Starting phenix.real_space_refine on Tue Sep 24 06:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyd_35818/09_2024/8iyd_35818.cif" } resolution = 3.1 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= -0.003 sd= 0.078 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 147 5.16 5 C 30891 2.51 5 N 8223 2.21 5 O 10083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49344 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "U" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "a" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "b" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "c" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "u" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1024 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "V" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "v" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "D" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "E" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "F" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "G" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "H" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "I" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "J" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1024 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "L" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "M" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "N" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "O" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "P" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "Q" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "R" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "S" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "T" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "W" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1024 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "X" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "Y" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1799 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Time building chain proxies: 21.28, per 1000 atoms: 0.43 Number of scatterers: 49344 At special positions: 0 Unit cell: (175.095, 177.243, 229.879, 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 147 16.00 O 10083 8.00 N 8223 7.00 C 30891 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: 8.92 Conformation dependent library (CDL) restraints added in 4.9 seconds 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12102 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 121 sheets defined 8.9% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.674A pdb=" N ALA B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 29 " --> pdb=" O PRO B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 25 through 29' Processing helix chain 'B' and resid 93 through 102 removed outlier: 3.987A pdb=" N GLU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'U' and resid 5 through 20 Processing helix chain 'U' and resid 76 through 88 removed outlier: 3.820A pdb=" N LEU U 80 " --> pdb=" O PRO U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 102 Processing helix chain 'a' and resid 92 through 103 Processing helix chain 'b' and resid 92 through 103 removed outlier: 3.671A pdb=" N LEU b 96 " --> pdb=" O GLY b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 155 removed outlier: 4.016A pdb=" N ARG b 155 " --> pdb=" O ALA b 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 103 Processing helix chain 'c' and resid 151 through 156 removed outlier: 3.681A pdb=" N SER c 156 " --> pdb=" O GLU c 153 " (cutoff:3.500A) Processing helix chain 'u' and resid 6 through 21 Processing helix chain 'u' and resid 76 through 88 removed outlier: 3.562A pdb=" N LEU u 80 " --> pdb=" O PRO u 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 88 through 93 Processing helix chain 'u' and resid 95 through 101 removed outlier: 3.962A pdb=" N LEU u 101 " --> pdb=" O ALA u 97 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 102 Processing helix chain 'v' and resid 92 through 103 Processing helix chain 'v' and resid 151 through 156 Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'E' and resid 93 through 102 removed outlier: 4.036A pdb=" N GLU E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 Processing helix chain 'F' and resid 151 through 155 Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 76 through 88 removed outlier: 3.817A pdb=" N LEU G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 95 through 102 Processing helix chain 'H' and resid 92 through 103 Processing helix chain 'I' and resid 92 through 103 removed outlier: 3.613A pdb=" N LEU I 96 " --> pdb=" O GLY I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 156 removed outlier: 3.729A pdb=" N ARG I 155 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER I 156 " --> pdb=" O GLU I 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 103 Processing helix chain 'J' and resid 151 through 156 removed outlier: 3.677A pdb=" N SER J 156 " --> pdb=" O GLU J 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 21 Processing helix chain 'K' and resid 76 through 88 removed outlier: 3.607A pdb=" N LEU K 80 " --> pdb=" O PRO K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 95 through 101 removed outlier: 4.071A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 102 Processing helix chain 'L' and resid 151 through 155 Processing helix chain 'M' and resid 92 through 103 Processing helix chain 'M' and resid 151 through 156 removed outlier: 3.688A pdb=" N ARG M 155 " --> pdb=" O ALA M 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 101 Processing helix chain 'O' and resid 93 through 102 removed outlier: 4.038A pdb=" N GLU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 102 Processing helix chain 'P' and resid 151 through 155 Processing helix chain 'Q' and resid 5 through 20 Processing helix chain 'Q' and resid 76 through 88 removed outlier: 3.895A pdb=" N LEU Q 80 " --> pdb=" O PRO Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'Q' and resid 95 through 102 Processing helix chain 'R' and resid 92 through 103 Processing helix chain 'S' and resid 92 through 103 Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.546A pdb=" N ASP S 154 " --> pdb=" O MET S 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG S 155 " --> pdb=" O ALA S 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 151 through 155' Processing helix chain 'T' and resid 93 through 102 Processing helix chain 'T' and resid 151 through 156 removed outlier: 3.665A pdb=" N SER T 156 " --> pdb=" O GLU T 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 21 Processing helix chain 'W' and resid 76 through 87 removed outlier: 3.634A pdb=" N LEU W 80 " --> pdb=" O PRO W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 93 Processing helix chain 'W' and resid 95 through 101 removed outlier: 4.153A pdb=" N LEU W 101 " --> pdb=" O ALA W 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 102 Processing helix chain 'X' and resid 151 through 155 Processing helix chain 'Y' and resid 92 through 103 Processing helix chain 'Y' and resid 151 through 156 removed outlier: 3.729A pdb=" N ARG Y 155 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.678A pdb=" N LEU A 17 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 117 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 150 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL A 119 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ARG A 148 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 85 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 42 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.326A pdb=" N LYS H 142 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE H 127 " --> pdb=" O THR H 140 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR H 140 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA H 85 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 42 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 36 through 38 removed outlier: 5.516A pdb=" N ALA H 107 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS H 142 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE H 127 " --> pdb=" O THR H 140 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR H 140 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR H 132 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 138 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 197 removed outlier: 4.123A pdb=" N PHE A 235 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.323A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA B 85 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 42 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.323A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR B 132 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 50 through 51 removed outlier: 5.170A pdb=" N ALA I 107 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.186A pdb=" N LYS I 142 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE I 127 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR I 140 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS I 129 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR I 138 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA I 85 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL I 42 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AB4, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.880A pdb=" N ILE B 214 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 195 through 197 Processing sheet with id=AB6, first strand: chain 'C' and resid 36 through 39 removed outlier: 4.897A pdb=" N LEU C 17 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 124 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR C 144 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 138 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR C 132 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA C 85 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 42 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 36 through 39 removed outlier: 4.897A pdb=" N LEU C 17 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA C 107 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 17.439A pdb=" N ARG C 121 " --> pdb=" O ASP c 56 " (cutoff:3.500A) removed outlier: 14.159A pdb=" N ASP c 56 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N TRP C 123 " --> pdb=" O SER c 54 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SER c 54 " --> pdb=" O TRP C 123 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER C 125 " --> pdb=" O ALA c 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU c 53 " --> pdb=" O GLN c 74 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN c 74 " --> pdb=" O GLU c 53 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TYR c 55 " --> pdb=" O GLN c 72 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN c 72 " --> pdb=" O TYR c 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.615A pdb=" N GLU C 49 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AC1, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AC3, first strand: chain 'C' and resid 196 through 197 removed outlier: 4.293A pdb=" N PHE C 235 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 25 through 28 removed outlier: 5.937A pdb=" N GLN U 62 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL U 129 " --> pdb=" O ALA U 107 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA U 107 " --> pdb=" O VAL U 129 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR U 131 " --> pdb=" O MET U 105 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N MET U 105 " --> pdb=" O THR U 131 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER U 108 " --> pdb=" O TYR u 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA u 49 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR U 112 " --> pdb=" O THR u 47 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR u 47 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 14.019A pdb=" N ARG U 114 " --> pdb=" O TYR u 45 " (cutoff:3.500A) removed outlier: 16.183A pdb=" N TYR u 45 " --> pdb=" O ARG U 114 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 25 through 28 removed outlier: 5.937A pdb=" N GLN U 62 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL U 129 " --> pdb=" O ALA U 107 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA U 107 " --> pdb=" O VAL U 129 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR U 131 " --> pdb=" O MET U 105 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N MET U 105 " --> pdb=" O THR U 131 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER U 108 " --> pdb=" O TYR u 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA u 49 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR U 112 " --> pdb=" O THR u 47 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR u 47 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 14.019A pdb=" N ARG U 114 " --> pdb=" O TYR u 45 " (cutoff:3.500A) removed outlier: 16.183A pdb=" N TYR u 45 " --> pdb=" O ARG U 114 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA u 49 " --> pdb=" O GLN u 62 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN u 62 " --> pdb=" O ALA u 49 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR u 51 " --> pdb=" O THR u 60 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR u 60 " --> pdb=" O TYR u 51 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER u 123 " --> pdb=" O TYR u 112 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR u 112 " --> pdb=" O SER u 123 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP u 125 " --> pdb=" O TYR u 110 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR u 110 " --> pdb=" O ASP u 125 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR u 127 " --> pdb=" O SER u 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER u 104 " --> pdb=" O THR u 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU u 133 " --> pdb=" O ILE u 102 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE u 102 " --> pdb=" O GLU u 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 36 through 38 removed outlier: 5.660A pdb=" N ALA a 107 " --> pdb=" O TYR a 20 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS a 142 " --> pdb=" O SER a 125 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE a 127 " --> pdb=" O THR a 140 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR a 140 " --> pdb=" O ILE a 127 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL a 136 " --> pdb=" O THR a 132 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N THR a 132 " --> pdb=" O VAL a 136 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR a 138 " --> pdb=" O ALA a 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 42 through 46 removed outlier: 6.925A pdb=" N VAL a 42 " --> pdb=" O ALA a 85 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA a 85 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR a 140 " --> pdb=" O ILE a 127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE a 127 " --> pdb=" O THR a 140 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS a 142 " --> pdb=" O SER a 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 52 through 56 removed outlier: 5.157A pdb=" N GLU a 53 " --> pdb=" O GLY a 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 164 through 167 Processing sheet with id=AD1, first strand: chain 'a' and resid 172 through 173 Processing sheet with id=AD2, first strand: chain 'b' and resid 36 through 38 removed outlier: 5.134A pdb=" N ALA b 107 " --> pdb=" O TYR b 