Starting phenix.real_space_refine on Fri Feb 6 15:04:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsf_60413/02_2026/8zsf_60413.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 sd= 0.077 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 60 5.16 5 C 16836 2.51 5 N 4176 2.21 5 O 4920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25992 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "A" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "C" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "K" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "E" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "I" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "G" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "L" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "F" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "J" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "H" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2166 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Time building chain proxies: 5.48, per 1000 atoms: 0.21 Number of scatterers: 25992 At special positions: 0 Unit cell: (111.3, 111.3, 159, 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 60 16.00 O 4920 8.00 N 4176 7.00 C 16836 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: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 12 sheets defined 52.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'D' and resid 1 through 9 removed outlier: 3.600A pdb=" N LEU D 5 " --> pdb=" O MET D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 42 removed outlier: 3.653A pdb=" N LEU D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 34 " --> pdb=" O TRP D 30 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.559A pdb=" N TRP D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 159 through 166 Processing helix chain 'D' and resid 170 through 180 removed outlier: 3.708A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 211 removed outlier: 3.764A pdb=" N ARG D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.511A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU D 233 " --> pdb=" O PRO D 229 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 removed outlier: 3.812A pdb=" N SER D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.589A pdb=" N LYS A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.832A pdb=" N SER A 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET A 23 " --> pdb=" O GLY A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.187A pdb=" N GLY A 52 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.749A pdb=" N LYS A 64 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.505A pdb=" N ARG A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.691A pdb=" N ILE A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 170 through 180 Processing helix chain 'A' and resid 195 through 211 removed outlier: 4.267A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.868A pdb=" N GLU A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 263 removed outlier: 3.542A pdb=" N SER A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.745A pdb=" N LYS C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 4.010A pdb=" N SER C 22 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET C 23 " --> pdb=" O GLY C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.557A pdb=" N LEU C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 53 through 60 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.741A pdb=" N LYS C 88 " --> pdb=" O ASP C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.503A pdb=" N GLU C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.771A pdb=" N ILE C 135 " --> pdb=" O ILE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 170 through 180 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.641A pdb=" N GLN C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.801A pdb=" N GLN C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.847A pdb=" N SER B 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 23 " --> pdb=" O GLY B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.616A pdb=" N LEU B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 68 through 79 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.703A pdb=" N GLU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.807A pdb=" N ILE B 135 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 195 through 211 removed outlier: 5.390A pdb=" N PHE B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 249 through 259 removed outlier: 3.617A pdb=" N SER B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'K' and resid 2 through 11 Processing helix chain 'K' and resid 19 through 23 removed outlier: 4.124A pdb=" N SER K 22 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET K 23 " --> pdb=" O GLY K 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 19 through 23' Processing helix chain 'K' and resid 29 through 42 Processing helix chain 'K' and resid 55 through 65 removed outlier: 3.606A pdb=" N LYS K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 80 removed outlier: 3.714A pdb=" N TRP K 74 " --> pdb=" O PRO K 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 88 removed outlier: 3.686A pdb=" N LYS K 88 " --> pdb=" O ASP K 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 88' Processing helix chain 'K' and resid 89 through 98 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'K' and resid 170 through 180 removed outlier: 3.625A pdb=" N LYS K 175 " --> pdb=" O PRO K 171 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 211 removed outlier: 3.940A pdb=" N ARG K 198 " --> pdb=" O ASP K 194 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN K 211 " --> pdb=" O LEU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 238 removed outlier: 3.751A pdb=" N GLU K 233 " --> pdb=" O PRO K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 263 removed outlier: 3.513A pdb=" N SER K 253 " --> pdb=" O ASN K 249 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE K 261 " --> pdb=" O PHE K 257 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU K 263 " --> pdb=" O LYS K 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.570A pdb=" N LYS E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.882A pdb=" N SER E 22 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET E 23 " --> pdb=" O GLY E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 23' Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.923A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL E 34 " --> pdb=" O TRP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 4.281A pdb=" N GLY E 52 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 3.709A pdb=" N LYS E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.525A pdb=" N LYS E 88 " --> pdb=" O ASP E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 170 through 180 Processing helix chain 'E' and resid 194 through 212 removed outlier: 4.257A pdb=" N ARG E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 249 through 262 removed outlier: 3.539A pdb=" N SER E 253 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.588A pdb=" N LYS I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 42 removed outlier: 3.722A pdb=" N LEU I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 50 removed outlier: 3.976A pdb=" N THR I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 68 through 79 removed outlier: 3.502A pdb=" N ARG I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 131 through 135 removed outlier: 3.660A pdb=" N ILE I 135 " --> pdb=" O ILE I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 167 removed outlier: 3.813A pdb=" N GLU I 167 " --> pdb=" O PHE I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 180 Processing helix chain 'I' and resid 198 through 211 removed outlier: 3.852A pdb=" N LEU I 204 " --> pdb=" O LEU I 200 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 236 Processing helix chain 'I' and resid 249 through 263 removed outlier: 3.664A pdb=" N SER I 253 " --> pdb=" O ASN I 249 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 255 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE I 261 " --> pdb=" O PHE I 257 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU I 263 " --> pdb=" O LYS I 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 10 removed outlier: 3.751A pdb=" N LYS