0.7242 (mtt) cc_final: 0.7024 (mtt) REVERT: R 232 ARG cc_start: 0.7358 (ptt90) cc_final: 0.6819 (mtm180) REVERT: S 119 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7350 (mt-10) REVERT: S 140 ILE cc_start: 0.7701 (pt) cc_final: 0.7457 (pt) REVERT: T 142 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.6543 (mpt) REVERT: Z 150 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: M 27 MET cc_start: 0.8867 (ttt) cc_final: 0.8481 (ttt) REVERT: M 38 ASP cc_start: 0.8074 (t70) cc_final: 0.7459 (t70) REVERT: M 93 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.4494 (pmt) REVERT: M 153 ASP cc_start: 0.7816 (m-30) cc_final: 0.7536 (m-30) REVERT: 1 51 ASP cc_start: 0.8453 (m-30) cc_final: 0.8158 (m-30) REVERT: 1 96 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: 1 122 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: 1 152 VAL cc_start: 0.8658 (p) cc_final: 0.8390 (t) REVERT: N 38 ASP cc_start: 0.8017 (t70) cc_final: 0.7449 (t0) REVERT: N 93 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.4792 (pmt) REVERT: N 153 ASP cc_start: 0.7890 (m-30) cc_final: 0.7608 (m-30) REVERT: 2 21 THR cc_start: 0.4806 (OUTLIER) cc_final: 0.4469 (t) REVERT: 2 26 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7665 (pt) REVERT: 2 90 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (p) REVERT: 2 138 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8283 (mt) REVERT: 2 150 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: H 53 GLN cc_start: 0.8452 (mt0) cc_final: 0.8245 (mt0) REVERT: H 149 ASP cc_start: 0.7290 (p0) cc_final: 0.6763 (p0) REVERT: H 153 ASP cc_start: 0.7889 (m-30) cc_final: 0.7481 (m-30) REVERT: V 51 ASP cc_start: 0.8355 (m-30) cc_final: 0.8152 (m-30) REVERT: V 70 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8009 (mmp80) REVERT: V 138 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8384 (mt) REVERT: V 152 VAL cc_start: 0.8771 (p) cc_final: 0.8366 (t) REVERT: I 71 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7613 (mtt90) REVERT: I 93 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.4251 (pmt) REVERT: I 112 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8115 (p) REVERT: I 153 ASP cc_start: 0.7726 (m-30) cc_final: 0.7289 (m-30) REVERT: W 14 MET cc_start: 0.8516 (mtp) cc_final: 0.8311 (mtt) REVERT: W 17 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: W 21 THR cc_start: 0.4524 (OUTLIER) cc_final: 0.4158 (t) REVERT: W 93 MET cc_start: 0.7073 (pmm) cc_final: 0.6633 (pmm) REVERT: J 17 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: J 77 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: J 146 MET cc_start: 0.9113 (mtm) cc_final: 0.8860 (mtp) REVERT: J 186 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: X 6 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8927 (pt) REVERT: K 21 THR cc_start: 0.5368 (OUTLIER) cc_final: 0.5095 (t) REVERT: K 93 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5101 (pmt) REVERT: K 153 ASP cc_start: 0.7845 (m-30) cc_final: 0.7508 (m-30) REVERT: Y 51 ASP cc_start: 0.8418 (m-30) cc_final: 0.7993 (m-30) REVERT: Y 122 ASP cc_start: 0.7550 (t0) cc_final: 0.7249 (m-30) REVERT: Y 138 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (mt) REVERT: L 22 MET cc_start: 0.1688 (OUTLIER) cc_final: 0.0971 (tmm) REVERT: L 27 MET cc_start: 0.8725 (ttt) cc_final: 0.8378 (ttt) REVERT: L 77 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: L 93 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.4923 (pmt) REVERT: L 122 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6397 (t70) REVERT: L 153 ASP cc_start: 0.7758 (m-30) cc_final: 0.7295 (m-30) REVERT: a 72 ASP cc_start: 0.8053 (t0) cc_final: 0.7785 (t70) REVERT: a 108 ASN cc_start: 0.8574 (t0) cc_final: 0.8364 (t160) REVERT: b 72 ASP cc_start: 0.7947 (t0) cc_final: 0.7654 (t70) REVERT: b 125 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7740 (tp-100) REVERT: b 161 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (mmtp) REVERT: b 201 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7051 (mm) REVERT: c 12 ILE cc_start: 0.6667 (tp) cc_final: 0.6266 (tt) REVERT: c 16 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8994 (p) REVERT: c 208 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5155 (mtmm) REVERT: c 221 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.7774 (t80) REVERT: d 198 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7908 (tptt) REVERT: d 228 GLU cc_start: 0.6729 (tp30) cc_final: 0.6161 (mp0) REVERT: e 84 ASP cc_start: 0.8879 (m-30) cc_final: 0.8635 (m-30) REVERT: e 150 ASP cc_start: 0.7986 (t70) cc_final: 0.7783 (t0) REVERT: e 161 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (mttm) REVERT: e 221 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.6798 (t80) REVERT: f 94 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9022 (mm) REVERT: f 228 GLU cc_start: 0.6964 (tp30) cc_final: 0.6632 (tp30) REVERT: g 152 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7508 (t0) REVERT: g 181 LYS cc_start: 0.7222 (mmtm) cc_final: 0.7012 (mmtm) outliers start: 396 outliers final: 256 residues processed: 1442 average time/residue: 1.2467 time to fit residues: 2345.3187 Evaluate side-chains 1466 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1151 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 VAL 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 52 LYS Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP 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 134 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 33 LYS 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 156 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 221 TYR 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 F residue 94 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain O residue 79 HIS 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 204 MET Chi-restraints excluded: chain Q residue 221 GLN 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 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 