20 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS b 142 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE b 127 " --> pdb=" O THR b 140 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR b 140 " --> pdb=" O ILE b 127 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS b 129 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR b 138 " --> pdb=" O LYS b 129 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA b 85 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL b 42 " --> pdb=" O ALA b 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 36 through 38 removed outlier: 5.134A pdb=" N ALA b 107 " --> pdb=" O TYR b 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 52 through 56 removed outlier: 5.137A pdb=" N GLU b 53 " --> pdb=" O GLY b 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 164 through 167 Processing sheet with id=AD6, first strand: chain 'b' and resid 195 through 197 removed outlier: 3.949A pdb=" N PHE b 235 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 36 through 38 removed outlier: 5.623A pdb=" N ALA c 107 " --> pdb=" O TYR c 20 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL c 124 " --> pdb=" O THR c 144 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR c 144 " --> pdb=" O VAL c 124 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR c 132 " --> pdb=" O VAL c 136 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL c 136 " --> pdb=" O THR c 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA c 85 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL c 42 " --> pdb=" O ALA c 85 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 164 through 167 Processing sheet with id=AD9, first strand: chain 'c' and resid 195 through 197 Processing sheet with id=AE1, first strand: chain 'V' and resid 36 through 39 removed outlier: 4.651A pdb=" N LEU V 17 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP V 118 " --> pdb=" O SER V 150 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER V 150 " --> pdb=" O ASP V 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE V 120 " --> pdb=" O ARG V 148 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ARG V 148 " --> pdb=" O PHE V 120 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY V 122 " --> pdb=" O VAL V 146 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL V 146 " --> pdb=" O GLY V 122 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL V 124 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR V 144 " --> pdb=" O VAL V 124 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR V 132 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL V 136 " --> pdb=" O THR V 132 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA V 85 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL V 42 " --> pdb=" O ALA V 85 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 36 through 39 removed outlier: 4.651A pdb=" N LEU V 17 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA V 107 " --> pdb=" O TYR V 20 " (cutoff:3.500A) removed outlier: 18.259A pdb=" N ARG V 121 " --> pdb=" O ASP v 56 " (cutoff:3.500A) removed outlier: 14.618A pdb=" N ASP v 56 " --> pdb=" O ARG V 121 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N TRP V 123 " --> pdb=" O SER v 54 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N SER v 54 " --> pdb=" O TRP V 123 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER V 125 " --> pdb=" O ALA v 52 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR v 51 " --> pdb=" O LYS v 75 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS v 75 " --> pdb=" O THR v 51 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU v 53 " --> pdb=" O GLY v 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 50 through 51 removed outlier: 5.821A pdb=" N ALA M 107 " --> pdb=" O TYR M 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 50 through 51 removed outlier: 5.522A pdb=" N VAL M 124 " --> pdb=" O THR M 144 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR M 144 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR M 132 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA M 85 " --> pdb=" O VAL M 42 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL M 42 " --> pdb=" O ALA M 85 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 54 through 56 Processing sheet with id=AE6, first strand: chain 'V' and resid 165 through 167 removed outlier: 3.934A pdb=" N ILE V 214 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 196 through 197 Processing sheet with id=AE8, first strand: chain 'v' and resid 36 through 38 removed outlier: 5.748A pdb=" N ALA v 107 " --> pdb=" O TYR v 20 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL v 124 " --> pdb=" O THR v 144 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR v 144 " --> pdb=" O VAL v 124 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR v 132 " --> pdb=" O VAL v 136 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL v 136 " --> pdb=" O THR v 132 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER v 81 " --> pdb=" O LEU v 45 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU v 45 " --> pdb=" O SER v 81 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR v 83 " --> pdb=" O LYS v 43 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'v' and resid 36 through 38 removed outlier: 5.748A pdb=" N ALA v 107 " --> pdb=" O TYR v 20 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'v' and resid 164 through 167 Processing sheet with id=AF2, first strand: chain 'v' and resid 172 through 173 removed outlier: 4.175A pdb=" N PHE v 235 " --> pdb=" O SER v 230 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 36 through 39 removed outlier: 4.576A pdb=" N LEU D 17 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA D 107 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 117 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER D 150 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 119 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG D 148 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG D 121 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS D 142 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE D 127 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 140 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 85 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 42 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.395A pdb=" N LYS R 142 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE R 127 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR R 140 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA R 85 " --> pdb=" O VAL R 42 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL R 42 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 36 through 38 removed outlier: 5.532A pdb=" N ALA R 107 " --> pdb=" O TYR R 20 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS R 142 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE R 127 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR R 140 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL R 136 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR R 132 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR R 138 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AF7, first strand: chain 'D' and resid 165 through 167 Processing sheet with id=AF8, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AF9, first strand: chain 'D' and resid 195 through 197 removed outlier: 4.216A pdb=" N PHE D 235 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 36 through 38 removed outlier: 5.293A pdb=" N ALA E 107 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS E 142 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 127 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR E 140 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA E 85 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 42 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 36 through 38 removed outlier: 5.293A pdb=" N ALA E 107 " --> pdb=" O TYR E 20 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS E 142 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 127 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR E 140 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR E 132 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 50 through 51 removed outlier: 5.137A pdb=" N ALA S 107 " --> pdb=" O TYR S 20 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.144A pdb=" N LYS S 142 " --> pdb=" O SER S 125 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE S 127 " --> pdb=" O THR S 140 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR S 140 " --> pdb=" O ILE S 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS S 129 " --> pdb=" O THR S 138 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR S 138 " --> pdb=" O LYS S 129 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA S 85 " --> pdb=" O VAL S 42 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL S 42 " --> pdb=" O ALA S 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 54 through 56 Processing sheet with id=AG6, first strand: chain 'E' and resid 165 through 167 removed outlier: 3.856A pdb=" N ILE E 214 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.530A pdb=" N VAL E 173 " --> pdb=" O THR E 242 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.876A pdb=" N LEU F 17 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA F 107 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL F 124 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR F 144 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N THR F 132 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA F 85 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F 42 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.876A pdb=" N LEU F 17 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA F 107 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 17.419A pdb=" N ARG F 121 " --> pdb=" O ASP J 56 " (cutoff:3.500A) removed outlier: 14.160A pdb=" N ASP J 56 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 12.086A pdb=" N TRP F 123 " --> pdb=" O SER J 54 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N SER J 54 " --> pdb=" O TRP F 123 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER F 125 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU J 53 " --> pdb=" O GLN J 74 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN J 74 " --> pdb=" O GLU J 53 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR J 55 " --> pdb=" O GLN J 72 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN J 72 " --> pdb=" O TYR J 55 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 49 through 50 removed outlier: 3.547A pdb=" N GLU F 49 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 54 through 56 Processing sheet with id=AH3, first strand: chain 'F' and resid 165 through 168 removed outlier: 4.786A pdb=" N ILE F 214 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 196 through 197 removed outlier: 4.265A pdb=" N PHE F 235 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 25 through 28 removed outlier: 5.990A pdb=" N GLN G 62 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL G 129 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA G 107 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR G 131 " --> pdb=" O MET G 105 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET G 105 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER G 108 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA K 49 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR G 112 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR K 47 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 14.041A pdb=" N ARG G 114 " --> pdb=" O TYR K 45 " (cutoff:3.500A) removed outlier: 16.138A pdb=" N TYR K 45 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 25 through 28 removed outlier: 5.990A pdb=" N GLN G 62 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL G 129 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA G 107 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR G 131 " --> pdb=" O MET G 105 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET G 105 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER G 108 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA K 49 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR G 112 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR K 47 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 14.041A pdb=" N ARG G 114 " --> pdb=" O TYR K 45 " (cutoff:3.500A) removed outlier: 16.138A pdb=" N TYR K 45 " --> pdb=" O ARG G 114 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA K 49 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN K 62 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYR K 51 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR K 60 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER K 123 " --> pdb=" O TYR K 112 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR K 112 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP K 125 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR K 110 " --> pdb=" O ASP K 125 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR K 127 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER K 104 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU K 133 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE K 102 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 52 through 56 removed outlier: 5.177A pdb=" N GLU H 53 " --> pdb=" O GLY H 73 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 164 through 167 Processing sheet with id=AH9, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AI1, first strand: chain 'I' and resid 52 through 56 removed outlier: 5.269A pdb=" N GLU I 53 " --> pdb=" O GLY I 73 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 164 through 167 Processing sheet with id=AI3, first strand: chain 'I' and resid 195 through 197 removed outlier: 3.962A pdb=" N PHE I 235 " --> pdb=" O SER I 230 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 36 through 38 removed outlier: 5.634A pdb=" N ALA J 107 " --> pdb=" O TYR J 20 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP J 118 " --> pdb=" O SER J 150 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER J 150 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE J 120 " --> pdb=" O ARG J 148 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ARG J 148 " --> pdb=" O PHE J 120 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY J 122 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL J 146 " --> pdb=" O GLY J 122 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL J 124 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR J 144 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR J 132 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J 85 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL J 42 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 164 through 167 Processing sheet with id=AI6, first strand: chain 'J' and resid 195 through 197 Processing sheet with id=AI7, first strand: chain 'L' and resid 36 through 39 removed outlier: 4.672A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL L 124 " --> pdb=" O THR L 144 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR L 144 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N THR L 132 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA L 85 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL L 42 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 36 through 39 removed outlier: 4.672A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA L 107 " --> pdb=" O TYR L 20 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 18.242A pdb=" N ARG L 121 " --> pdb=" O ASP M 56 " (cutoff:3.500A) removed outlier: 14.586A pdb=" N ASP M 56 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N TRP L 123 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N SER M 54 " --> pdb=" O TRP L 123 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N SER L 125 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU M 53 " --> pdb=" O GLN M 74 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN M 74 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR M 55 " --> pdb=" O GLN M 72 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN M 72 " --> pdb=" O TYR M 55 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 50 through 51 removed outlier: 5.493A pdb=" N ALA Y 107 " --> pdb=" O TYR Y 20 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 50 through 51 removed outlier: 5.542A pdb=" N VAL Y 124 " --> pdb=" O THR Y 144 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR Y 144 " --> pdb=" O VAL Y 124 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR Y 132 " --> pdb=" O VAL Y 136 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL Y 136 " --> pdb=" O THR Y 132 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA Y 85 " --> pdb=" O VAL Y 42 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL Y 42 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 54 through 56 Processing sheet with id=AJ3, first strand: chain 'L' and resid 165 through 167 removed outlier: 4.101A pdb=" N ILE L 214 " --> pdb=" O LEU L 181 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 196 through 197 Processing sheet with id=AJ5, first strand: chain 'M' and resid 164 through 167 Processing sheet with id=AJ6, first strand: chain 'M' and resid 172 through 173 removed outlier: 4.177A pdb=" N PHE M 235 " --> pdb=" O SER M 230 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.660A pdb=" N LEU N 17 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA N 107 " --> pdb=" O TYR N 20 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL N 117 " --> pdb=" O SER N 150 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER N 150 " --> pdb=" O VAL N 117 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL N 119 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG N 148 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG N 121 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS N 142 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE N 127 " --> pdb=" O THR N 140 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR N 140 " --> pdb=" O ILE N 127 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA N 85 " --> pdb=" O VAL N 42 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL N 42 " --> pdb=" O ALA N 85 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 54 through 56 Processing sheet with id=AJ9, first strand: chain 'N' and resid 165 through 167 Processing sheet with id=AK1, first strand: chain 'N' and resid 179 through 180 Processing sheet with id=AK2, first strand: chain 'N' and resid 195 through 197 removed outlier: 4.216A pdb=" N PHE N 235 " --> pdb=" O SER N 230 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 36 through 38 removed outlier: 5.276A pdb=" N ALA O 107 " --> pdb=" O TYR O 20 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS O 142 " --> pdb=" O SER O 125 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE O 127 " --> pdb=" O THR O 140 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR O 140 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA O 85 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL O 42 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 36 through 38 removed outlier: 5.276A pdb=" N ALA O 107 " --> pdb=" O TYR O 20 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS O 142 " --> pdb=" O SER O 125 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE O 127 " --> pdb=" O THR O 140 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR O 140 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR O 132 " --> pdb=" O VAL O 136 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 54 through 56 Processing sheet with id=AK6, first strand: chain 'O' and resid 165 through 167 removed outlier: 3.882A pdb=" N ILE O 214 " --> pdb=" O LEU O 181 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'O' and resid 172 through 173 removed outlier: 3.619A pdb=" N VAL O 173 " --> pdb=" O THR O 242 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'P' and resid 36 through 38 removed outlier: 5.660A pdb=" N ALA P 107 " --> pdb=" O TYR P 20 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL P 124 " --> pdb=" O THR P 144 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR P 144 " --> pdb=" O VAL P 124 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N THR P 132 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA P 85 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL P 42 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 36 through 38 removed outlier: 5.660A pdb=" N ALA P 107 " --> pdb=" O TYR P 20 " (cutoff:3.500A) removed outlier: 17.382A pdb=" N ARG P 121 " --> pdb=" O ASP T 56 " (cutoff:3.500A) removed outlier: 14.182A pdb=" N ASP T 56 " --> pdb=" O ARG P 121 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N TRP P 123 " --> pdb=" O SER T 54 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N SER T 54 " --> pdb=" O TRP P 123 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER P 125 " --> pdb=" O ALA T 52 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU T 53 " --> pdb=" O GLN T 74 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN T 74 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR T 55 " --> pdb=" O GLN T 72 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN T 72 " --> pdb=" O TYR T 55 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'P' and resid 49 through 50 Processing sheet with id=AL2, first strand: chain 'P' and resid 54 through 56 Processing sheet with id=AL3, first strand: chain 'P' and resid 165 through 168 removed outlier: 4.709A pdb=" N ILE P 214 " --> pdb=" O LEU P 181 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 196 through 197 removed outlier: 4.306A pdb=" N PHE P 235 " --> pdb=" O SER P 230 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Q' and resid 25 through 28 removed outlier: 5.948A pdb=" N GLN Q 62 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL Q 129 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR Q 131 " --> pdb=" O MET Q 105 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET Q 105 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER Q 108 " --> pdb=" O TYR W 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA W 49 " --> pdb=" O TYR Q 110 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR Q 112 " --> pdb=" O THR W 47 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR W 47 " --> pdb=" O TYR Q 112 " (cutoff:3.500A) removed outlier: 14.008A pdb=" N ARG Q 114 " --> pdb=" O TYR W 45 " (cutoff:3.500A) removed outlier: 16.155A pdb=" N TYR W 45 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'Q' and resid 25 through 28 removed outlier: 5.948A pdb=" N GLN Q 62 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL Q 129 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR Q 131 " --> pdb=" O MET Q 105 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET Q 105 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER Q 108 " --> pdb=" O TYR W 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA W 49 " --> pdb=" O TYR Q 110 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR Q 112 " --> pdb=" O THR W 47 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR W 47 " --> pdb=" O TYR Q 112 " (cutoff:3.500A) removed outlier: 14.008A pdb=" N ARG Q 114 " --> pdb=" O TYR W 45 " (cutoff:3.500A) removed outlier: 16.155A pdb=" N TYR W 45 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA W 49 " --> pdb=" O GLN W 62 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN W 62 " --> pdb=" O ALA W 49 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR W 51 " --> pdb=" O THR W 60 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR W 60 " --> pdb=" O TYR W 51 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER W 123 " --> pdb=" O TYR W 112 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR W 112 " --> pdb=" O SER W 123 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP W 125 " --> pdb=" O TYR W 110 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR W 110 " --> pdb=" O ASP W 125 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR W 127 " --> pdb=" O SER W 108 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER W 104 " --> pdb=" O THR W 131 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU W 133 " --> pdb=" O ILE W 102 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE W 102 " --> pdb=" O GLU W 133 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'R' and resid 52 through 56 removed outlier: 5.140A pdb=" N GLU R 53 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'R' and resid 164 through 167 Processing sheet with id=AL9, first strand: chain 'R' and resid 172 through 173 Processing sheet with id=AM1, first strand: chain 'S' and resid 52 through 56 removed outlier: 5.380A pdb=" N GLU S 53 " --> pdb=" O GLY S 73 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'S' and resid 164 through 167 Processing sheet with id=AM3, first strand: chain 'S' and resid 195 through 197 removed outlier: 3.897A pdb=" N PHE S 235 " --> pdb=" O SER S 230 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'T' and resid 36 through 38 removed outlier: 5.625A pdb=" N ALA T 107 " --> pdb=" O TYR T 20 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP T 118 " --> pdb=" O SER T 150 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER T 150 " --> pdb=" O ASP T 118 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE T 120 " --> pdb=" O ARG T 148 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ARG T 148 " --> pdb=" O PHE T 120 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY T 122 " --> pdb=" O VAL T 146 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL T 146 " --> pdb=" O GLY T 122 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL T 124 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR T 144 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR T 132 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA T 85 " --> pdb=" O VAL T 42 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL T 42 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'T' and resid 164 through 167 Processing sheet with id=AM6, first strand: chain 'T' and resid 195 through 197 Processing sheet with id=AM7, first strand: chain 'X' and resid 36 through 39 removed outlier: 4.644A pdb=" N LEU X 17 " --> pdb=" O LEU X 39 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA X 107 " --> pdb=" O TYR X 20 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS X 142 " --> pdb=" O SER X 125 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE X 127 " --> pdb=" O THR X 140 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR X 140 " --> pdb=" O ILE X 127 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS X 129 " --> pdb=" O THR X 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR X 138 " --> pdb=" O LYS X 129 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL X 131 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL X 136 " --> pdb=" O VAL X 131 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA X 85 " --> pdb=" O VAL X 42 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL X 42 " --> pdb=" O ALA X 85 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'X' and resid 36 through 39 removed outlier: 4.644A pdb=" N LEU X 17 " --> pdb=" O LEU X 39 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA X 107 " --> pdb=" O TYR X 20 " (cutoff:3.500A) removed outlier: 18.216A pdb=" N ARG X 121 " --> pdb=" O ASP Y 56 " (cutoff:3.500A) removed outlier: 14.585A pdb=" N ASP Y 56 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 12.187A pdb=" N TRP X 123 " --> pdb=" O SER Y 54 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N SER Y 54 " --> pdb=" O TRP X 123 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER X 125 " --> pdb=" O ALA Y 52 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR Y 51 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS Y 75 " --> pdb=" O THR Y 51 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU Y 53 " --> pdb=" O GLY Y 73 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'X' and resid 54 through 56 Processing sheet with id=AN1, first strand: chain 'X' and resid 165 through 167 removed outlier: 4.119A pdb=" N ILE X 214 " --> pdb=" O LEU X 181 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'X' and resid 196 through 197 Processing sheet with id=AN3, first strand: chain 'Y' and resid 164 through 167 Processing sheet with id=AN4, first strand: chain 'Y' and resid 172 through 173 removed outlier: 4.202A pdb=" N PHE Y 235 " --> pdb=" O SER Y 230 " (cutoff:3.500A) 2111 hydrogen bonds defined for protein. 5565 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: 21.40 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8605 1.32 - 1.44: 13037 1.44 - 1.57: 28401 1.57 - 1.70: 3 1.70 - 1.83: 294 Bond restraints: 50340 Sorted by residual: bond pdb=" C GLY P 222 " pdb=" O GLY P 222 " ideal model delta sigma weight residual 1.236 1.197 0.039 5.30e-03 3.56e+04 5.34e+01 bond pdb=" C PRO O 9 " pdb=" O PRO O 9 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" N ASP T 64 " pdb=" CA ASP T 64 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N ASP c 64 " pdb=" CA ASP c 64 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.46e+00 bond pdb=" N VAL O 10 " pdb=" CA VAL O 10 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.32e+00 ... (remaining 50335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 67864 2.88 - 5.77: 793 5.77 - 8.65: 88 8.65 - 11.54: 17 11.54 - 14.42: 4 Bond angle restraints: 68766 Sorted by residual: angle pdb=" N ALA Q 37 " pdb=" CA ALA Q 37 " pdb=" C ALA Q 37 " ideal model delta sigma weight residual 112.38 103.62 8.76 1.22e+00 6.72e-01 5.16e+01 angle pdb=" N PRO c 187 " pdb=" CA PRO c 187 " pdb=" C PRO c 187 " ideal model delta sigma weight residual 112.47 98.05 14.42 2.06e+00 2.36e-01 4.90e+01 angle pdb=" N PRO F 187 " pdb=" CA PRO F 187 " pdb=" C PRO F 187 " ideal model delta sigma weight residual 112.47 99.88 12.59 2.06e+00 2.36e-01 3.74e+01 angle pdb=" C ALA Q 73 " pdb=" CA ALA Q 73 " pdb=" CB ALA Q 73 " ideal model delta sigma weight residual 116.63 109.78 6.85 1.16e+00 7.43e-01 3.48e+01 angle pdb=" C PHE Q 39 " pdb=" CA PHE Q 39 " pdb=" CB PHE Q 39 " ideal model delta sigma weight residual 110.17 121.63 -11.46 1.97e+00 2.58e-01 3.38e+01 ... (remaining 68761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25772 17.99 - 35.99: 2953 35.99 - 53.98: 805 53.98 - 71.98: 125 71.98 - 89.97: 75 Dihedral angle restraints: 29730 sinusoidal: 10857 harmonic: 18873 Sorted by residual: dihedral pdb=" CA PHE U 39 " pdb=" C PHE U 39 " pdb=" N PRO U 40 " pdb=" CA PRO U 40 " ideal model delta harmonic sigma weight residual -180.00 -103.34 -76.66 0 5.00e+00 4.00e-02 2.35e+02 dihedral pdb=" CA PHE W 39 " pdb=" C PHE W 39 " pdb=" N PRO W 40 " pdb=" CA PRO W 40 " ideal model delta harmonic sigma weight residual -180.00 -129.07 -50.93 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA PHE u 39 " pdb=" C PHE u 39 " pdb=" N PRO u 40 " pdb=" CA PRO u 40 " ideal model delta harmonic sigma weight residual -180.00 -129.85 -50.15 