G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 24 removed outlier: 3.917A pdb=" N MET G 23 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN G 24 " --> pdb=" O VAL G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 20 through 24' Processing helix chain 'G' and resid 29 through 42 removed outlier: 3.682A pdb=" N LEU G 33 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 50 removed outlier: 4.080A pdb=" N THR G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.703A pdb=" N ALA G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 Processing helix chain 'G' and resid 85 through 88 removed outlier: 3.836A pdb=" N LYS G 88 " --> pdb=" O ASP G 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 85 through 88' Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 110 through 119 removed outlier: 3.510A pdb=" N TYR G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 removed outlier: 3.731A pdb=" N ILE G 135 " --> pdb=" O ILE G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 170 through 180 Processing helix chain 'G' and resid 195 through 211 removed outlier: 5.290A pdb=" N PHE G 201 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 237 removed outlier: 4.100A pdb=" N GLN G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 259 removed outlier: 4.114A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 262 No H-bonds generated for 'chain 'G' and resid 260 through 262' Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.681A pdb=" N LYS L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 42 Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 55 through 65 Processing helix chain 'L' and resid 68 through 80 removed outlier: 3.527A pdb=" N TRP L 74 " --> pdb=" O PRO L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 98 Processing helix chain 'L' and resid 110 through 119 Processing helix chain 'L' and resid 158 through 166 Processing helix chain 'L' and resid 173 through 180 Processing helix chain 'L' and resid 194 through 211 removed outlier: 3.950A pdb=" N ARG L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 237 removed outlier: 3.851A pdb=" N GLU L 232 " --> pdb=" O ASN L 228 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU L 233 " --> pdb=" O PRO L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 261 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.623A pdb=" N SER F 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET F 23 " --> pdb=" O GLY F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 23' Processing helix chain 'F' and resid 29 through 42 removed outlier: 3.822A pdb=" N LEU F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 34 " --> pdb=" O TRP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.872A pdb=" N ARG F 49 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 64 removed outlier: 3.714A pdb=" N LEU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 64 " --> pdb=" O TYR F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 158 through 167 removed outlier: 3.924A pdb=" N GLU F 167 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.578A pdb=" N GLN F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 removed outlier: 3.662A pdb=" N GLU F 233 " --> pdb=" O PRO F 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 263 removed outlier: 3.786A pdb=" N SER F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 10 removed outlier: 3.625A pdb=" N LYS J 10 " --> pdb=" O ALA J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 23 removed outlier: 3.853A pdb=" N SER J 22 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET J 23 " --> pdb=" O GLY J 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 19 through 23' Processing helix chain 'J' and resid 29 through 42 removed outlier: 3.655A pdb=" N LEU J 33 " --> pdb=" O SER J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 50 removed outlier: 4.066A pdb=" N THR J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 68 through 79 Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 110 through 118 Processing helix chain 'J' and resid 128 through 135 removed outlier: 3.605A pdb=" N ASP J 131 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA J 133 " --> pdb=" O SER J 130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE J 135 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 167 removed outlier: 3.666A pdb=" N GLU J 167 " --> pdb=" O PHE J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 180 Processing helix chain 'J' and resid 198 through 211 removed outlier: 4.234A pdb=" N LEU J 204 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 237 removed outlier: 3.660A pdb=" N GLN J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 263 removed outlier: 3.612A pdb=" N LEU J 254 " --> pdb=" O PRO J 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE J 261 " --> pdb=" O PHE J 257 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU J 263 " --> pdb=" O LYS J 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 10 removed outlier: 3.561A pdb=" N LYS H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.953A pdb=" N MET H 23 " --> pdb=" O GLY H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.684A pdb=" N LEU H 33 " --> pdb=" O SER H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 49 Processing helix chain 'H' and resid 53 through 63 removed outlier: 3.943A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.820A pdb=" N GLU H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.642A pdb=" N ASP H 131 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 165 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 170 through 180 Processing helix chain 'H' and resid 194 through 211 removed outlier: 3.711A pdb=" N GLN H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 236 Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 249 through 259 removed outlier: 3.893A pdb=" N SER H 253 " --> pdb=" O ASN H 249 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 254 " --> pdb=" O PRO H 250 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU H 255 " --> pdb=" O GLY H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing sheet with id=AA1, first strand: chain 'D' and resid 103 through 105 removed outlier: 6.123A pdb=" N ILE D 14 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE D 188 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE D 16 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL D 185 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE D 223 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE D 187 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 126 removed outlier: 6.397A pdb=" N ILE A 124 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 144 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE A 102 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 14 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE A 188 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 16 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A 185 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE A 223 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 187 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 141 through 144 removed outlier: 7.300A pdb=" N VAL C 13 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 104 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU C 15 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 188 " --> pdb=" O PHE C 16 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL C 185 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE C 223 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 187 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER C 220 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 243 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE C 222 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.694A pdb=" N ILE B 103 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 102 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 14 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 188 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE B 16 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL B 185 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE B 223 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 187 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER B 220 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE B 243 