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 84 SER 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 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 123 ILE 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 6 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 37 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 175 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 2 THR 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 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 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 41 THR Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 84 SER Chi-restraints excluded: chain 2 residue 90 VAL Chi-restraints excluded: chain 2 residue 119 SER Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 LEU Chi-restraints excluded: chain 2 residue 150 GLU 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 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 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 178 ILE 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 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 137 VAL 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 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 167 SER 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 2 THR 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 41 THR 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 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 J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 ASP 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 45 ILE 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 134 VAL Chi-restraints excluded: chain X residue 155 VAL 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 21 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 134 VAL 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 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 84 SER 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 140 SER Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 203 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 26 ILE 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 79 VAL Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 131 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 a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 53 LYS 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 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 201 LEU 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 53 LYS Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 208 LYS Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 36 THR 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 184 LEU Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 216 THR 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 53 LYS 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 161 LYS Chi-restraints excluded: chain e residue 200 SER 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 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 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 152 ASP 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: 4.9990 chunk 698 optimal weight: 5.9990 chunk 426 optimal weight: 0.8980 chunk 331 optimal weight: 0.5980 chunk 485 optimal weight: 1.9990 chunk 732 optimal weight: 6.9990 chunk 673 optimal weight: 3.9990 chunk 583 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 450 optimal weight: 7.9990 chunk 357 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN C 44 ASN D 23 GLN D 98 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN F 44 ASN G 122 GLN O 79 HIS P 79 HIS ** P 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS Q 79 HIS R 47 HIS R 79 HIS ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS U 79 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN M 88 ASN M 89 GLN N 88 ASN 2 141 GLN H 36 GLN H 88 ASN H 89 GLN V 88 ASN V 89 GLN V 141 GLN I 141 GLN J 30 ASN J 36 GLN J 88 ASN X 88 ASN X 141 GLN K 88 ASN ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN L 88 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 183 ASN ** c 121 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 59129 Z= 0.258 Angle : 0.661 16.441 79856 Z= 0.353 Chirality : 0.044 0.333 9338 Planarity : 0.004 0.060 10255 Dihedral : 5.587 55.378 8320 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 5.29 % Allowed : 26.69 % Favored : 68.02 % 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: 0.53 (0.10), residues: 7462 helix: 2.05 (0.09), residues: 3493 sheet: -0.63 (0.13), residues: 1463 loop : -1.49 (0.11), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 28 HIS 0.015 0.002 HIS U 79 PHE 0.031 0.002 PHE b 42 TYR 0.026 0.002 TYR 1 124 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 1509 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1178 time to evaluate : 4.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7074 (pt0) REVERT: B 93 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8266 (mtt-85) REVERT: B 94 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8693 (mp) REVERT: B 221 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 231 LYS cc_start: 0.8433 (ptmm) cc_final: 0.8127 (ptpp) REVERT: C 68 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: C 72 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: C 94 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8548 (mp) REVERT: C 208 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7990 (mtmm) REVERT: D 33 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8563 (mtmm) REVERT: D 40 MET cc_start: 0.8501 (ptp) cc_final: 0.8211 (ptm) REVERT: D 94 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 208 LYS cc_start: 0.8208 (mppt) cc_final: 0.7778 (mtpm) REVERT: D 231 LYS cc_start: 0.8101 (ptpt) cc_final: 0.7798 (pttm) REVERT: E 28 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7727 (mtp-110) REVERT: E 40 MET cc_start: 0.8177 (ptp) cc_final: 0.7806 (ptp) REVERT: E 81 