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 29727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7030 0.080 - 0.160: 1023 0.160 - 0.240: 23 0.240 - 0.320: 8 0.320 - 0.401: 1 Chirality restraints: 8085 Sorted by residual: chirality pdb=" CA PHE Q 39 " pdb=" N PHE Q 39 " pdb=" C PHE Q 39 " pdb=" CB PHE Q 39 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB THR W 52 " pdb=" CA THR W 52 " pdb=" OG1 THR W 52 " pdb=" CG2 THR W 52 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PRO K 72 " pdb=" N PRO K 72 " pdb=" C PRO K 72 " pdb=" CB PRO K 72 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 8082 not shown) Planarity restraints: 8859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE u 39 " 0.093 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO u 40 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO u 40 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO u 40 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 74 " 0.020 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" CD GLN C 74 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLN C 74 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN C 74 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 209 " 0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C VAL b 209 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL b 209 " 0.027 2.00e-02 2.50e+03 pdb=" N SER b 210 " 0.023 2.00e-02 2.50e+03 ... (remaining 8856 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1318 2.65 - 3.21: 47359 3.21 - 3.78: 75578 3.78 - 4.34: 103535 4.34 - 4.90: 172113 Nonbonded interactions: 399903 Sorted by model distance: nonbonded pdb=" OG SER v 126 " pdb=" OE1 GLU X 49 " model vdw 2.090 3.040 nonbonded pdb=" O PHE L 185 " pdb=" OG1 THR L 191 " model vdw 2.091 3.040 nonbonded pdb=" OG1 THR C 206 " pdb=" OD1 ASN C 217 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR P 206 " pdb=" OD1 ASN P 217 " model vdw 2.095 3.040 nonbonded pdb=" OE1 GLU L 49 " pdb=" OG SER Y 126 " model vdw 2.096 3.040 ... (remaining 399898 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'v' } ncs_group { reference = (chain 'G' and resid 5 through 134) selection = chain 'K' selection = (chain 'Q' and resid 5 through 134) selection = (chain 'U' and resid 5 through 134) selection = chain 'W' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 90.730 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 50340 Z= 0.287 Angle : 0.809 14.420 68766 Z= 0.439 Chirality : 0.051 0.401 8085 Planarity : 0.006 0.145 8859 Dihedral : 17.220 89.974 17628 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.47 % Favored : 89.77 % Rotamer: Outliers : 0.98 % Allowed : 31.62 % Favored : 67.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 6579 helix: -0.63 (0.22), residues: 486 sheet: -0.91 (0.10), residues: 3030 loop : -2.30 (0.10), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 18 HIS 0.005 0.001 HIS U 66 PHE 0.054 0.003 PHE K 39 TYR 0.040 0.002 TYR O 55 ARG 0.009 0.001 ARG u 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 441 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7034 (pp20) REVERT: C 75 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7553 (mmtp) REVERT: U 34 PHE cc_start: 0.7981 (m-80) cc_final: 0.7436 (m-80) REVERT: c 63 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: c 135 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7280 (tm-30) REVERT: v 53 GLU cc_start: 0.8289 (pm20) cc_final: 0.7668 (pm20) REVERT: v 90 GLU cc_start: 0.5968 (mp0) cc_final: 0.5647 (mp0) REVERT: F 75 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7621 (mttm) REVERT: N 44 ASP cc_start: 0.8526 (t70) cc_final: 0.8175 (t0) REVERT: N 63 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: P 74 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: Q 27 PHE cc_start: 0.7462 (m-80) cc_final: 0.7014 (m-80) REVERT: Q 36 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: Q 40 PRO cc_start: 0.7881 (OUTLIER) cc_final: 0.7595 (Cg_endo) REVERT: Q 74 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8417 (tm-30) REVERT: R 64 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (p0) REVERT: X 20 TYR cc_start: 0.7416 (t80) cc_final: 0.7037 (t80) REVERT: Y 153 GLU cc_start: 0.7611 (tp30) cc_final: 0.6874 (tp30) outliers start: 52 outliers final: 23 residues processed: 475 average time/residue: 0.4939 time to fit residues: 398.0741 Evaluate side-chains 451 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 419 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 212 MET Chi-restraints excluded: chain b residue 213 THR Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 63 GLU Chi-restraints excluded: chain N residue 64 ASP Chi-restraints excluded: chain O residue 8 MET Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 40 PRO Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain S residue 151 MET Chi-restraints excluded: chain T residue 188 GLU Chi-restraints excluded: chain T residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 552 optimal weight: 9.9990 chunk 495 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 512 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 381 optimal weight: 3.9990 chunk 593 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN H 177 GLN O 101 ASN S 101 ASN Y 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 50340 Z= 0.299 Angle : 0.672 8.260 68766 Z= 0.351 Chirality : 0.048 0.238 8085 Planarity : 0.005 0.119 8859 Dihedral : 6.617 86.594 7081 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.55 % Favored : 92.00 % Rotamer: Outliers : 5.78 % Allowed : 28.70 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6579 helix: -0.18 (0.22), residues: 504 sheet: -0.91 (0.10), residues: 3045 loop : -2.17 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 18 HIS 0.005 0.001 HIS Q 6 PHE 0.019 0.002 PHE W 39 TYR 0.015 0.002 TYR O 55 ARG 0.005 0.000 ARG c 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 497 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: A 142 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (tttp) REVERT: U 34 PHE cc_start: 0.8009 (m-80) cc_final: 0.7377 (m-80) REVERT: U 74 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8603 (tm-30) REVERT: a 32 SER cc_start: 0.6845 (OUTLIER) cc_final: 0.6509 (p) REVERT: a 102 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7879 (tm-30) REVERT: b 134 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8735 (ptmt) REVERT: b 135 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7112 (tm-30) REVERT: c 59 TYR cc_start: 0.9025 (m-10) cc_final: 0.8798 (m-10) REVERT: c 135 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6930 (tm-30) REVERT: c 185 PHE cc_start: 0.3388 (OUTLIER) cc_final: 0.3164 (m-80) REVERT: u 54 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: u 79 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7731 (tm-30) REVERT: v 87 MET cc_start: 0.8372 (mtp) cc_final: 0.7872 (mtp) REVERT: v 90 GLU cc_start: 0.6494 (mp0) cc_final: 0.5946 (mp0) REVERT: v 94 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: D 39 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8222 (mm) REVERT: D 84 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7946 (pp) REVERT: D 102 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: H 32 SER cc_start: 0.7065 (OUTLIER) cc_final: 0.6770 (p) REVERT: H 63 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7964 (tp30) REVERT: I 84 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7473 (pp) REVERT: I 155 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7486 (pmm-80) REVERT: J 151 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: K 79 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7770 (tm-30) REVERT: L 20 TYR cc_start: 0.7751 (t80) cc_final: 0.7486 (t80) REVERT: L 49 GLU cc_start: 0.8647 (pt0) cc_final: 0.7857 (pt0) REVERT: L 102 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7447 (pm20) REVERT: M 135 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: N 102 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: P 8 MET cc_start: 0.7938 (mpp) cc_final: 0.7406 (mpp) REVERT: P 64 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6964 (p0) REVERT: P 75 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7331 (mttm) REVERT: Q 27 PHE cc_start: 0.7557 (m-80) cc_final: 0.6925 (m-80) REVERT: Q 74 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8411 (tm-30) REVERT: R 111 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7424 (mtp180) REVERT: T 93 GLN cc_start: 0.8206 (mp10) cc_final: 0.7748 (mp10) REVERT: W 64 GLU cc_start: 0.7780 (mp0) cc_final: 0.7579 (mp0) REVERT: W 79 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7599 (tm-30) REVERT: X 20 TYR cc_start: 0.7243 (t80) cc_final: 0.7019 (t80) REVERT: Y 20 TYR cc_start: 0.7860 (t80) cc_final: 0.7552 (t80) REVERT: Y 53 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: Y 142 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: Y 153 GLU cc_start: 0.7518 (tp30) cc_final: 0.7221 (tp30) REVERT: Y 164 MET cc_start: 0.5248 (pmm) cc_final: 0.3801 (tpp) outliers start: 307 outliers final: 162 residues processed: 747 average time/residue: 0.4772 time to fit residues: 605.3003 Evaluate side-chains 636 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 451 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 178 SER Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 212 MET Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 62 ASP Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 185 PHE Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 87 ARG Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain v residue 94 GLN Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 81 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain P residue 18 TRP Chi-restraints excluded: chain P residue 59 TYR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 75 LYS Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 142 LYS Chi-restraints excluded: chain Y residue 150 SER Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 330 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 494 optimal weight: 2.9990 chunk 404 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 594 optimal weight: 6.9990 chunk 642 optimal weight: 10.0000 chunk 529 optimal weight: 3.9990 chunk 590 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 477 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 50340 Z= 0.385 Angle : 0.695 8.572 68766 Z= 0.365 Chirality : 0.049 0.256 8085 Planarity : 0.005 0.116 8859 Dihedral : 6.114 85.565 7019 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.39 % Favored : 91.17 % Rotamer: Outliers : 8.22 % Allowed : 27.23 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.10), residues: 6579 helix: -0.18 (0.22), residues: 504 sheet: -1.04 (0.10), residues: 3045 loop : -2.16 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 18 HIS 0.005 0.001 HIS u 66 PHE 0.031 0.002 PHE L 82 TYR 0.018 0.002 TYR O 55 ARG 0.006 0.000 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 463 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7889 (ttp) REVERT: A 63 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: A 142 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8215 (tttp) REVERT: B 90 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: C 45 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8745 (tp) REVERT: C 61 ASP cc_start: 0.8074 (m-30) cc_final: 0.7817 (m-30) REVERT: C 87 MET cc_start: 0.9346 (mtm) cc_final: 0.9068 (mtp) REVERT: U 34 PHE cc_start: 0.8118 (m-80) cc_final: 0.7535 (m-80) REVERT: U 74 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8592 (tm-30) REVERT: U 94 ASP cc_start: 0.8003 (m-30) cc_final: 0.7586 (p0) REVERT: a 32 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6472 (p) REVERT: b 134 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8775 (ptmt) REVERT: b 135 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7123 (tm-30) REVERT: c 59 TYR cc_start: 0.9044 (m-10) cc_final: 0.8761 (m-10) REVERT: c 135 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6704 (tm-30) REVERT: c 151 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8480 (mmm) REVERT: c 185 PHE cc_start: 0.3453 (OUTLIER) cc_final: 0.3158 (m-80) REVERT: u 54 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: u 64 GLU cc_start: 0.7721 (mp0) cc_final: 0.7495 (mp0) REVERT: u 87 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8001 (mpp-170) REVERT: V 135 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7589 (tm-30) REVERT: v 35 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7726 (p0) REVERT: v 87 MET cc_start: 0.8491 (mtp) cc_final: 0.7950 (mtp) REVERT: v 90 GLU cc_start: 0.6679 (mp0) cc_final: 0.6296 (mp0) REVERT: D 39 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8260 (mm) REVERT: D 84 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7967 (pp) REVERT: D 101 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8909 (m-40) REVERT: D 102 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: F 75 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7850 (mttm) REVERT: F 90 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: H 32 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.6797 (p) REVERT: H 63 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: H 177 GLN cc_start: 0.4302 (OUTLIER) cc_final: 0.3980 (pm20) REVERT: I 155 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7478 (pmm-80) REVERT: J 93 GLN cc_start: 0.8351 (mp10) cc_final: 0.8049 (mp10) REVERT: J 151 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: K 64 GLU cc_start: 0.7578 (mp0) cc_final: 0.7353 (mp0) REVERT: L 20 TYR cc_start: 0.7657 (t80) cc_final: 0.7306 (t80) REVERT: L 102 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: L 111 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7731 (ttp80) REVERT: M 35 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7848 (t0) REVERT: M 94 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: M 102 GLU cc_start: 0.6966 (pp20) cc_final: 0.6493 (pp20) REVERT: M 135 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: N 84 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8039 (pp) REVERT: N 102 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: P 8 MET cc_start: 0.7916 (mpp) cc_final: 0.7371 (mpp) REVERT: P 64 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7059 (p0) REVERT: P 72 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: P 75 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7328 (mttm) REVERT: Q 27 PHE cc_start: 0.7603 (m-80) cc_final: 0.7085 (m-80) REVERT: Q 74 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8393 (tm-30) REVERT: R 111 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: S 155 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7881 (pmm-80) REVERT: W 64 GLU cc_start: 0.7763 (mp0) cc_final: 0.7485 (mp0) REVERT: W 79 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7614 (tm-30) REVERT: X 8 MET cc_start: 0.8836 (mpp) cc_final: 0.8441 (mpp) REVERT: X 102 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: X 111 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: Y 20 TYR cc_start: 0.7948 (t80) cc_final: 0.7726 (t80) REVERT: Y 153 GLU cc_start: 0.7412 (tp30) cc_final: 0.6926 (tp30) REVERT: Y 164 MET cc_start: 0.5207 (pmm) cc_final: 0.3722 (tpp) outliers start: 436 outliers final: 297 residues processed: 823 average time/residue: 0.4705 time to fit residues: 664.1472 Evaluate side-chains 776 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 442 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 51 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 118 ASP Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 