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B 222 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 103 through 105 removed outlier: 8.243A pdb=" N TYR K 104 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU K 15 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE K 188 " --> pdb=" O PHE K 16 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL K 185 " --> pdb=" O TYR K 221 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE K 223 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE K 187 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE K 222 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 123 through 126 removed outlier: 7.161A pdb=" N VAL E 13 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TYR E 104 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 15 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL E 185 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE E 223 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE E 187 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER E 220 " --> pdb=" O GLY E 241 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE E 243 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 222 " --> pdb=" O ILE E 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 141 through 144 removed outlier: 7.236A pdb=" N VAL I 13 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR I 104 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU I 15 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE I 14 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE I 188 " --> pdb=" O ILE I 14 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE I 16 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL I 185 " --> pdb=" O TYR I 221 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE I 223 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE I 187 " --> pdb=" O PHE I 223 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N SER I 220 " --> pdb=" O GLY I 241 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE I 243 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE I 222 " --> pdb=" O ILE I 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 123 through 126 removed outlier: 5.092A pdb=" N ILE G 102 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 102 through 105 removed outlier: 4.733A pdb=" N ILE L 102 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE L 14 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE L 188 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE L 16 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL L 185 " --> pdb=" O TYR L 221 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE L 223 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE L 187 " --> pdb=" O PHE L 223 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE L 222 " --> pdb=" O ILE L 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 123 through 126 removed outlier: 6.848A pdb=" N ILE F 103 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 13 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TYR F 104 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU F 15 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL F 185 " --> pdb=" O TYR F 221 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE F 223 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE F 187 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 141 through 144 removed outlier: 7.253A pdb=" N VAL J 13 " --> pdb=" O ILE J 102 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR J 104 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU J 15 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE J 14 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE J 188 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE J 16 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER J 220 " --> pdb=" O GLY J 241 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE J 243 " --> pdb=" O SER J 220 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE J 222 " --> pdb=" O ILE J 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.892A pdb=" N ILE H 124 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS H 144 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE H 126 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE H 103 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL H 13 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR H 104 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 15 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE H 14 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL H 185 " --> pdb=" O TYR H 221 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE H 223 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE H 187 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 224 " --> pdb=" O ILE H 243 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2757 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: 4.21 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8078 1.34 - 1.46: 5211 1.46 - 1.58: 13205 1.58 - 1.69: 2 1.69 - 1.81: 120 Bond restraints: 26616 Sorted by residual: bond pdb=" CB ASN F 196 " pdb=" CG ASN F 196 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.91e+00 bond pdb=" CB PHE E 223 " pdb=" CG PHE E 223 " ideal model delta sigma weight residual 1.502 1.553 -0.051 2.30e-02 1.89e+03 4.95e+00 bond pdb=" CA ASP H 136 " pdb=" CB ASP H 136 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.69e-02 3.50e+03 4.28e+00 bond pdb=" CB ASN J 99 " pdb=" CG ASN J 99 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.26e+00 bond pdb=" CB ASP G 136 " pdb=" CG ASP G 136 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.09e+00 ... (remaining 26611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 35345 3.01 - 6.02: 538 6.02 - 9.02: 76 9.02 - 12.03: 22 12.03 - 15.04: 7 Bond angle restraints: 35988 Sorted by residual: angle pdb=" N ILE G 197 " pdb=" CA ILE G 197 " pdb=" C ILE G 197 " ideal model delta sigma weight residual 111.91 105.56 6.35 8.90e-01 1.26e+00 5.09e+01 angle pdb=" N ILE C 197 " pdb=" CA ILE C 197 " pdb=" C ILE C 197 " ideal model delta sigma weight residual 112.83 106.27 6.56 9.90e-01 1.02e+00 4.39e+01 angle pdb=" N ILE J 197 " pdb=" CA ILE J 197 " pdb=" C ILE J 197 " ideal model delta sigma weight residual 111.91 106.41 5.50 8.90e-01 1.26e+00 3.81e+01 angle pdb=" C ILE G 135 " pdb=" N ASP G 136 " pdb=" CA ASP G 136 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" N ILE B 68 " pdb=" CA ILE B 68 " pdb=" C ILE B 68 " ideal model delta sigma weight residual 112.29 106.68 5.61 9.40e-01 1.13e+00 3.56e+01 ... (remaining 35983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13292 17.87 - 35.74: 2037 35.74 - 53.62: 513 53.62 - 71.49: 78 71.49 - 89.36: 28 Dihedral angle restraints: 15948 sinusoidal: 6624 harmonic: 9324 Sorted by residual: dihedral pdb=" CA ASP G 248 " pdb=" C ASP G 248 " pdb=" N ASN G 249 " pdb=" CA ASN G 249 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LYS H 64 " pdb=" C LYS H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLU I 59 " pdb=" C GLU I 59 " pdb=" N TYR I 60 " pdb=" CA TYR I 60 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 15945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3271 0.077 - 0.153: 554 0.153 - 0.230: 37 0.230 - 0.307: 10 0.307 - 0.383: 4 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE K 124 " pdb=" CA ILE K 124 " pdb=" CG1 ILE K 124 " pdb=" CG2 ILE K 124 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE K 103 " pdb=" CA ILE K 103 " pdb=" CG1 ILE K 103 " pdb=" CG2 ILE K 103 " both_signs ideal model delta sigma weight residual False 2.64 3.03 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB ILE L 103 " pdb=" CA ILE L 103 " pdb=" CG1 ILE L 103 " pdb=" CG2 ILE L 103 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3873 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 226 " 0.090 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO E 227 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 217 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO L 218 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO L 218 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO L 218 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 124 " 0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C ILE K 124 " -0.083 2.00e-02 2.50e+03 pdb=" O ILE K 124 " 0.031 2.00e-02 2.50e+03 pdb=" N LYS K 125 " 0.028 2.00e-02 2.50e+03 