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8596 (mt) REVERT: E 221 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7479 (t80) REVERT: F 94 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8638 (mp) REVERT: F 103 TYR cc_start: 0.8995 (m-80) cc_final: 0.8490 (m-80) REVERT: F 231 LYS cc_start: 0.8432 (ptpp) cc_final: 0.8201 (ptpp) REVERT: P 232 ARG cc_start: 0.7086 (ptt90) cc_final: 0.6444 (mtm180) REVERT: Q 82 TYR cc_start: 0.8692 (t80) cc_final: 0.8395 (t80) REVERT: Q 204 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6946 (mtp) REVERT: Q 221 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: R 51 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7453 (ttp-170) REVERT: R 101 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: R 232 ARG cc_start: 0.7257 (ptt90) cc_final: 0.6794 (mtm180) REVERT: S 41 LYS cc_start: 0.7892 (mptt) cc_final: 0.7597 (mmtm) REVERT: S 119 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7311 (mt-10) REVERT: S 140 ILE cc_start: 0.7781 (pt) cc_final: 0.7572 (pt) REVERT: T 204 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7498 (mtt) REVERT: U 125 LEU cc_start: 0.7396 (tp) cc_final: 0.7113 (mt) REVERT: Z 39 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8540 (p) REVERT: M 27 MET cc_start: 0.8858 (ttt) cc_final: 0.8422 (ttt) REVERT: M 38 ASP cc_start: 0.7810 (t70) cc_final: 0.7210 (t70) REVERT: M 93 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.4458 (pmt) REVERT: M 131 SER cc_start: 0.8729 (t) cc_final: 0.8416 (p) REVERT: M 153 ASP cc_start: 0.7760 (m-30) cc_final: 0.7475 (m-30) REVERT: 1 51 ASP cc_start: 0.8346 (m-30) cc_final: 0.8079 (m-30) REVERT: 1 122 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: 1 152 VAL cc_start: 0.8563 (p) cc_final: 0.8301 (t) REVERT: N 26 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7232 (pp) REVERT: N 38 ASP cc_start: 0.7830 (t70) cc_final: 0.7243 (t0) REVERT: N 93 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.4721 (pmt) REVERT: N 153 ASP cc_start: 0.7837 (m-30) cc_final: 0.7564 (m-30) REVERT: 2 21 THR cc_start: 0.4591 (OUTLIER) cc_final: 0.4309 (t) REVERT: 2 26 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7404 (pt) REVERT: 2 150 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: H 53 GLN cc_start: 0.8511 (mt0) cc_final: 0.8283 (mt0) REVERT: H 149 ASP cc_start: 0.7280 (p0) cc_final: 0.6760 (p0) REVERT: H 153 ASP cc_start: 0.7864 (m-30) cc_final: 0.7470 (m-30) REVERT: V 70 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7990 (mmp80) REVERT: V 138 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (mt) REVERT: I 93 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.4260 (pmt) REVERT: I 112 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8003 (p) REVERT: I 153 ASP cc_start: 0.7630 (m-30) cc_final: 0.7232 (m-30) REVERT: W 14 MET cc_start: 0.8494 (mtp) cc_final: 0.8243 (mtm) REVERT: W 17 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6983 (pp20) REVERT: W 21 THR cc_start: 0.4701 (OUTLIER) cc_final: 0.4349 (t) REVERT: W 26 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7609 (pt) REVERT: W 93 MET cc_start: 0.7037 (pmm) cc_final: 0.6704 (pmm) REVERT: J 77 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: J 146 MET cc_start: 0.9103 (mtm) cc_final: 0.8869 (mtp) REVERT: J 186 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: X 6 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8893 (pt) REVERT: K 21 THR cc_start: 0.5153 (OUTLIER) cc_final: 0.4861 (t) REVERT: K 93 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5275 (pmt) REVERT: K 153 ASP cc_start: 0.7825 (m-30) cc_final: 0.7485 (m-30) REVERT: Y 51 ASP cc_start: 0.8318 (m-30) cc_final: 0.7944 (m-30) REVERT: Y 122 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: L 22 MET cc_start: 0.1810 (OUTLIER) cc_final: 0.1136 (tmm) REVERT: L 26 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7675 (pt) REVERT: L 27 MET cc_start: 0.8681 (ttt) cc_final: 0.8369 (ttt) REVERT: L 71 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7246 (mpp80) REVERT: L 77 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: L 93 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5172 (pmt) REVERT: L 153 ASP cc_start: 0.7713 (m-30) cc_final: 0.7120 (m-30) REVERT: a 72 ASP cc_start: 0.8071 (t0) cc_final: 0.7800 (t70) REVERT: b 125 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7433 (tp-100) REVERT: b 161 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7563 (mmtp) REVERT: b 201 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6891 (mm) REVERT: b 221 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: c 12 ILE cc_start: 0.6533 (tp) cc_final: 0.6174 (tt) REVERT: c 16 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8965 (p) REVERT: c 90 ASP cc_start: 0.6983 (m-30) cc_final: 0.6554 (m-30) REVERT: c 221 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7818 (t80) REVERT: d 20 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7438 (mtp85) REVERT: d 198 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7856 (tptt) REVERT: d 228 GLU cc_start: 0.6719 (tp30) cc_final: 0.6238 (mp0) REVERT: e 84 ASP cc_start: 0.8852 (m-30) cc_final: 0.8632 (m-30) REVERT: e 161 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.6994 (mmpt) REVERT: e 221 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.6788 (t80) REVERT: f 12 ILE cc_start: 0.7086 (tp) cc_final: 0.6666 (tt) REVERT: f 94 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9034 (mm) REVERT: f 228 GLU cc_start: 0.6931 (tp30) cc_final: 0.6591 (tp30) REVERT: g 152 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7347 (t0) outliers start: 331 outliers final: 237 residues processed: 1396 average time/residue: 1.2287 time to fit residues: 2241.3909 Evaluate side-chains 1431 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1139 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain B residue 225 ASP 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 134 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 33 LYS 