178 SER Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 212 MET Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 185 PHE Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 214 ILE Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 87 ARG Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 140 THR Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 35 ASP Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 198 VAL Chi-restraints excluded: chain v residue 213 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 81 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 18 TRP Chi-restraints excluded: chain P residue 59 TYR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain P residue 75 LYS Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 90 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 142 LYS Chi-restraints excluded: chain Y residue 150 SER Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 587 optimal weight: 6.9990 chunk 447 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 65 optimal weight: 0.0470 chunk 283 optimal weight: 30.0000 chunk 399 optimal weight: 4.9990 chunk 597 optimal weight: 2.9990 chunk 632 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 565 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 50340 Z= 0.326 Angle : 0.668 8.528 68766 Z= 0.349 Chirality : 0.049 0.252 8085 Planarity : 0.005 0.116 8859 Dihedral : 5.958 86.527 7019 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.86 % Favored : 91.73 % Rotamer: Outliers : 8.72 % Allowed : 27.59 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.10), residues: 6579 helix: -0.05 (0.22), residues: 504 sheet: -1.03 (0.10), residues: 3045 loop : -2.13 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 18 HIS 0.004 0.001 HIS u 66 PHE 0.027 0.002 PHE K 39 TYR 0.018 0.002 TYR O 55 ARG 0.005 0.000 ARG O 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 463 poor density : 481 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7937 (ttp) REVERT: A 63 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 102 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: A 142 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8205 (tttp) REVERT: B 90 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: C 45 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8761 (tp) REVERT: C 61 ASP cc_start: 0.7981 (m-30) cc_final: 0.7719 (m-30) REVERT: C 75 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7368 (mmtp) REVERT: C 87 MET cc_start: 0.9349 (mtm) cc_final: 0.8899 (mtp) REVERT: C 90 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: U 34 PHE cc_start: 0.8141 (m-80) cc_final: 0.7718 (m-80) REVERT: U 74 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8573 (tm-30) REVERT: a 32 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.6501 (p) REVERT: a 63 GLU cc_start: 0.8669 (tp30) cc_final: 0.8330 (tp30) REVERT: b 74 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: b 134 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8774 (ptmt) REVERT: b 135 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7099 (tm-30) REVERT: c 93 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: c 135 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6654 (tm-30) REVERT: c 151 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8479 (mmm) REVERT: c 185 PHE cc_start: 0.3702 (OUTLIER) cc_final: 0.3418 (m-80) REVERT: c 219 VAL cc_start: 0.2113 (OUTLIER) cc_final: 0.1889 (m) REVERT: u 30 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7299 (ttt180) REVERT: u 54 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: u 64 GLU cc_start: 0.7781 (mp0) cc_final: 0.7468 (mp0) REVERT: u 79 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7722 (tm-30) REVERT: u 87 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7979 (mpp-170) REVERT: V 135 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7641 (tm-30) REVERT: v 35 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.7770 (p0) REVERT: v 87 MET cc_start: 0.8561 (mtp) cc_final: 0.7961 (mtp) REVERT: v 90 GLU cc_start: 0.6849 (mp0) cc_final: 0.6580 (mp0) REVERT: D 39 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8264 (mm) REVERT: D 84 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7926 (pp) REVERT: D 102 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: F 90 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: F 196 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.4494 (ptp-110) REVERT: G 74 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8287 (tm-30) REVERT: G 89 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: H 32 SER cc_start: 0.7110 (OUTLIER) cc_final: 0.6815 (p) REVERT: H 63 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: H 177 GLN cc_start: 0.3736 (OUTLIER) cc_final: 0.2671 (pm20) REVERT: I 84 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7544 (pp) REVERT: I 155 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7464 (pmm-80) REVERT: J 93 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: J 102 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8350 (pp20) REVERT: J 151 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: K 64 GLU cc_start: 0.7676 (mp0) cc_final: 0.7370 (mp0) REVERT: K 79 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7699 (tm-30) REVERT: L 20 TYR cc_start: 0.7613 (t80) cc_final: 0.7272 (t80) REVERT: L 49 GLU cc_start: 0.8658 (pt0) cc_final: 0.7894 (pt0) REVERT: L 102 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: L 111 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7677 (ttp80) REVERT: L 135 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7298 (tm-30) REVERT: M 38 ARG cc_start: 0.8808 (ttp-170) cc_final: 0.8506 (ttt180) REVERT: M 94 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: M 135 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: N 102 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: O 212 MET cc_start: 0.3651 (ttt) cc_final: 0.2310 (mtm) REVERT: P 8 MET cc_start: 0.7856 (mpp) cc_final: 0.7315 (mpp) REVERT: P 64 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7066 (p0) REVERT: P 72 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: P 75 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7288 (mttm) REVERT: P 90 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: Q 4 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7382 (ptp) REVERT: Q 27 PHE cc_start: 0.7587 (m-80) cc_final: 0.7031 (m-80) REVERT: Q 74 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8374 (tm-30) REVERT: R 111 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7449 (mtp180) REVERT: S 21 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: S 75 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: S 155 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7874 (pmm-80) REVERT: T 93 GLN cc_start: 0.8200 (mp10) cc_final: 0.7619 (mp10) REVERT: T 135 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6686 (tm-30) REVERT: W 64 GLU cc_start: 0.7824 (mp0) cc_final: 0.7520 (mp0) REVERT: W 79 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7569 (tm-30) REVERT: W 105 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7606 (tpt) REVERT: X 8 MET cc_start: 0.8894 (mpp) cc_final: 0.8568 (mpp) REVERT: X 90 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: X 102 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: X 111 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7864 (ttp80) REVERT: X 148 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7561 (ttp-110) REVERT: Y 20 TYR cc_start: 0.7975 (t80) cc_final: 0.7753 (t80) REVERT: Y 148 ARG cc_start: 0.7228 (tpt170) cc_final: 0.6972 (tpp-160) REVERT: Y 164 MET cc_start: 0.5346 (pmm) cc_final: 0.3830 (tpp) outliers start: 463 outliers final: 317 residues processed: 863 average time/residue: 0.4642 time to fit residues: 678.7187 Evaluate side-chains 824 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 456 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 51 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 118 ASP Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 178 SER Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 212 MET Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 185 PHE Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 214 ILE Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 87 ARG Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain u residue 117 ASP Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 140 THR Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 35 ASP Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 81 SER Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 18 TRP Chi-restraints excluded: chain P residue 59 TYR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 75 LYS Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 39 LEU Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 90 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 150 SER Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 526 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 470 optimal weight: 4.9990 chunk 260 optimal weight: 0.6980 chunk 539 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 567 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 177 GLN v 74 GLN H 177 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 50340 Z= 0.322 Angle : 0.667 8.594 68766 Z= 0.348 Chirality : 0.048 0.257 8085 Planarity : 0.005 0.117 8859 Dihedral : 5.803 71.178 7013 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.04 % Favored : 91.55 % Rotamer: Outliers : 9.76 % Allowed : 26.68 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.10), residues: 6579 helix: -0.01 (0.22), residues: 504 sheet: -0.96 (0.10), residues: 2985 loop : -2.12 (0.10), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP V 67 HIS 0.004 0.001 HIS Q 6 PHE 0.036 0.002 PHE X 82 TYR 0.014 0.002 TYR O 55 ARG 0.005 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 518 poor density : 474 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: A 62 ASP cc_start: 0.8124 (t0) cc_final: 0.7890 (t0) REVERT: A 63 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: A 102 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: B 90 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: C 45 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8762 (tp) REVERT: C 61 ASP cc_start: 0.7972 (m-30) cc_final: 0.7753 (m-30) REVERT: C 75 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7389 (mmtp) REVERT: C 87 MET cc_start: 0.9348 (mtm) cc_final: 0.8818 (mtp) REVERT: C 90 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: U 34 PHE cc_start: 0.8166 (m-80) cc_final: 0.7617 (m-80) REVERT: U 35 ASP cc_start: 0.7615 (t70) cc_final: 0.7272 (m-30) REVERT: U 74 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8545 (tm-30) REVERT: U 134 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7764 (tpt) REVERT: a 32 SER cc_start: 0.6812 (OUTLIER) cc_final: 0.6567 (p) REVERT: a 63 GLU cc_start: 0.8724 (tp30) cc_final: 0.8257 (tp30) REVERT: a 116 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7976 (p) REVERT: b 74 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: b 134 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8775 (ptmt) REVERT: b 135 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7127 (tm-30) REVERT: c 59 TYR cc_start: 0.9031 (m-10) cc_final: 0.8744 (m-10) REVERT: c 93 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: c 135 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6410 (tm-30) REVERT: c 151 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8588 (mmt) REVERT: c 219 VAL cc_start: 0.2211 (OUTLIER) cc_final: 0.1950 (m) REVERT: u 30 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7295 (ttt180) REVERT: u 54 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6236 (pm20) REVERT: u 64 GLU cc_start: 0.7819 (mp0) cc_final: 0.7469 (mp0) REVERT: u 79 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7706 (tm-30) REVERT: u 87 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8011 (mpp-170) REVERT: V 111 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7872 (ttp80) REVERT: V 135 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7611 (tm-30) REVERT: V 212 MET cc_start: 0.3317 (mpp) cc_final: 0.2873 (mpp) REVERT: v 35 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8147 (p0) REVERT: D 39 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8258 (mm) REVERT: D 84 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7928 (pp) REVERT: D 101 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8861 (m110) REVERT: D 102 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: D 235 PHE cc_start: 0.4836 (OUTLIER) cc_final: 0.4212 (t80) REVERT: E 53 GLU cc_start: 0.8153 (pp20) cc_final: 0.7821 (pm20) REVERT: F 90 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: F 196 ARG cc_start: 0.4721 (OUTLIER) cc_final: 0.4502 (ptp-110) REVERT: G 74 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8266 (tm-30) REVERT: G 89 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: H 32 SER cc_start: 0.7345 (OUTLIER) cc_final: 0.7075 (p) REVERT: H 63 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: I 84 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7538 (pp) REVERT: I 155 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7466 (pmm-80) REVERT: J 93 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: J 102 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8351 (pp20) REVERT: J 151 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8014 (mtp) REVERT: K 54 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: K 64 GLU cc_start: 0.7707 (mp0) cc_final: 0.7399 (mp0) REVERT: K 79 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7800 (tm-30) REVERT: L 20 TYR cc_start: 0.7592 (t80) cc_final: 0.7206 (t80) REVERT: L 49 GLU cc_start: 0.8668 (pt0) cc_final: 0.7925 (pt0) REVERT: L 102 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: L 111 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7678 (ttp80) REVERT: L 135 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7348 (tm-30) REVERT: L 145 ASN cc_start: 0.7834 (t0) cc_final: 0.6901 (m110) REVERT: M 35 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8059 (t0) REVERT: M 94 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: M 135 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: N 102 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: O 38 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.6961 (ttp-170) REVERT: P 8 MET cc_start: 0.7844 (mpp) cc_final: 0.7305 (mpp) REVERT: P 63 GLU cc_start: 0.7864 (mp0) cc_final: 0.7523 (mm-30) REVERT: P 64 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7055 (p0) REVERT: P 72 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: P 75 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7250 (mttm) REVERT: P 90 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: Q 4 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7428 (ptp) REVERT: Q 27 PHE cc_start: 0.7605 (m-80) cc_final: 0.6971 (m-80) REVERT: Q 74 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8586 (tm-30) REVERT: R 45 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8515 (tt) REVERT: R 111 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: S 21 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8274 (ptpp) REVERT: S 75 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7490 (ptpp) REVERT: S 155 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7898 (pmm-80) REVERT: T 93 GLN cc_start: 0.8206 (mp10) cc_final: 0.7780 (mp10) REVERT: T 135 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6708 (tm-30) REVERT: W 64 GLU cc_start: 0.7827 (mp0) cc_final: 0.7461 (mp0) REVERT: W 79 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7562 (tm-30) REVERT: W 105 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7514 (tpt) REVERT: X 8 MET cc_start: 0.8919 (mpp) cc_final: 0.8624 (mpp) REVERT: X 74 GLN cc_start: 0.7889 (mt0) cc_final: 0.7534 (mt0) REVERT: X 90 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: X 102 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: X 111 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7825 (ttp80) REVERT: X 148 ARG cc_start: 0.7837 (ttt90) cc_final: 0.7521 (ttp-110) REVERT: Y 53 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: Y 148 ARG cc_start: 0.7322 (tpt170) cc_final: 0.7092 (tpp-160) REVERT: Y 164 MET cc_start: 0.5454 (pmm) cc_final: 0.3792 (tpp) outliers start: 518 outliers final: 375 residues processed: 915 average time/residue: 0.4662 time to fit residues: 724.8814 Evaluate side-chains 886 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 453 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 51 THR Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 118 ASP Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 138 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 178 SER Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 87 MET Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 132 THR Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 212 MET Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 125 SER Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 214 ILE Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 87 ARG Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain u residue 117 ASP Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 51 THR Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 140 THR Chi-restraints excluded: chain v residue 3 VAL Chi-restraints excluded: chain v residue 10 VAL Chi-restraints excluded: chain v residue 17 LEU Chi-restraints excluded: chain v residue 35 ASP Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 213 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 81 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 18 TRP Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 75 LYS Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 118 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 90 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 9 LEU Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 58 SER Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 84 LEU Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 102 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 140 THR Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 150 SER Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 212 optimal weight: 1.9990 chunk 569 optimal weight: 0.7980 chunk 124 optimal weight: 0.0670 chunk 371 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 632 optimal weight: 8.9990 chunk 525 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 217 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 GLN H 177 GLN O 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 50340 Z= 0.178 Angle : 0.605 9.308 68766 Z= 0.312 Chirality : 0.046 0.232 8085 Planarity : 0.005 0.117 8859 Dihedral : 5.212 65.774 7011 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.23 % Favored : 93.40 % Rotamer: Outliers : 5.90 % Allowed : 30.39 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.10), residues: 6579 helix: 0.51 (0.23), residues: 504 sheet: -0.78 (0.10), residues: 2991 loop : -1.96 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP X 67 HIS 0.002 0.001 HIS U 66 PHE 0.024 0.001 PHE X 82 TYR 0.013 0.001 TYR Q 110 ARG 0.004 0.000 ARG v 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 522 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8047 (t0) cc_final: 0.7812 (t0) REVERT: B 90 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: C 87 MET cc_start: 0.9237 (mtm) cc_final: 0.9021 (mtp) REVERT: C 181 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4050 (mt) REVERT: U 74 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8557 (tm-30) REVERT: U 134 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7705 (tpt) REVERT: a 32 SER cc_start: 0.6958 (OUTLIER) cc_final: 0.6740 (p) REVERT: a 49 GLU cc_start: 0.8229 (pm20) cc_final: 0.8011 (pm20) REVERT: a 63 GLU cc_start: 0.8737 (tp30) cc_final: 0.8227 (tp30) REVERT: a 111 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: a 212 MET cc_start: 0.2828 (tpt) cc_final: 0.2596 (tpp) REVERT: b 59 TYR cc_start: 0.8674 (m-80) cc_final: 0.8458 (m-80) REVERT: b 74 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: b 134 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8627 (ptmt) REVERT: b 135 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7145 (tm-30) REVERT: c 93 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: c 102 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8372 (pp20) REVERT: c 151 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: u 54 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6129 (pm20) REVERT: u 64 GLU cc_start: 0.7862 (mp0) cc_final: 0.7476 (mp0) REVERT: u 79 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7724 (tm-30) REVERT: V 102 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: V 111 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7786 (ttp80) REVERT: V 135 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7588 (tm-30) REVERT: v 56 ASP cc_start: 0.7647 (t0) cc_final: 0.7350 (t0) REVERT: v 90 GLU cc_start: 0.6248 (mp0) cc_final: 0.6001 (mp0) REVERT: D 62 ASP cc_start: 0.7872 (t0) cc_final: 0.7639 (t0) REVERT: D 101 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.8850 (m110) REVERT: D 164 MET cc_start: 0.7455 (tpp) cc_final: 0.4655 (ttt) REVERT: D 196 ARG cc_start: 0.5238 (mtt180) cc_final: 0.4749 (tpp-160) REVERT: D 235 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.4518 (t80) REVERT: E 53 GLU cc_start: 0.8191 (pp20) cc_final: 0.7833 (pm20) REVERT: E 63 GLU cc_start: 0.7922 (mp0) cc_final: 0.7684 (mp0) REVERT: E 151 MET cc_start: 0.7841 (mmm) cc_final: 0.7549 (mmm) REVERT: F 142 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8004 (tttm) REVERT: F 235 PHE cc_start: 0.5915 (m-80) cc_final: 0.5447 (m-80) REVERT: G 89 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8205 (m-10) REVERT: H 32 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.7133 (p) REVERT: H 63 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: I 84 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7507 (pp) REVERT: J 93 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: J 102 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: J 151 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: K 64 GLU cc_start: 0.7627 (mp0) cc_final: 0.7245 (mp0) REVERT: K 79 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7875 (tm-30) REVERT: L 20 TYR cc_start: 0.7630 (t80) cc_final: 0.7236 (t80) REVERT: L 49 GLU cc_start: 0.8673 (pt0) cc_final: 0.8096 (pt0) REVERT: L 55 TYR cc_start: 0.6691 (p90) cc_final: 0.6476 (p90) REVERT: L 102 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: L 111 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7471 (ttp80) REVERT: L 135 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7314 (tm-30) REVERT: L 145 ASN cc_start: 0.7790 (t0) cc_final: 0.6984 (m110) REVERT: L 212 MET cc_start: 0.3885 (mpp) cc_final: 0.3499 (mpp) REVERT: M 135 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: N 62 ASP cc_start: 0.8070 (t0) cc_final: 0.7822 (t0) REVERT: N 196 ARG cc_start: 0.5199 (mtt180) cc_final: 0.4749 (tpp-160) REVERT: O 90 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: O 212 MET cc_start: 0.4309 (ttt) cc_final: 0.2901 (mtm) REVERT: P 8 MET cc_start: 0.7825 (mpp) cc_final: 0.7312 (mpp) REVERT: P 63 GLU cc_start: 0.7825 (mp0) cc_final: 0.7481 (mm-30) REVERT: P 64 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6912 (p0) REVERT: P 72 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: P 87 MET cc_start: 0.9301 (ptp) cc_final: 0.8822 (mtp) REVERT: Q 9 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8062 (mp) REVERT: Q 27 PHE cc_start: 0.7478 (m-80) cc_final: 0.6674 (m-80) REVERT: Q 74 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8414 (tm-30) REVERT: Q 89 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: S 21 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8356 (ptpp) REVERT: S 155 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8056 (pmm-80) REVERT: T 93 GLN cc_start: 0.8186 (mp10) cc_final: 0.7670 (mp10) REVERT: T 135 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6505 (tm-30) REVERT: T 151 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8338 (mtp) REVERT: W 64 GLU cc_start: 0.7784 (mp0) cc_final: 0.7493 (mp0) REVERT: W 79 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7675 (tm-30) REVERT: W 105 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7438 (tpt) REVERT: W 125 ASP cc_start: 0.8117 (p0) cc_final: 0.7917 (p0) REVERT: X 8 MET cc_start: 0.8845 (mpp) cc_final: 0.8617 (mpp) REVERT: X 90 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7925 (pp20) REVERT: X 111 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7634 (ttp80) REVERT: X 148 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7409 (ttp-110) REVERT: Y 53 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: Y 164 MET cc_start: 0.5196 (pmm) cc_final: 0.3481 (tpp) outliers start: 313 outliers final: 182 residues processed: 775 average time/residue: 0.4635 time to fit residues: 612.1016 Evaluate side-chains 704 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 484 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 92 MET Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 74 GLN Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 111 ARG Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 91 GLN Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 89 TYR Chi-restraints excluded: chain Q residue 93 SER Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 151 MET Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 610 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 360 optimal weight: 7.9990 chunk 462 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 chunk 532 optimal weight: 4.9990 chunk 353 optimal weight: 0.0870 chunk 630 optimal weight: 0.0980 chunk 394 optimal weight: 20.0000 chunk 384 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 overall best weight: 1.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 50340 Z= 0.208 Angle : 0.614 13.028 68766 Z= 0.315 Chirality : 0.047 0.233 8085 Planarity : 0.005 0.117 8859 Dihedral : 5.101 65.417 7003 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.81 % Favored : 92.83 % Rotamer: Outliers : 5.99 % Allowed : 29.83 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.10), residues: 6579 helix: 0.62 (0.23), residues: 504 sheet: -0.76 (0.10), residues: 3009 loop : -1.90 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP V 67 HIS 0.002 0.001 HIS G 6 PHE 0.021 0.001 PHE X 82 TYR 0.022 0.001 TYR u 110 ARG 0.003 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 492 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8083 (t0) cc_final: 0.7817 (t0) REVERT: B 90 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: C 45 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8855 (tp) REVERT: C 87 MET cc_start: 0.9267 (mtm) cc_final: 0.9043 (mtp) REVERT: U 74 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8549 (tm-30) REVERT: U 134 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7689 (tpt) REVERT: a 32 SER cc_start: 0.7028 (OUTLIER) cc_final: 0.6805 (p) REVERT: a 49 GLU cc_start: 0.8307 (pm20) cc_final: 0.8084 (pm20) REVERT: a 63 GLU cc_start: 0.8744 (tp30) cc_final: 0.8263 (tp30) REVERT: a 111 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7408 (mtp85) REVERT: b 59 TYR cc_start: 0.8688 (m-80) cc_final: 0.8430 (m-80) REVERT: b 74 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: b 134 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8705 (ptmt) REVERT: b 135 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7127 (tm-30) REVERT: c 102 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8389 (pp20) REVERT: c 151 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (mmt) REVERT: u 54 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: u 64 GLU cc_start: 0.7817 (mp0) cc_final: 0.7463 (mp0) REVERT: u 79 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7702 (tm-30) REVERT: V 135 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7596 (tm-30) REVERT: v 56 ASP cc_start: 0.7648 (t0) cc_final: 0.7355 (t0) REVERT: D 101 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8848 (m110) REVERT: D 164 MET cc_start: 0.7489 (tpp) cc_final: 0.7128 (tpp) REVERT: D 196 ARG cc_start: 0.5474 (mtt180) cc_final: 0.4813 (tpp-160) REVERT: D 235 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4729 (t80) REVERT: E 63 GLU cc_start: 0.7957 (mp0) cc_final: 0.7683 (mp0) REVERT: E 151 MET cc_start: 0.7923 (mmm) cc_final: 0.7580 (mmm) REVERT: F 142 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8012 (tttm) REVERT: F 235 PHE cc_start: 0.5983 (m-80) cc_final: 0.5563 (m-80) REVERT: G 89 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8170 (m-10) REVERT: H 32 SER cc_start: 0.7330 (OUTLIER) cc_final: 0.7043 (p) REVERT: H 63 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: H 135 GLU cc_start: 0.8402 (mp0) cc_final: 0.7803 (mp0) REVERT: I 84 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7549 (pp) REVERT: J 93 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: J 102 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8253 (pp20) REVERT: J 151 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: K 54 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: K 64 GLU cc_start: 0.7671 (mp0) cc_final: 0.7286 (mp0) REVERT: K 79 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7995 (tm-30) REVERT: L 20 TYR cc_start: 0.7623 (t80) cc_final: 0.7240 (t80) REVERT: L 49 GLU cc_start: 0.8625 (pt0) cc_final: 0.8087 (pt0) REVERT: L 55 TYR cc_start: 0.6693 (p90) cc_final: 0.6489 (p90) REVERT: L 90 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: L 102 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: L 111 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7643 (ttp80) REVERT: L 135 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7326 (tm-30) REVERT: L 145 ASN cc_start: 0.7821 (t0) cc_final: 0.6774 (m110) REVERT: M 53 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: M 135 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: N 62 ASP cc_start: 0.8087 (t0) cc_final: 0.7848 (t0) REVERT: N 235 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.5182 (t80) REVERT: O 90 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: O 91 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: O 164 MET cc_start: 0.6795 (tmm) cc_final: 0.6284 (tmm) REVERT: O 212 MET cc_start: 0.3681 (ttt) cc_final: 0.2281 (mtm) REVERT: P 8 MET cc_start: 0.7842 (mpp) cc_final: 0.7281 (mpp) REVERT: P 63 GLU cc_start: 0.7802 (mp0) cc_final: 0.7454 (mm-30) REVERT: P 64 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6924 (p0) REVERT: P 72 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: P 87 MET cc_start: 0.9307 (ptp) cc_final: 0.8558 (mtp) REVERT: P 90 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: Q 9 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8098 (mp) REVERT: Q 74 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8399 (tm-30) REVERT: Q 89 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: S 21 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8309 (ptpp) REVERT: S 155 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8010 (pmm-80) REVERT: T 90 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: T 93 GLN cc_start: 0.8260 (mp10) cc_final: 0.7649 (mp10) REVERT: T 135 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6593 (tm-30) REVERT: T 151 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: W 64 GLU cc_start: 0.7847 (mp0) cc_final: 0.7461 (mp0) REVERT: W 105 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7390 (tpt) REVERT: X 53 GLU cc_start: 0.7364 (pm20) cc_final: 0.7080 (pm20) REVERT: X 74 GLN cc_start: 0.8004 (mt0) cc_final: 0.7691 (mt0) REVERT: X 90 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8078 (pp20) REVERT: X 111 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7753 (ttp80) REVERT: X 148 ARG cc_start: 0.7703 (ttt90) cc_final: 0.7418 (ttp-110) REVERT: Y 53 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: Y 90 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6510 (mp0) REVERT: Y 164 MET cc_start: 0.4993 (pmm) cc_final: 0.3380 (tpp) outliers start: 318 outliers final: 238 residues processed: 752 average time/residue: 0.5010 time to fit residues: 651.6166 Evaluate side-chains 756 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 476 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 18 TRP Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 39 PHE Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 94 GLN Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 207 VAL Chi-restraints excluded: chain v residue 3 VAL Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 209 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain N residue 235 PHE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 91 GLN Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 89 TYR Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 90 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 151 MET Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 182 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 389 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 429 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 495 optimal weight: 2.