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2526 2.75 - 3.28: 24295 3.28 - 3.82: 43577 3.82 - 4.36: 52301 4.36 - 4.90: 91025 Nonbonded interactions: 213724 Sorted by model distance: nonbonded pdb=" OG1 THR F 170 " pdb=" OD2 ASP F 173 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" OD2 ASP B 173 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR J 170 " pdb=" OD2 ASP J 173 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR E 108 " pdb=" O VAL E 156 " model vdw 2.334 3.040 nonbonded pdb=" OE1 GLU I 40 " pdb=" OH TYR I 61 " model vdw 2.337 3.040 ... (remaining 213719 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.280 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.840 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.005 0.079 26616 Z= 0.230 Angle : 0.947 15.039 35988 Z= 0.512 Chirality : 0.058 0.383 3876 Planarity : 0.008 0.134 4560 Dihedral : 17.938 89.361 9948 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 0.62 % Allowed : 28.37 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3144 helix: -2.04 (0.11), residues: 1404 sheet: -1.17 (0.25), residues: 492 loop : -1.72 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 72 TYR 0.036 0.002 TYR I 60 PHE 0.079 0.003 PHE H 201 TRP 0.025 0.002 TRP F 79 HIS 0.009 0.001 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00529 (26616) covalent geometry : angle 0.94701 (35988) hydrogen bonds : bond 0.14800 ( 932) hydrogen bonds : angle 6.76447 ( 2757) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 409 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8501 (m-30) REVERT: K 110 ARG cc_start: 0.8500 (mtt90) cc_final: 0.8132 (mtt180) REVERT: E 210 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8463 (mt-10) REVERT: I 78 MET cc_start: 0.8715 (mmm) cc_final: 0.8451 (tpp) REVERT: I 209 LYS cc_start: 0.8081 (mttt) cc_final: 0.7834 (mtmm) REVERT: G 226 ARG cc_start: 0.8301 (mmt180) cc_final: 0.7775 (mmm160) REVERT: G 242 MET cc_start: 0.7129 (tpp) cc_final: 0.6926 (tpp) REVERT: L 261 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7494 (t80) REVERT: H 214 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7219 (mt-10) outliers start: 18 outliers final: 7 residues processed: 418 average time/residue: 0.1956 time to fit residues: 122.6253 Evaluate side-chains 400 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 391 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 158 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 107 ASN A 237 GLN C 92 HIS B 3 GLN K 164 GLN E 24 ASN E 32 GLN E 217 GLN I 32 GLN I 211 GLN I 260 ASN G 247 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN J 12 ASN H 260 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112220 restraints weight = 34454.384| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.42 r_work: 0.3204 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26616 Z= 0.153 Angle : 0.558 8.897 35988 Z= 0.292 Chirality : 0.046 0.235 3876 Planarity : 0.005 0.079 4560 Dihedral : 5.634 70.524 3462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 3.33 % Allowed : 25.31 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.14), residues: 3144 helix: -0.77 (0.13), residues: 1440 sheet: -1.07 (0.23), residues: 540 loop : -1.55 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.018 0.001 TYR F 61 PHE 0.029 0.001 PHE G 201 TRP 0.016 0.001 TRP H 74 HIS 0.004 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00361 (26616) covalent geometry : angle 0.55780 (35988) hydrogen bonds : bond 0.03381 ( 932) hydrogen bonds : angle 4.69181 ( 2757) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 430 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 258 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8212 (mm) REVERT: C 57 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 60 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: C 123 TYR cc_start: 0.8542 (p90) cc_final: 0.8139 (p90) REVERT: C 136 ASP cc_start: 0.7837 (t70) cc_final: 0.7611 (t0) REVERT: C 236 GLU cc_start: 0.8755 (tp30) cc_final: 0.8471 (tp30) REVERT: B 116 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8997 (mp) REVERT: K 125 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8580 (ttmm) REVERT: K 162 TYR cc_start: 0.8284 (t80) cc_final: 0.7981 (t80) REVERT: K 201 PHE cc_start: 0.8570 (m-10) cc_final: 0.8315 (m-80) REVERT: E 214 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: I 59 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: I 60 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.4790 (m-10) REVERT: I 63 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8153 (mm) REVERT: I 67 LYS cc_start: 0.8318 (pttm) cc_final: 0.8087 (pttm) REVERT: I 78 MET cc_start: 0.8903 (mmm) cc_final: 0.8598 (tpp) REVERT: I 113 GLU cc_start: 0.8535 (mp0) cc_final: 0.8309 (mp0) REVERT: I 242 MET cc_start: 0.8613 (tpp) cc_final: 0.7985 (ttt) REVERT: G 226 ARG cc_start: 0.8413 (mmt180) cc_final: 0.7761 (mmm160) REVERT: F 88 LYS cc_start: 0.9047 (tptt) cc_final: 0.8794 (mmmt) REVERT: J 232 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7183 (tm-30) REVERT: H 78 MET cc_start: 0.7327 (pmm) cc_final: 0.7030 (pmm) outliers start: 96 outliers final: 44 residues processed: 503 average time/residue: 0.1850 time to fit residues: 142.0777 Evaluate side-chains 438 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 52 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 68 optimal weight: 0.0040 chunk 292 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 ASN C 32 GLN C 211 GLN E 32 GLN E 164 GLN I 260 ASN G 211 GLN G 247 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN F 260 ASN J 99 ASN H 118 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109291 restraints weight = 34643.436| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.47 r_work: 0.3154 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26616 Z= 0.183 Angle : 0.561 9.338 35988 Z= 0.293 Chirality : 0.046 0.215 3876 Planarity : 0.004 0.063 4560 Dihedral : 5.385 69.736 3448 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.72 % Rotamer: Outliers : 4.20 % Allowed : 24.51 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 3144 helix: -0.30 (0.13), residues: 1452 sheet: -0.53 (0.32), residues: 288 loop : -1.31 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 77 TYR 0.023 0.001 TYR E 61 PHE 0.035 0.002 PHE H 201 TRP 0.014 0.001 TRP H 74 HIS 0.003 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00437 (26616) covalent geometry : angle 0.56098 (35988) hydrogen bonds : bond 0.03237 ( 932) hydrogen bonds : angle 4.43406 ( 2757) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 411 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6834 (mtt180) REVERT: D 233 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: D 258 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 263 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4851 (pp) REVERT: C 57 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8226 (mp) REVERT: C 60 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: C 123 TYR cc_start: 0.8799 (p90) cc_final: 0.8315 (p90) REVERT: C 136 ASP cc_start: 0.7906 (t70) cc_final: 0.7689 (t70) REVERT: C 198 ARG cc_start: 0.7415 (mtm110) cc_final: 0.7030 (mtm180) REVERT: C 210 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: C 236 GLU cc_start: 0.8853 (tp30) cc_final: 0.8531 (tp30) REVERT: C 258 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8326 (mm) REVERT: B 32 GLN cc_start: 0.8364 (mp10) cc_final: 0.8072 (mp10) REVERT: B 116 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9029 (mp) REVERT: K 57 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7832 (mp) REVERT: K 201 PHE cc_start: 0.8581 (m-10) cc_final: 0.8315 (m-10) REVERT: E 210 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8549 (mt-10) REVERT: E 214 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: E 258 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8458 (mm) REVERT: I 59 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: I 60 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.4799 (m-10) REVERT: I 63 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8359 (mm) REVERT: I 67 LYS cc_start: 0.8312 (pttm) cc_final: 0.8035 (pttm) REVERT: I 113 GLU cc_start: 0.8575 (mp0) cc_final: 0.8326 (mp0) REVERT: I 242 MET cc_start: 0.8710 (tpp) cc_final: 0.8308 (ttt) REVERT: G 217 GLN cc_start: 0.7265 (tt0) cc_final: 