Starting phenix.real_space_refine on Sun Feb 8 09:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.map" model { file = "/net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9z_70267/02_2026/9o9z_70267.cif" } resolution = 2.4 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= 0.001 sd= 0.025 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 44 5.16 5 C 27555 2.51 5 N 7843 2.21 5 O 8294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s 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: 43736 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "B" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "C" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "E" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "F" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "G" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "H" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "I" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "J" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "K" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1882 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain: "a" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "b" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "c" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "d" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "e" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "f" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "g" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "h" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "i" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "j" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "k" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2094 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Time building chain proxies: 9.92, per 1000 atoms: 0.23 Number of scatterers: 43736 At special positions: 0 Unit cell: (208.05, 210.24, 118.99, 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 44 16.00 O 8294 8.00 N 7843 7.00 C 27555 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: 3.86 Conformation dependent library (CDL) restraints added in 1.8 seconds 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10538 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 64 sheets defined 57.3% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 113 through 132 Proline residue: A 120 - end of helix removed outlier: 4.018A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.958A pdb=" N THR A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 232 removed outlier: 3.996A pdb=" N ARG A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 113 through 132 Proline residue: B 120 - end of helix removed outlier: 4.089A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 142 through 160 removed outlier: 3.875A pdb=" N THR B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 232 removed outlier: 3.974A pdb=" N ARG B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 113 through 132 Proline residue: C 120 - end of helix removed outlier: 4.261A pdb=" N THR C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 132 " --> pdb=" O LYS C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 142 through 160 removed outlier: 4.011A pdb=" N THR C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 232 removed outlier: 3.984A pdb=" N ARG C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 113 through 132 Proline residue: D 120 - end of helix removed outlier: 4.078A pdb=" N THR D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 142 through 160 removed outlier: 3.951A pdb=" N THR D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 232 removed outlier: 4.002A pdb=" N ARG D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 251 Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 113 through 132 Proline residue: E 120 - end of helix removed outlier: 3.971A pdb=" N THR E 124 " --> pdb=" O PRO E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 142 through 160 removed outlier: 4.005A pdb=" N THR E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 232 removed outlier: 4.001A pdb=" N ARG E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 251 Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'F' and resid 23 through 25 No H-bonds generated for 'chain 'F' and resid 23 through 25' Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 113 through 132 Proline residue: F 120 - end of helix removed outlier: 4.110A pdb=" N THR F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 Processing helix chain 'F' and resid 142 through 160 removed outlier: 3.993A pdb=" N THR F 160 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 232 removed outlier: 3.991A pdb=" N ARG F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 113 through 132 Proline residue: G 120 - end of helix removed outlier: 4.097A pdb=" N THR G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 142 Processing helix chain 'G' and resid 142 through 160 removed outlier: 3.988A pdb=" N THR G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 232 removed outlier: 3.993A pdb=" N ARG G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 251 Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'H' and resid 23 through 25 No H-bonds generated for 'chain 'H' and resid 23 through 25' Processing helix chain 'H' and resid 102 through 110 Processing helix chain 'H' and resid 113 through 132 Proline residue: H 120 - end of helix removed outlier: 4.041A pdb=" N THR H 124 " --> pdb=" O PRO H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 142 through 160 removed outlier: 3.981A pdb=" N THR H 160 " --> pdb=" O GLU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 232 removed outlier: 3.970A pdb=" N ARG H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE H 198 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'I' and resid 23 through 25 No H-bonds generated for 'chain 'I' and resid 23 through 25' Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 113 through 132 Proline residue: I 120 - end of helix removed outlier: 4.070A pdb=" N THR I 124 " --> pdb=" O PRO I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 142 Processing helix chain 'I' and resid 142 through 160 removed outlier: 3.991A pdb=" N THR I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 232 removed outlier: 3.983A pdb=" N ARG I 197 " --> pdb=" O ALA I 193 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE I 198 " --> pdb=" O GLU I 194 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 251 Processing helix chain 'I' and resid 252 through 254 No H-bonds generated for 'chain 'I' and resid 252 through 254' Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 113 through 132 Proline residue: J 120 - end of helix removed outlier: 4.055A pdb=" N THR J 124 " --> pdb=" O PRO J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 142 Processing helix chain 'J' and resid 142 through 160 removed outlier: 3.975A pdb=" N THR J 160 " --> pdb=" O GLU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 232 removed outlier: 3.972A pdb=" N ARG J 197 " --> pdb=" O ALA J 193 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE J 198 " --> pdb=" O GLU J 194 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 251 Processing helix chain 'J' and resid 252 through 254 No H-bonds generated for 'chain 'J' and resid 252 through 254' Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 