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 156 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 221 TYR 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 F residue 94 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain G residue 221 TYR 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 140 ILE Chi-restraints excluded: chain Q residue 204 MET Chi-restraints excluded: chain Q residue 221 GLN 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 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 204 MET Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 39 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 84 SER 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 175 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 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 123 ILE 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 41 THR Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 84 SER 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 1 residue 203 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain N residue 22 MET 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 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 175 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain 2 residue 17 GLU 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 84 SER Chi-restraints excluded: chain 2 residue 119 SER 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 175 VAL Chi-restraints excluded: chain 2 residue 178 ILE 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 77 GLU 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 203 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain V residue 74 MET Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 123 ILE Chi-restraints excluded: chain V residue 137 VAL 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 93 MET Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 120 VAL 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 2 THR 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 41 THR 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 155 VAL Chi-restraints excluded: chain W residue 164 GLN 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 77 GLU Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 ASP 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 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 134 VAL Chi-restraints excluded: chain X residue 155 VAL 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 21 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 134 VAL 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 21 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 84 SER 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 175 VAL 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 71 ARG 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 120 VAL Chi-restraints excluded: chain L residue 131 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 a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 53 LYS 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 31 VAL Chi-restraints excluded: chain b residue 38 LEU Chi-restraints excluded: chain b residue 125 GLN Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 161 LYS Chi-restraints excluded: chain b residue 200 SER Chi-restraints excluded: chain b residue 201 LEU 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 53 LYS Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 216 THR Chi-restraints excluded: chain c residue 221 TYR Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 36 THR 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 184 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 198 LYS Chi-restraints excluded: chain d residue 200 SER Chi-restraints excluded: chain d residue 216 THR 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 53 LYS Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 151 CYS Chi-restraints excluded: chain e residue 161 LYS Chi-restraints excluded: chain e residue 200 SER 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 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 38 LEU Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 53 LYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 151 CYS Chi-restraints excluded: chain g residue 152 ASP 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: 0.0570 chunk 621 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 537 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 584 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 599 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 44 ASN D 98 GLN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN F 44 ASN G 122 GLN ** 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 47 HIS R 79 HIS ** S 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS U 79 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN M 88 ASN N 88 ASN 2 141 GLN H 36 GLN H 88 ASN H 89 GLN V 88 ASN V 89 GLN V 141 GLN J 88 ASN X 141 GLN Y 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** ** 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 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116119 restraints weight = 65038.395| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.03 r_work: 0.3173 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 59129 Z= 0.245 Angle : 0.661 16.907 79856 Z= 0.352 Chirality : 0.044 0.328 9338 Planarity : 0.004 0.059 10255 Dihedral : 5.544 55.702 8320 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.47 % Favored : 96.38 % Rotamer: Outliers : 5.13 % Allowed : 27.07 % Favored : 67.80 % 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: 0.61 (0.10), residues: 7462 helix: 2.11 (0.09), residues: 3486 sheet: -0.60 (0.13), residues: 1463 loop : -1.44 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 28 HIS 0.014 0.002 HIS R 79 PHE 0.029 0.002 PHE f 42 TYR 0.022 0.002 TYR L 184 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: 32638.78 seconds wall clock time: 554 minutes 6.64 seconds (33246.64 seconds total)