0.6988 (tt0) REVERT: G 226 ARG cc_start: 0.8360 (mmt180) cc_final: 0.7780 (mmm160) REVERT: G 230 ILE cc_start: 0.8754 (mp) cc_final: 0.7643 (mp) REVERT: G 247 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6626 (t0) REVERT: L 49 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8258 (tpp80) REVERT: F 136 ASP cc_start: 0.7913 (t0) cc_final: 0.7474 (t0) REVERT: F 173 ASP cc_start: 0.8950 (m-30) cc_final: 0.8319 (m-30) REVERT: J 164 GLN cc_start: 0.8295 (mt0) cc_final: 0.8069 (mt0) REVERT: J 232 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7326 (tm-30) REVERT: H 109 ASP cc_start: 0.7937 (m-30) cc_final: 0.7495 (p0) REVERT: H 164 GLN cc_start: 0.8249 (tt0) cc_final: 0.8047 (tt0) REVERT: H 198 ARG cc_start: 0.7383 (mtm180) cc_final: 0.6948 (mtm180) REVERT: H 199 LEU cc_start: 0.7712 (tt) cc_final: 0.7106 (mp) REVERT: H 201 PHE cc_start: 0.8345 (m-80) cc_final: 0.8032 (m-80) outliers start: 121 outliers final: 75 residues processed: 500 average time/residue: 0.1781 time to fit residues: 136.5824 Evaluate side-chains 466 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 375 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 197 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 199 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 ASN C 211 GLN B 247 ASN E 32 GLN E 164 GLN I 260 ASN G 211 GLN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN J 99 ASN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126839 restraints weight = 33757.203| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.54 r_work: 0.3374 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26616 Z= 0.133 Angle : 0.522 9.751 35988 Z= 0.272 Chirality : 0.045 0.255 3876 Planarity : 0.004 0.057 4560 Dihedral : 5.209 69.053 3448 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 4.62 % Allowed : 24.34 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 3144 helix: -0.05 (0.14), residues: 1476 sheet: -1.18 (0.23), residues: 540 loop : -1.34 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 77 TYR 0.021 0.001 TYR I 60 PHE 0.027 0.001 PHE H 201 TRP 0.011 0.001 TRP H 74 HIS 0.004 0.000 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00316 (26616) covalent geometry : angle 0.52228 (35988) hydrogen bonds : bond 0.02876 ( 932) hydrogen bonds : angle 4.22409 ( 2757) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 407 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 233 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: D 258 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 64 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8141 (ptpp) REVERT: A 236 GLU cc_start: 0.8678 (tp30) cc_final: 0.8424 (tt0) REVERT: A 263 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4934 (pp) REVERT: C 60 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6628 (m-10) REVERT: C 123 TYR cc_start: 0.8641 (p90) cc_final: 0.8207 (p90) REVERT: C 136 ASP cc_start: 0.7775 (t70) cc_final: 0.7558 (t70) REVERT: C 144 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8746 (mmtt) REVERT: C 198 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7196 (mtm180) REVERT: C 210 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 236 GLU cc_start: 0.8763 (tp30) cc_final: 0.8445 (tp30) REVERT: B 116 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9063 (mp) REVERT: B 201 PHE cc_start: 0.8563 (m-80) cc_final: 0.8243 (m-80) REVERT: K 57 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7858 (mp) REVERT: K 125 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (ttmm) REVERT: E 75 MET cc_start: 0.9254 (mtm) cc_final: 0.8936 (mtp) REVERT: E 214 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7679 (pt0) REVERT: E 258 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8526 (mm) REVERT: I 60 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.5125 (m-10) REVERT: I 113 GLU cc_start: 0.8480 (mp0) cc_final: 0.8279 (mp0) REVERT: I 242 MET cc_start: 0.8684 (tpp) cc_final: 0.8295 (ttt) REVERT: G 213 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7196 (pp) REVERT: G 226 ARG cc_start: 0.8433 (mmt180) cc_final: 0.7796 (mmm160) REVERT: G 230 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.7850 (mp) REVERT: L 49 ARG cc_start: 0.8522 (tpp80) cc_final: 0.7941 (mmm160) REVERT: F 67 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5053 (mttt) REVERT: F 136 ASP cc_start: 0.7914 (t0) cc_final: 0.7472 (t0) REVERT: F 173 ASP cc_start: 0.8917 (m-30) cc_final: 0.8302 (m-30) REVERT: F 215 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7693 (tp30) REVERT: F 217 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: J 232 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7360 (tm-30) REVERT: H 61 TYR cc_start: 0.7424 (t80) cc_final: 0.7178 (t80) REVERT: H 109 ASP cc_start: 0.7972 (m-30) cc_final: 0.7556 (p0) REVERT: H 198 ARG cc_start: 0.7308 (mtm180) cc_final: 0.6847 (mtm180) REVERT: H 201 PHE cc_start: 0.8451 (m-80) cc_final: 0.8176 (m-80) REVERT: H 232 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7085 (tp30) outliers start: 133 outliers final: 74 residues processed: 512 average time/residue: 0.1706 time to fit residues: 134.3259 Evaluate side-chains 461 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 370 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 270 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 211 GLN E 32 GLN E 164 GLN I 260 ASN G 211 GLN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125849 restraints weight = 33976.747| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.63 r_work: 0.3357 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26616 Z= 0.154 Angle : 0.537 10.656 35988 Z= 0.277 Chirality : 0.046 0.254 3876 Planarity : 0.004 0.056 4560 Dihedral : 5.155 68.339 3448 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 4.90 % Allowed : 24.31 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3144 helix: 0.12 (0.14), residues: 1464 sheet: -0.36 (0.28), residues: 336 loop : -1.30 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.023 0.001 TYR I 60 PHE 0.030 0.001 PHE K 201 TRP 0.013 0.001 TRP I 30 HIS 0.004 0.001 HIS I 36 Details of bonding type rmsd covalent geometry : bond 0.00369 (26616) covalent geometry : angle 0.53703 (35988) hydrogen bonds : bond 0.02889 ( 932) hydrogen bonds : angle 4.18111 ( 2757) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 396 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6897 (mtt180) REVERT: D 233 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: D 258 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 64 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8185 (ptpp) REVERT: A 167 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7540 (pt0) REVERT: A 236 GLU cc_start: 0.8712 (tp30) cc_final: 0.8432 (tt0) REVERT: A 263 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4900 (pp) REVERT: C 60 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6633 (m-10) REVERT: C 123 TYR cc_start: 0.8720 (p90) cc_final: 0.8369 (p90) REVERT: C 136 ASP cc_start: 0.7683 (t70) cc_final: 0.7466 (t70) REVERT: C 144 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8745 (mmtt) REVERT: C 210 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 236 GLU cc_start: 0.8811 (tp30) cc_final: 0.8472 (tp30) REVERT: C 258 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8341 (mm) REVERT: B 32 GLN cc_start: 0.8300 (mp10) cc_final: 0.8049 (mp10) REVERT: B 116 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 201 PHE cc_start: 0.8678 (m-80) cc_final: 0.8257 (m-80) REVERT: K 125 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8509 (ttmm) REVERT: E 213 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7019 (pp) REVERT: E 214 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: E 258 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8562 (mm) REVERT: I 49 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8150 (mtm110) REVERT: I 60 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5359 (m-10) REVERT: I 113 GLU cc_start: 0.8496 (mp0) cc_final: 0.8276 (mp0) REVERT: I 242 MET cc_start: 0.8709 (tpp) cc_final: 0.8336 (ttt) REVERT: G 226 ARG cc_start: 0.8452 (mmt180) cc_final: 0.7747 (mmm160) REVERT: G 230 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8037 (mp) REVERT: L 199 LEU cc_start: 0.7958 (tt) cc_final: 0.6882 (mp) REVERT: F 67 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5059 (mttt) REVERT: F 136 