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50340 Z= 0.237 Angle : 0.628 11.619 68766 Z= 0.322 Chirality : 0.047 0.234 8085 Planarity : 0.005 0.118 8859 Dihedral : 5.139 65.430 7003 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.92 % Favored : 92.70 % Rotamer: Outliers : 6.54 % Allowed : 29.36 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.10), residues: 6579 helix: 0.71 (0.23), residues: 486 sheet: -0.76 (0.10), residues: 3009 loop : -1.93 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP V 67 HIS 0.003 0.001 HIS W 66 PHE 0.021 0.002 PHE T 120 TYR 0.023 0.001 TYR u 110 ARG 0.004 0.000 ARG c 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 483 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8095 (t0) cc_final: 0.7836 (t0) REVERT: A 139 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7975 (tpp-160) REVERT: B 90 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: C 45 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8861 (tp) REVERT: C 87 MET cc_start: 0.9295 (mtm) cc_final: 0.8788 (mtp) REVERT: C 90 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: U 74 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8550 (tm-30) REVERT: U 134 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: a 32 SER cc_start: 0.6995 (OUTLIER) cc_final: 0.6781 (p) REVERT: a 49 GLU cc_start: 0.8336 (pm20) cc_final: 0.8113 (pm20) REVERT: a 63 GLU cc_start: 0.8752 (tp30) cc_final: 0.8261 (tp30) REVERT: a 111 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7460 (mtp85) REVERT: b 59 TYR cc_start: 0.8733 (m-80) cc_final: 0.8460 (m-80) REVERT: b 74 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: b 134 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (ptmt) REVERT: b 135 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7240 (tm-30) REVERT: c 93 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: c 102 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8389 (pp20) REVERT: c 148 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.6759 (ttp-170) REVERT: c 151 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8526 (mmt) REVERT: u 54 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6133 (pm20) REVERT: u 64 GLU cc_start: 0.7897 (mp0) cc_final: 0.7501 (mp0) REVERT: u 79 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7700 (tm-30) REVERT: v 56 ASP cc_start: 0.7649 (t0) cc_final: 0.7360 (t0) REVERT: D 101 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8857 (m110) REVERT: D 164 MET cc_start: 0.7528 (tpp) cc_final: 0.7209 (tpp) REVERT: D 235 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4393 (t80) REVERT: E 53 GLU cc_start: 0.8187 (pp20) cc_final: 0.7904 (pm20) REVERT: E 63 GLU cc_start: 0.7987 (mp0) cc_final: 0.7767 (mp0) REVERT: E 151 MET cc_start: 0.7810 (mmm) cc_final: 0.7444 (mmm) REVERT: F 142 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8025 (tttm) REVERT: F 235 PHE cc_start: 0.6115 (m-80) cc_final: 0.5662 (m-80) REVERT: G 89 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8186 (m-10) REVERT: H 32 SER cc_start: 0.7371 (OUTLIER) cc_final: 0.7141 (p) REVERT: H 63 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: H 135 GLU cc_start: 0.8409 (mp0) cc_final: 0.7801 (mp0) REVERT: H 154 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: H 164 MET cc_start: 0.2095 (tpp) cc_final: 0.1745 (tpt) REVERT: I 75 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7973 (mtmt) REVERT: I 84 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7496 (pp) REVERT: I 155 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7315 (pmm-80) REVERT: J 93 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: J 102 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: J 151 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7818 (mtp) REVERT: K 54 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: K 64 GLU cc_start: 0.7675 (mp0) cc_final: 0.7285 (mp0) REVERT: K 79 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7835 (tm-30) REVERT: L 20 TYR cc_start: 0.7622 (t80) cc_final: 0.7254 (t80) REVERT: L 49 GLU cc_start: 0.8651 (pt0) cc_final: 0.8065 (pt0) REVERT: L 55 TYR cc_start: 0.6691 (p90) cc_final: 0.6485 (p90) REVERT: L 102 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: L 111 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7571 (ttp80) REVERT: L 135 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7331 (tm-30) REVERT: L 145 ASN cc_start: 0.7754 (t0) cc_final: 0.6570 (m110) REVERT: M 35 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8137 (t0) REVERT: M 53 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: M 135 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: N 49 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: N 62 ASP cc_start: 0.8108 (t0) cc_final: 0.7857 (t0) REVERT: N 196 ARG cc_start: 0.5530 (mtt180) cc_final: 0.4949 (tpp-160) REVERT: N 235 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.5183 (t80) REVERT: O 90 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: O 164 MET cc_start: 0.6701 (tmm) cc_final: 0.6182 (tmm) REVERT: O 212 MET cc_start: 0.3794 (ttt) cc_final: 0.2441 (mtm) REVERT: P 8 MET cc_start: 0.7848 (mpp) cc_final: 0.7278 (mpp) REVERT: P 63 GLU cc_start: 0.7845 (mp0) cc_final: 0.7526 (mm-30) REVERT: P 64 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.7010 (p0) REVERT: P 72 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: P 90 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: P 235 PHE cc_start: 0.6659 (m-80) cc_final: 0.6157 (m-80) REVERT: Q 9 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (mp) REVERT: Q 74 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8409 (tm-30) REVERT: Q 89 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: R 111 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7077 (mtp85) REVERT: R 116 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7934 (p) REVERT: S 21 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8289 (ptpp) REVERT: S 75 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7248 (ptpp) REVERT: S 155 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7999 (pmm-80) REVERT: T 93 GLN cc_start: 0.8210 (mp10) cc_final: 0.7864 (mp10) REVERT: T 102 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8289 (pp20) REVERT: T 135 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6600 (tm-30) REVERT: T 148 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.6888 (ttp-170) REVERT: W 64 GLU cc_start: 0.7872 (mp0) cc_final: 0.7496 (mp0) REVERT: W 105 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7293 (tpt) REVERT: X 53 GLU cc_start: 0.7166 (pm20) cc_final: 0.6865 (pm20) REVERT: X 90 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: X 111 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: X 148 ARG cc_start: 0.7713 (ttt90) cc_final: 0.7375 (ttp-110) REVERT: Y 53 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: Y 90 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6577 (mp0) REVERT: Y 164 MET cc_start: 0.4998 (pmm) cc_final: 0.3252 (tpp) outliers start: 347 outliers final: 273 residues processed: 772 average time/residue: 0.4545 time to fit residues: 598.5237 Evaluate side-chains 795 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 472 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 18 TRP Chi-restraints excluded: chain a residue 32 SER Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 219 VAL Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 214 ILE Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 39 PHE Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 207 VAL Chi-restraints excluded: chain v residue 3 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 209 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain N residue 235 PHE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 89 TYR Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 182 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 573 optimal weight: 7.9990 chunk 603 optimal weight: 3.9990 chunk 550 optimal weight: 0.5980 chunk 587 optimal weight: 7.9990 chunk 353 optimal weight: 0.0970 chunk 255 optimal weight: 2.9990 chunk 461 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 530 optimal weight: 3.9990 chunk 555 optimal weight: 0.9990 chunk 585 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 50340 Z= 0.191 Angle : 0.616 11.956 68766 Z= 0.315 Chirality : 0.046 0.232 8085 Planarity : 0.005 0.119 8859 Dihedral : 4.978 64.194 7001 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.55 % Favored : 93.07 % Rotamer: Outliers : 6.20 % Allowed : 29.58 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 6579 helix: 0.69 (0.23), residues: 504 sheet: -0.70 (0.10), residues: 2991 loop : -1.88 (0.10), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP V 67 HIS 0.003 0.001 HIS Q 66 PHE 0.018 0.001 PHE T 120 TYR 0.020 0.001 TYR u 110 ARG 0.003 0.000 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 487 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8083 (t0) cc_final: 0.7815 (t0) REVERT: A 139 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7944 (tpp-160) REVERT: A 196 ARG cc_start: 0.5028 (mtt180) cc_final: 0.4444 (mmp80) REVERT: B 90 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: C 45 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8862 (tp) REVERT: C 87 MET cc_start: 0.9270 (mtm) cc_final: 0.9068 (mtp) REVERT: C 235 PHE cc_start: 0.5019 (m-80) cc_final: 0.4579 (m-10) REVERT: U 74 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8555 (tm-30) REVERT: U 134 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7736 (tpt) REVERT: a 49 GLU cc_start: 0.8279 (pm20) cc_final: 0.8049 (pm20) REVERT: a 63 GLU cc_start: 0.8750 (tp30) cc_final: 0.8248 (tp30) REVERT: a 111 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7384 (mtp85) REVERT: b 59 TYR cc_start: 0.8723 (m-80) cc_final: 0.8431 (m-80) REVERT: b 74 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: b 134 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8746 (ptmt) REVERT: b 135 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7241 (tm-30) REVERT: b 185 PHE cc_start: 0.2525 (m-10) cc_final: 0.2310 (m-80) REVERT: c 93 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: c 102 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (pp20) REVERT: c 151 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8461 (mmt) REVERT: u 54 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6075 (pm20) REVERT: u 64 GLU cc_start: 0.7903 (mp0) cc_final: 0.7513 (mp0) REVERT: u 79 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7727 (tm-30) REVERT: v 56 ASP cc_start: 0.7674 (t0) cc_final: 0.7386 (t0) REVERT: D 164 MET cc_start: 0.7443 (tpp) cc_final: 0.7169 (tpp) REVERT: D 196 ARG cc_start: 0.5415 (mtt180) cc_final: 0.4792 (tpp-160) REVERT: D 235 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.4399 (t80) REVERT: E 53 GLU cc_start: 0.8230 (pp20) cc_final: 0.7918 (pm20) REVERT: E 63 GLU cc_start: 0.7846 (mp0) cc_final: 0.7566 (mp0) REVERT: E 151 MET cc_start: 0.7919 (mmm) cc_final: 0.7577 (mmm) REVERT: F 142 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: F 235 PHE cc_start: 0.6198 (m-80) cc_final: 0.5755 (m-80) REVERT: G 89 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: H 63 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: H 135 GLU cc_start: 0.8410 (mp0) cc_final: 0.7812 (mp0) REVERT: I 75 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7983 (mtmt) REVERT: I 84 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7534 (pp) REVERT: I 155 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7306 (pmm-80) REVERT: J 93 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: J 102 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8184 (pp20) REVERT: J 151 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7809 (mtp) REVERT: K 54 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: K 64 GLU cc_start: 0.7657 (mp0) cc_final: 0.7261 (mp0) REVERT: K 79 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8029 (tm-30) REVERT: L 20 TYR cc_start: 0.7591 (t80) cc_final: 0.7206 (t80) REVERT: L 49 GLU cc_start: 0.8659 (pt0) cc_final: 0.8148 (pt0) REVERT: L 55 TYR cc_start: 0.6621 (p90) cc_final: 0.6409 (p90) REVERT: L 102 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: L 111 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7532 (ttp80) REVERT: L 135 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7276 (tm-30) REVERT: L 145 ASN cc_start: 0.7710 (t0) cc_final: 0.6523 (m110) REVERT: M 53 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: M 135 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: N 49 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: N 62 ASP cc_start: 0.8102 (t0) cc_final: 0.7839 (t0) REVERT: N 196 ARG cc_start: 0.5322 (mtt180) cc_final: 0.4786 (tpp-160) REVERT: N 235 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5195 (t80) REVERT: O 90 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: O 164 MET cc_start: 0.6698 (tmm) cc_final: 0.5945 (ttt) REVERT: O 212 MET cc_start: 0.4102 (ttt) cc_final: 0.2598 (mtm) REVERT: P 8 MET cc_start: 0.7846 (mpp) cc_final: 0.7277 (mpp) REVERT: P 63 GLU cc_start: 0.7885 (mp0) cc_final: 0.7580 (mm-30) REVERT: P 64 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.7034 (p0) REVERT: P 72 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: P 87 MET cc_start: 0.9289 (ptp) cc_final: 0.8862 (mtp) REVERT: P 235 PHE cc_start: 0.6535 (m-80) cc_final: 0.6206 (m-80) REVERT: Q 9 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8106 (mp) REVERT: Q 74 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8450 (tm-30) REVERT: Q 89 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (m-10) REVERT: R 111 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: S 21 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8315 (ptpp) REVERT: S 155 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8001 (pmm-80) REVERT: S 212 MET cc_start: 0.5091 (tmm) cc_final: 0.4744 (tmm) REVERT: T 93 GLN cc_start: 0.8179 (mp10) cc_final: 0.7683 (mp10) REVERT: T 102 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8322 (pp20) REVERT: T 135 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6546 (tm-30) REVERT: T 148 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.6775 (ptt180) REVERT: W 64 GLU cc_start: 0.7860 (mp0) cc_final: 0.7523 (mp0) REVERT: W 105 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7314 (tpt) REVERT: X 53 GLU cc_start: 0.7319 (pm20) cc_final: 0.6992 (pm20) REVERT: X 90 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (pp20) REVERT: X 111 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7728 (ttp80) REVERT: X 148 ARG cc_start: 0.7673 (ttt90) cc_final: 0.7343 (ttp-110) REVERT: Y 53 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: Y 164 MET cc_start: 0.4947 (pmm) cc_final: 0.3222 (tpp) outliers start: 329 outliers final: 259 residues processed: 763 average time/residue: 0.4644 time to fit residues: 606.6657 Evaluate side-chains 774 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 474 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 219 VAL Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 134 LYS Chi-restraints excluded: chain b residue 144 THR Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 39 PHE Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 88 ILE Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain v residue 3 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 179 THR Chi-restraints excluded: chain v residue 209 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 185 PHE Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain N residue 235 PHE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 91 GLN Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 89 TYR Chi-restraints excluded: chain Q residue 105 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 182 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 110 ILE Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 385 optimal weight: 7.9990 chunk 621 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 651 optimal weight: 30.0000 chunk 599 optimal weight: 4.9990 chunk 518 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 318 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 177 GLN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** H 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN L 94 GLN ** M 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN R 93 GLN R 217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 50340 Z= 0.531 Angle : 0.776 12.187 68766 Z= 0.406 Chirality : 0.052 0.248 8085 Planarity : 0.006 0.120 8859 Dihedral : 5.919 69.704 7001 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.91 % Favored : 90.67 % Rotamer: Outliers : 6.65 % Allowed : 29.15 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 6579 helix: -0.21 (0.22), residues: 492 sheet: -1.01 (0.10), residues: 3069 loop : -2.14 (0.10), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP V 67 HIS 0.008 0.002 HIS u 66 PHE 0.032 0.003 PHE K 39 TYR 0.030 0.002 TYR O 55 ARG 0.009 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13158 Ramachandran restraints generated. 6579 Oldfield, 0 Emsley, 6579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 451 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8402 (t0) cc_final: 0.8164 (t0) REVERT: A 139 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8041 (tpp-160) REVERT: B 90 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: C 45 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (tp) REVERT: C 61 ASP cc_start: 0.7866 (m-30) cc_final: 0.7567 (m-30) REVERT: C 90 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: C 235 PHE cc_start: 0.5041 (m-80) cc_final: 0.4412 (m-10) REVERT: U 74 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8481 (tm-30) REVERT: U 134 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7822 (tpt) REVERT: a 63 GLU cc_start: 0.8770 (tp30) cc_final: 0.8224 (tp30) REVERT: b 135 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7406 (tm-30) REVERT: c 35 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7146 (p0) REVERT: c 59 TYR cc_start: 0.9078 (m-10) cc_final: 0.8837 (m-10) REVERT: c 93 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: c 102 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8395 (pp20) REVERT: c 135 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6261 (tm-30) REVERT: c 151 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8571 (mmp) REVERT: u 54 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6166 (pm20) REVERT: u 64 GLU cc_start: 0.7980 (mp0) cc_final: 0.7625 (mp0) REVERT: u 79 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7654 (tm-30) REVERT: V 20 TYR cc_start: 0.7709 (t80) cc_final: 0.7445 (t80) REVERT: v 53 GLU cc_start: 0.7899 (pm20) cc_final: 0.7638 (pm20) REVERT: v 164 MET cc_start: 0.4421 (tpp) cc_final: 0.3218 (pmm) REVERT: E 63 GLU cc_start: 0.7979 (mp0) cc_final: 0.7715 (mp0) REVERT: G 74 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8317 (tm-30) REVERT: G 89 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: H 21 LYS cc_start: 0.8612 (pttt) cc_final: 0.8383 (pttm) REVERT: H 63 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: H 154 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: I 75 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8157 (mtmt) REVERT: I 84 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7650 (pp) REVERT: I 155 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7305 (pmm-80) REVERT: J 93 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: J 102 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8430 (pp20) REVERT: J 151 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: K 64 GLU cc_start: 0.7749 (mp0) cc_final: 0.7416 (mp0) REVERT: K 79 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7967 (tm-30) REVERT: L 20 TYR cc_start: 0.7637 (t80) cc_final: 0.7350 (t80) REVERT: L 102 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: L 111 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: L 135 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7430 (tm-30) REVERT: L 145 ASN cc_start: 0.7815 (t0) cc_final: 0.6805 (m110) REVERT: M 35 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8108 (t0) REVERT: M 135 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: N 49 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: O 90 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: P 8 MET cc_start: 0.7917 (mpp) cc_final: 0.7302 (mpp) REVERT: P 63 GLU cc_start: 0.7780 (mp0) cc_final: 0.7468 (mm-30) REVERT: P 90 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: P 235 PHE cc_start: 0.6402 (m-80) cc_final: 0.6114 (m-10) REVERT: Q 27 PHE cc_start: 0.7637 (m-80) cc_final: 0.6891 (m-80) REVERT: Q 74 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8363 (tm-30) REVERT: Q 89 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8243 (m-10) REVERT: R 111 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7486 (mtp85) REVERT: R 164 MET cc_start: 0.1784 (tpp) cc_final: 0.1560 (tpt) REVERT: S 21 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8160 (ptpp) REVERT: S 75 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7825 (mtmm) REVERT: S 155 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7848 (pmm-80) REVERT: T 59 TYR cc_start: 0.9126 (m-80) cc_final: 0.8890 (m-10) REVERT: T 93 GLN cc_start: 0.8114 (mp10) cc_final: 0.7450 (mp10) REVERT: T 102 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8447 (pp20) REVERT: T 135 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6630 (tm-30) REVERT: T 151 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8538 (mtp) REVERT: W 64 GLU cc_start: 0.7873 (mp0) cc_final: 0.7546 (mp0) REVERT: W 79 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7587 (tm-30) REVERT: W 87 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7539 (mpt180) REVERT: W 105 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7530 (tpt) REVERT: X 53 GLU cc_start: 0.7193 (pm20) cc_final: 0.6912 (pm20) REVERT: X 74 GLN cc_start: 0.8017 (mt0) cc_final: 0.7542 (mt0) REVERT: X 111 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: X 148 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7425 (ttp-110) REVERT: Y 20 TYR cc_start: 0.7964 (t80) cc_final: 0.7564 (t80) REVERT: Y 53 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: Y 87 MET cc_start: 0.8430 (mtp) cc_final: 0.8190 (mtp) REVERT: Y 164 MET cc_start: 0.4971 (pmm) cc_final: 0.3166 (tpp) outliers start: 353 outliers final: 286 residues processed: 752 average time/residue: 0.4691 time to fit residues: 598.1401 Evaluate side-chains 761 residues out of total 5307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 438 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 TRP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 89 TYR Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 18 TRP Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 61 ASP Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 110 ILE Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 154 ASP Chi-restraints excluded: chain a residue 158 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 207 VAL Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 213 THR Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 219 VAL Chi-restraints excluded: chain b residue 74 GLN Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 146 VAL Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain b residue 165 THR Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain c residue 105 THR Chi-restraints excluded: chain c residue 116 THR Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 145 ASN Chi-restraints excluded: chain c residue 151 MET Chi-restraints excluded: chain c residue 174 VAL Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 213 THR Chi-restraints excluded: chain c residue 214 ILE Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain c residue 242 THR Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 54 GLU Chi-restraints excluded: chain u residue 58 SER Chi-restraints excluded: chain u residue 113 ARG Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 207 VAL Chi-restraints excluded: chain v residue 3 VAL Chi-restraints excluded: chain v residue 127 ILE Chi-restraints excluded: chain v residue 132 THR Chi-restraints excluded: chain v residue 150 SER Chi-restraints excluded: chain v residue 158 VAL Chi-restraints excluded: chain v residue 209 VAL Chi-restraints excluded: chain v residue 213 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 217 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 39 PHE Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 138 THR Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 155 ARG Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 213 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 74 GLN Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 125 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 182 THR Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 134 MET Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 102 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 140 THR Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 183 VAL Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 35 ASP Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 135 GLU Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 209 VAL Chi-restraints excluded: chain M residue 213 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 139 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 166 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 186 GLN Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 195 PHE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 196 ARG Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 140 THR Chi-restraints excluded: chain P residue 157 THR Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 215 THR Chi-restraints excluded: chain P residue 217 ASN Chi-restraints excluded: chain P residue 224 VAL Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 84 MET Chi-restraints excluded: chain Q residue 89 TYR Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ARG Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 21 LYS Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 90 GLU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain S residue 155 ARG Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 185 PHE Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 102 GLU Chi-restraints excluded: chain T residue 116 THR Chi-restraints excluded: chain T residue 125 SER Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 132 THR Chi-restraints excluded: chain T residue 143 VAL Chi-restraints excluded: chain T residue 145 ASN Chi-restraints excluded: chain T residue 151 MET Chi-restraints excluded: chain T residue 159 THR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 182 THR Chi-restraints excluded: chain T residue 214 ILE Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 226 ILE Chi-restraints excluded: chain W residue 7 THR Chi-restraints excluded: chain W residue 39 PHE Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 104 SER Chi-restraints excluded: chain W residue 105 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 130 ILE Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 90 GLU Chi-restraints excluded: chain X residue 111 ARG Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain X residue 129 LYS Chi-restraints excluded: chain X residue 164 MET Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 53 GLU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 165 THR Chi-restraints excluded: chain Y residue 209 VAL Chi-restraints excluded: chain Y residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 654 random chunks: chunk 412 optimal weight: 0.7980 chunk 552 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 478 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 519 optimal weight: 7.9990 chunk 217 optimal weight: 30.0000 chunk 533 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 177 GLN G 66 HIS ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN I 225 ASN J 74 GLN ** M 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.147724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102722 restraints weight = 106754.285| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.43 r_work: 0.3326 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 50340 Z= 0.223 Angle : 0.655 12.263 68766 Z= 0.337 Chirality : 0.047 0.252 8085 Planarity : 0.005 0.121 8859 Dihedral : 5.430 67.178 7001 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.86 % Favored : 92.78 % Rotamer: Outliers : 5.71 % Allowed : 30.02 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6579 helix: 0.39 (0.23), residues: 468 sheet: -0.82 (0.10), residues: 2985 loop : -2.01 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP V 67 HIS 0.003 0.001 HIS Q 66 PHE 0.021 0.002 PHE T 120 TYR 0.026 0.001 TYR K 110 ARG 0.003 0.000 ARG N 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11860.12 seconds wall clock time: 206 minutes 7.77 seconds (12367.77 seconds total)