ASP cc_start: 0.7898 (t0) cc_final: 0.7421 (t0) REVERT: F 173 ASP cc_start: 0.8932 (m-30) cc_final: 0.8310 (m-30) REVERT: F 215 GLU cc_start: 0.8838 (mm-30) cc_final: 0.7775 (tp30) REVERT: F 217 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: J 62 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7782 (tttm) REVERT: J 232 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7366 (tm-30) REVERT: H 198 ARG cc_start: 0.7507 (mtm180) cc_final: 0.6948 (mtm180) REVERT: H 199 LEU cc_start: 0.7680 (tt) cc_final: 0.7152 (mt) REVERT: H 201 PHE cc_start: 0.8584 (m-80) cc_final: 0.8327 (m-80) REVERT: H 232 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7050 (tp30) outliers start: 141 outliers final: 91 residues processed: 499 average time/residue: 0.2027 time to fit residues: 153.7397 Evaluate side-chains 484 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 32 GLN Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 137 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN E 32 GLN E 164 GLN I 260 ASN ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN G 217 GLN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125509 restraints weight = 33871.613| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.58 r_work: 0.3354 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26616 Z= 0.162 Angle : 0.543 11.334 35988 Z= 0.281 Chirality : 0.046 0.260 3876 Planarity : 0.004 0.056 4560 Dihedral : 5.159 68.515 3448 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 5.00 % Allowed : 24.13 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3144 helix: 0.17 (0.14), residues: 1476 sheet: -0.39 (0.28), residues: 336 loop : -1.31 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 77 TYR 0.024 0.001 TYR I 60 PHE 0.056 0.001 PHE K 201 TRP 0.014 0.001 TRP H 74 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00389 (26616) covalent geometry : angle 0.54340 (35988) hydrogen bonds : bond 0.02898 ( 932) hydrogen bonds : angle 4.16358 ( 2757) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 394 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8306 (tttp) REVERT: D 198 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6909 (mtt180) REVERT: D 233 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: D 258 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8311 (mm) REVERT: A 64 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8149 (ptpp) REVERT: A 167 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7603 (pt0) REVERT: A 236 GLU cc_start: 0.8713 (tp30) cc_final: 0.8431 (tt0) REVERT: A 263 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4958 (pp) REVERT: C 60 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: C 123 TYR cc_start: 0.8624 (p90) cc_final: 0.8173 (p90) REVERT: C 136 ASP cc_start: 0.7687 (t70) cc_final: 0.7430 (t70) REVERT: C 144 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8760 (mmtt) REVERT: C 198 ARG cc_start: 0.7598 (mtm110) cc_final: 0.6936 (mtm180) REVERT: C 210 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: C 236 GLU cc_start: 0.8798 (tp30) cc_final: 0.8472 (tp30) REVERT: C 258 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8382 (mm) REVERT: B 32 GLN cc_start: 0.8302 (mp10) cc_final: 0.8065 (mp10) REVERT: B 62 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8221 (tttt) REVERT: B 116 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 201 PHE cc_start: 0.8689 (m-80) cc_final: 0.8312 (m-80) REVERT: K 57 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7869 (mp) REVERT: K 125 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8511 (ttmm) REVERT: E 213 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7325 (pp) REVERT: E 214 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: E 258 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8563 (mm) REVERT: I 49 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8132 (mtm110) REVERT: I 60 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.5568 (m-10) REVERT: I 113 GLU cc_start: 0.8502 (mp0) cc_final: 0.8267 (mp0) REVERT: I 242 MET cc_start: 0.8724 (tpp) cc_final: 0.8356 (ttt) REVERT: G 230 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8219 (mp) REVERT: F 67 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5055 (mttt) REVERT: F 136 ASP cc_start: 0.7881 (t0) cc_final: 0.7397 (t0) REVERT: F 173 ASP cc_start: 0.8936 (m-30) cc_final: 0.8302 (m-30) REVERT: F 215 GLU cc_start: 0.8868 (mm-30) cc_final: 0.7762 (tp30) REVERT: F 217 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: J 62 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7837 (tttm) REVERT: J 214 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7562 (mm-30) REVERT: J 232 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7474 (tm-30) REVERT: H 198 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6799 (mtm180) REVERT: H 199 LEU cc_start: 0.7668 (tt) cc_final: 0.7414 (tt) REVERT: H 201 PHE cc_start: 0.8667 (m-80) cc_final: 0.8311 (m-80) REVERT: H 232 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: H 242 MET cc_start: 0.8574 (tpt) cc_final: 0.8064 (tpp) outliers start: 144 outliers final: 94 residues processed: 504 average time/residue: 0.2034 time to fit residues: 155.9427 Evaluate side-chains 494 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 378 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 32 GLN Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 255 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN C 211 GLN E 32 GLN E 164 GLN I 260 ASN G 137 ASN G 196 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127405 restraints weight = 33741.040| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.53 r_work: 0.3361 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26616 Z= 0.130 Angle : 0.527 11.423 35988 Z= 0.273 Chirality : 0.045 0.260 3876 Planarity : 0.004 0.056 4560 Dihedral : 5.077 68.627 3448 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 4.79 % Allowed : 24.38 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3144 helix: 0.10 (0.13), residues: 1548 sheet: -0.31 (0.28), residues: 336 loop : -1.24 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 77 TYR 0.022 0.001 TYR I 60 PHE 0.032 0.001 PHE K 201 TRP 0.013 0.001 TRP H 74 HIS 0.003 0.000 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00312 (26616) covalent geometry : angle 0.52684 (35988) hydrogen bonds : bond 0.02767 ( 932) hydrogen bonds : angle 4.09335 ( 2757) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 399 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8269 (tttp) REVERT: D 198 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6881 (mtt180) REVERT: D 258 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 167 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7490 (pt0) REVERT: A 236 GLU cc_start: 0.8699 (tp30) cc_final: 0.8408 (tt0) REVERT: A 263 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4887 (pp) REVERT: C 60 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6636 (m-10) REVERT: C 123 TYR cc_start: 0.8609 (p90) cc_final: 0.8135 (p90) REVERT: C 136 ASP cc_start: 0.7676 (t70) cc_final: 0.7415 (t70) REVERT: C 144 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8749 (mmtt) REVERT: C 198 ARG cc_start: 0.7548 (mtm110) cc_final: 0.6991 (mtm180) REVERT: C 210 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: C 236 GLU cc_start: 0.8750 (tp30) cc_final: 0.8391 (tp30) REVERT: C 258 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8382 (mm) REVERT: B 1 MET cc_start: 0.6640 (tpt) cc_final: 0.5032 (mtt) REVERT: B 62 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8190 (tttt) REVERT: B 116 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9027 (mp) REVERT: K 57 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7828 (mp) REVERT: K 67 LYS cc_start: 0.8809 (mttm) cc_final: 0.8347 (mtmt) REVERT: E 213 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7205 (pp) REVERT: E 214 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: E 258 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8553 (mm) REVERT: I 49 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8080 (mtm110) REVERT: I 60 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.5705 (m-10) REVERT: I 113 GLU cc_start: 0.8509 (mp0) cc_final: 0.8267 (mp0) REVERT: I 233 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: I 242 MET cc_start: 0.8721 (tpp) cc_final: 0.8352 (ttt) REVERT: G 226 ARG cc_start: 0.8472 (mmt180) cc_final: 0.7755 (tpp-160) REVERT: G 230 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8138 (mp) REVERT: F 1 MET cc_start: 0.8091 (tmm) cc_final: 0.7752 (tmm) REVERT: F 67 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5044 (mttt) REVERT: F 136 ASP cc_start: 0.7812 (t0) cc_final: 0.7295 (t0) REVERT: F 173 ASP cc_start: 0.8941 (m-30) cc_final: 0.8280 (m-30) REVERT: F 215 GLU cc_start: 0.8831 (mm-30) cc_final: 0.7677 (tp30) REVERT: F 217 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: J 62 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7828 (tttm) REVERT: J 232 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7436 (tm-30) REVERT: H 56 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6947 (mt-10) REVERT: H 109 ASP cc_start: 0.8138 (m-30) cc_final: 0.7687 (p0) REVERT: H 198 ARG cc_start: 0.7378 (mtm180) cc_final: 0.7084 (mtp180) REVERT: H 199 LEU cc_start: 0.7643 (tt) cc_final: 0.7199 (mt) REVERT: H 201 PHE cc_start: 0.8621 (m-80) cc_final: 0.8418 (m-80) REVERT: H 214 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7215 (mt-10) REVERT: H 232 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7024 (tp30) outliers start: 138 outliers final: 93 residues processed: 503 average time/residue: 0.1996 time to fit residues: 153.0991 Evaluate side-chains 488 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 375 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 217 GLN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 229 optimal weight: 0.0870 chunk 110 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN E 32 GLN I 260 ASN G 137 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.158910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128307 restraints weight = 33792.732| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.60 r_work: 0.3396 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26616 Z= 0.111 Angle : 0.522 10.805 35988 Z= 0.269 Chirality : 0.045 0.263 3876 Planarity : 0.004 0.056 4560 Dihedral : 4.977 68.459 3448 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 4.10 % Allowed : 25.31 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3144 helix: 0.29 (0.14), residues: 1524 sheet: -0.20 (0.29), residues: 336 loop : -1.16 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 77 TYR 0.023 0.001 TYR K 61 PHE 0.025 0.001 PHE K 201 TRP 0.012 0.001 TRP H 74 HIS 0.004 0.000 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00262 (26616) covalent geometry : angle 0.52192 (35988) hydrogen bonds : bond 0.02656 ( 932) hydrogen bonds : angle 4.03262 ( 2757) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 396 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 198 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6943 (mtt180) REVERT: D 233 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: D 258 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 167 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7409 (pt0) REVERT: A 236 GLU cc_start: 0.8695 (tp30) cc_final: 0.8429 (tt0) REVERT: C 60 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6590 (m-10) REVERT: C 123 TYR cc_start: 0.8567 (p90) cc_final: 0.8152 (p90) REVERT: C 144 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8748 (mmtt) REVERT: C 198 ARG cc_start: 0.7641 (mtm110) cc_final: 0.7204 (mtm180) REVERT: C 210 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 236 GLU cc_start: 0.8688 (tp30) cc_final: 0.8300 (tp30) REVERT: C 258 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 1 MET cc_start: 0.6531 (tpt) cc_final: 0.5055 (mtt) REVERT: B 62 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8219 (tttt) REVERT: B 116 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9031 (mp) REVERT: K 67 LYS cc_start: 0.8774 (mttm) cc_final: 0.8358 (mtmt) REVERT: K 196 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7643 (t0) REVERT: E 75 MET cc_start: 0.9230 (mtm) cc_final: 0.8948 (mtp) REVERT: E 213 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7214 (pp) REVERT: E 214 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: E 258 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (mm) REVERT: I 49 ARG cc_start: 0.8429 (mtm110) cc_final: 0.8057 (mtm110) REVERT: I 60 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.5700 (m-10) REVERT: I 113 GLU cc_start: 0.8468 (mp0) cc_final: 0.8242 (mp0) REVERT: I 233 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: I 242 MET cc_start: 0.8668 (tpp) cc_final: 0.8283 (ttt) REVERT: I 259 LYS cc_start: 0.8222 (tptt) cc_final: 0.7905 (tptt) REVERT: G 226 ARG cc_start: 0.8430 (mmt180) cc_final: 0.7749 (tpp-160) REVERT: G 230 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8151 (mp) REVERT: L 49 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8015 (tpp80) REVERT: L 199 LEU cc_start: 0.7854 (tt) cc_final: 0.7160 (mm) REVERT: L 261 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.6984 (t80) REVERT: F 1 MET cc_start: 0.8102 (tmm) cc_final: 0.7820 (tmm) REVERT: F 67 LYS cc_start: 0.5963 (OUTLIER) cc_final: 0.4935 (mttt) REVERT: F 136 ASP cc_start: 0.7778 (t0) cc_final: 0.7260 (t0) REVERT: F 173 ASP cc_start: 0.8909 (m-30) cc_final: 0.8236 (m-30) REVERT: F 215 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7637 (tp30) REVERT: F 217 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: J 62 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (tttm) REVERT: J 232 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 109 ASP cc_start: 0.8111 (m-30) cc_final: 0.7738 (p0) REVERT: H 198 ARG cc_start: 0.7340 (mtm180) cc_final: 0.7076 (mtp180) REVERT: H 199 LEU cc_start: 0.7594 (tt) cc_final: 0.7109 (mt) REVERT: H 214 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7259 (mt-10) REVERT: H 232 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7061 (tp30) outliers start: 118 outliers final: 83 residues processed: 490 average time/residue: 0.1805 time to fit residues: 135.3707 Evaluate side-chains 483 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 380 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 255 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN E 32 GLN E 164 GLN I 260 ASN G 137 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126846 restraints weight = 33710.022| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.60 r_work: 0.3370 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26616 Z= 0.146 Angle : 0.545 11.247 35988 Z= 0.280 Chirality : 0.046 0.272 3876 Planarity : 0.004 0.056 4560 Dihedral : 5.016 68.352 3448 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 4.41 % Allowed : 24.90 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3144 helix: 0.28 (0.14), residues: 1524 sheet: -0.25 (0.29), residues: 336 loop : -1.15 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 77 TYR 0.023 0.001 TYR I 60 PHE 0.029 0.001 PHE K 201 TRP 0.013 0.001 TRP H 74 HIS 0.005 0.001 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00352 (26616) covalent geometry : angle 0.54473 (35988) hydrogen bonds : bond 0.02830 ( 932) hydrogen bonds : angle 4.09079 ( 2757) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 379 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8459 (tttm) REVERT: D 198 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6890 (mtt180) REVERT: D 233 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: D 258 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 167 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7466 (pt0) REVERT: C 60 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: C 123 TYR cc_start: 0.8626 (p90) cc_final: 0.8216 (p90) REVERT: C 144 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8756 (mmtt) REVERT: C 198 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7177 (mtm180) REVERT: C 210 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: C 236 GLU cc_start: 0.8729 (tp30) cc_final: 0.8346 (tp30) REVERT: C 258 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8402 (mm) REVERT: B 1 MET cc_start: 0.6555 (tpt) cc_final: 0.5042 (mtt) REVERT: B 62 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8228 (tttt) REVERT: B 116 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9036 (mp) REVERT: K 67 LYS cc_start: 0.8798 (mttm) cc_final: 0.8370 (mtmt) REVERT: E 75 MET cc_start: 0.9266 (mtm) cc_final: 0.9016 (mtp) REVERT: E 213 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7207 (pp) REVERT: E 214 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: E 258 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8579 (mm) REVERT: I 49 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8102 (mtm110) REVERT: I 60 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5648 (m-10) REVERT: I 113 GLU cc_start: 0.8497 (mp0) cc_final: 0.8254 (mp0) REVERT: I 233 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: I 242 MET cc_start: 0.8707 (tpp) cc_final: 0.8345 (ttt) REVERT: G 230 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8186 (mp) REVERT: L 49 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8022 (tpp80) REVERT: F 1 MET cc_start: 0.8145 (tmm) cc_final: 0.7818 (tmm) REVERT: F 67 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.4879 (mttt) REVERT: F 136 ASP cc_start: 0.7909 (t0) cc_final: 0.7387 (t0) REVERT: F 173 ASP cc_start: 0.8938 (m-30) cc_final: 0.8262 (m-30) REVERT: F 215 GLU cc_start: 0.8831 (mm-30) cc_final: 0.7727 (tp30) REVERT: F 217 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: J 62 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7793 (tttm) REVERT: J 99 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7362 (m110) REVERT: J 214 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7494 (mm-30) REVERT: J 232 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7476 (tm-30) REVERT: H 56 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6730 (mt-10) REVERT: H 109 ASP cc_start: 0.8150 (m-30) cc_final: 0.7697 (p0) REVERT: H 198 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6815 (mtm180) REVERT: H 199 LEU cc_start: 0.7760 (tt) cc_final: 0.7131 (mt) REVERT: H 214 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7265 (mt-10) REVERT: H 232 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7044 (tp30) outliers start: 127 outliers final: 91 residues processed: 478 average time/residue: 0.1879 time to fit residues: 136.9867 Evaluate side-chains 478 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 367 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 158 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 217 GLN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 299 optimal weight: 0.0980 chunk 252 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN E 32 GLN I 260 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** H 80 HIS ** 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 = 0.3943 r_free = 0.3943 target = 0.161849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132710 restraints weight = 34036.849| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.46 r_work: 0.3382 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26616 Z= 0.114 Angle : 0.539 10.761 35988 Z= 0.277 Chirality : 0.045 0.264 3876 Planarity : 0.004 0.075 4560 Dihedral : 4.963 68.571 3448 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 3.92 % Allowed : 25.62 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3144 helix: 0.35 (0.14), residues: 1524 sheet: -0.21 (0.29), residues: 336 loop : -1.12 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 77 TYR 0.021 0.001 TYR I 60 PHE 0.023 0.001 PHE K 201 TRP 0.016 0.001 TRP H 74 HIS 0.005 0.000 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00269 (26616) covalent geometry : angle 0.53870 (35988) hydrogen bonds : bond 0.02730 ( 932) hydrogen bonds : angle 4.04292 ( 2757) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 377 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8196 (tttp) REVERT: D 198 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6889 (mtt180) REVERT: D 233 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: D 258 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 167 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7444 (pt0) REVERT: A 236 GLU cc_start: 0.8606 (tp30) cc_final: 0.8388 (tt0) REVERT: C 60 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: C 123 TYR cc_start: 0.8590 (p90) cc_final: 0.8164 (p90) REVERT: C 198 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7216 (mtm180) REVERT: C 210 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 236 GLU cc_start: 0.8745 (tp30) cc_final: 0.8313 (tp30) REVERT: C 258 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 1 MET cc_start: 0.6548 (tpt) cc_final: 0.5021 (mtt) REVERT: B 62 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8227 (tttt) REVERT: B 116 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9034 (mp) REVERT: B 226 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7899 (ptm-80) REVERT: K 67 LYS cc_start: 0.8777 (mttm) cc_final: 0.8397 (mtmt) REVERT: K 196 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7572 (t0) REVERT: E 75 MET cc_start: 0.9239 (mtm) cc_final: 0.8955 (mtp) REVERT: E 199 LEU cc_start: 0.7262 (tt) cc_final: 0.6867 (tt) REVERT: E 214 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: E 258 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8532 (mm) REVERT: I 49 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8049 (mtm110) REVERT: I 60 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5709 (m-10) REVERT: I 113 GLU cc_start: 0.8486 (mp0) cc_final: 0.8252 (mp0) REVERT: I 233 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: I 242 MET cc_start: 0.8705 (tpp) cc_final: 0.8317 (ttt) REVERT: G 230 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8160 (mp) REVERT: L 199 LEU cc_start: 0.7858 (tt) cc_final: 0.7157 (mm) REVERT: L 261 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.6997 (t80) REVERT: F 1 MET cc_start: 0.8050 (tmm) cc_final: 0.7776 (tmm) REVERT: F 67 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.4858 (mttt) REVERT: F 136 ASP cc_start: 0.7918 (t0) cc_final: 0.7471 (t0) REVERT: F 173 ASP cc_start: 0.8912 (m-30) cc_final: 0.8240 (m-30) REVERT: F 215 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7686 (tp30) REVERT: F 217 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: J 99 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7440 (m110) REVERT: J 232 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7484 (tm-30) REVERT: H 109 ASP cc_start: 0.8131 (m-30) cc_final: 0.7764 (p0) REVERT: H 198 ARG cc_start: 0.7243 (mtm180) cc_final: 0.6777 (mtm180) REVERT: H 214 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7240 (mt-10) REVERT: H 232 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7039 (tp30) outliers start: 113 outliers final: 87 residues processed: 469 average time/residue: 0.1908 time to fit residues: 136.1368 Evaluate side-chains 477 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 371 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 208 TRP Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 68 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 184 SER Chi-restraints excluded: chain I residue 196 ASN Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 260 ASN Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 196 ASN Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 170 THR Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 86 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 210 optimal weight: 0.0980 chunk 219 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 260 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN C 211 GLN E 32 GLN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** H 80 HIS ** 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 = 0.3990 r_free = 0.3990 target = 0.165970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135819 restraints weight = 33901.966| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.46 r_work: 0.3526 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26616 Z= 0.092 Angle : 0.525 10.825 35988 Z= 0.269 Chirality : 0.044 0.258 3876 Planarity : 0.004 0.059 4560 Dihedral : 4.801 69.443 3448 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 26.22 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3144 helix: 0.46 (0.14), residues: 1524 sheet: -0.04 (0.29), residues: 336 loop : -1.08 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 77 TYR 0.020 0.001 TYR K 61 PHE 0.018 0.001 PHE J 100 TRP 0.016 0.001 TRP H 74 HIS 0.004 0.000 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00204 (26616) covalent geometry : angle 0.52543 (35988) hydrogen bonds : bond 0.02547 ( 932) hydrogen bonds : angle 3.92922 ( 2757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5233.24 seconds wall clock time: 90 minutes 58.41 seconds (5458.41 seconds total)