113 through 132 Proline residue: K 120 - end of helix removed outlier: 4.019A pdb=" N THR K 124 " --> pdb=" O PRO K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 142 Processing helix chain 'K' and resid 142 through 160 removed outlier: 3.968A pdb=" N THR K 160 " --> pdb=" O GLU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 232 removed outlier: 3.971A pdb=" N ARG K 197 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE K 198 " --> pdb=" O GLU K 194 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 251 Processing helix chain 'K' and resid 252 through 254 No H-bonds generated for 'chain 'K' and resid 252 through 254' Processing helix chain 'a' and resid 34 through 38 removed outlier: 3.656A pdb=" N GLU a 38 " --> pdb=" O TYR a 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 34 through 38' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 127 through 146 Proline residue: a 134 - end of helix removed outlier: 4.422A pdb=" N ASN a 138 " --> pdb=" O PRO a 134 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA a 146 " --> pdb=" O LYS a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 156 through 174 removed outlier: 3.547A pdb=" N GLU a 170 " --> pdb=" O ARG a 166 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP a 174 " --> pdb=" O GLU a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 245 removed outlier: 3.837A pdb=" N GLN a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE a 212 " --> pdb=" O GLN a 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU a 213 " --> pdb=" O ARG a 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL a 214 " --> pdb=" O ALA a 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU a 215 " --> pdb=" O GLN a 211 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET a 237 " --> pdb=" O GLU a 233 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS a 244 " --> pdb=" O GLU a 240 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN a 245 " --> pdb=" O ALA a 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 266 removed outlier: 3.736A pdb=" N LYS a 250 " --> pdb=" O PRO a 246 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR a 266 " --> pdb=" O LYS a 262 " (cutoff:3.500A) Processing helix chain 'a' and resid 276 through 279 Processing helix chain 'a' and resid 284 through 287 Processing helix chain 'a' and resid 288 through 293 Processing helix chain 'b' and resid 34 through 39 Processing helix chain 'b' and resid 116 through 124 Processing helix chain 'b' and resid 127 through 146 Proline residue: b 134 - end of helix removed outlier: 4.467A pdb=" N ASN b 138 " --> pdb=" O PRO b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 156 Processing helix chain 'b' and resid 156 through 174 removed outlier: 4.014A pdb=" N ASP b 174 " --> pdb=" O GLU b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 245 removed outlier: 3.834A pdb=" N GLN b 211 " --> pdb=" O ALA b 207 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE b 212 " --> pdb=" O GLN b 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU b 213 " --> pdb=" O ARG b 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU b 215 " --> pdb=" O GLN b 211 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN b 219 " --> pdb=" O GLU b 215 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU b 240 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA b 241 " --> pdb=" O MET b 237 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS b 244 " --> pdb=" O GLU b 240 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN b 245 " --> pdb=" O ALA b 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 246 through 266 removed outlier: 3.702A pdb=" N LYS b 250 " --> pdb=" O PRO b 246 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR b 266 " --> pdb=" O LYS b 262 " (cutoff:3.500A) Processing helix chain 'b' and resid 276 through 279 Processing helix chain 'b' and resid 284 through 287 Processing helix chain 'b' and resid 288 through 293 Processing helix chain 'c' and resid 34 through 38 Processing helix chain 'c' and resid 116 through 124 Processing helix chain 'c' and resid 127 through 146 Proline residue: c 134 - end of helix removed outlier: 4.507A pdb=" N ASN c 138 " --> pdb=" O PRO c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 149 through 156 Processing helix chain 'c' and resid 156 through 174 removed outlier: 4.149A pdb=" N ASP c 174 " --> pdb=" O GLU c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 245 removed outlier: 3.833A pdb=" N GLN c 211 " --> pdb=" O ALA c 207 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE c 212 " --> pdb=" O GLN c 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU c 213 " --> pdb=" O ARG c 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU c 215 " --> pdb=" O GLN c 211 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN c 219 " --> pdb=" O GLU c 215 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET c 237 " --> pdb=" O GLU c 233 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS c 244 " --> pdb=" O GLU c 240 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN c 245 " --> pdb=" O ALA c 241 " (cutoff:3.500A) Processing helix chain 'c' and resid 246 through 266 removed outlier: 3.690A pdb=" N LYS c 250 " --> pdb=" O PRO c 246 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR c 266 " --> pdb=" O LYS c 262 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 279 Processing helix chain 'c' and resid 284 through 287 Processing helix chain 'c' and resid 288 through 293 Processing helix chain 'd' and resid 34 through 38 Processing helix chain 'd' and resid 116 through 124 Processing helix chain 'd' and resid 127 through 146 Proline residue: d 134 - end of helix removed outlier: 4.498A pdb=" N ASN d 138 " --> pdb=" O PRO d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 156 Processing helix chain 'd' and resid 156 through 174 removed outlier: 4.067A pdb=" N ASP d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 243 removed outlier: 3.840A pdb=" N GLN d 211 " --> pdb=" O ALA d 207 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE d 212 " --> pdb=" O GLN d 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU d 213 " --> pdb=" O ARG d 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL d 214 " --> pdb=" O ALA d 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU d 215 " --> pdb=" O GLN d 211 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN d 219 " --> pdb=" O GLU d 215 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET d 237 " --> pdb=" O GLU d 233 " (cutoff:3.500A) Processing helix chain 'd' and resid 246 through 266 removed outlier: 3.805A pdb=" N LYS d 250 " --> pdb=" O PRO d 246 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR d 266 " --> pdb=" O LYS d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 276 through 279 Processing helix chain 'd' and resid 284 through 287 Processing helix chain 'd' and resid 288 through 293 Processing helix chain 'e' and resid 34 through 39 Processing helix chain 'e' and resid 116 through 124 Processing helix chain 'e' and resid 127 through 146 Proline residue: e 134 - end of helix removed outlier: 4.561A pdb=" N ASN e 138 " --> pdb=" O PRO e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 156 Processing helix chain 'e' and resid 156 through 174 removed outlier: 4.055A pdb=" N ASP e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 245 removed outlier: 3.834A pdb=" N GLN e 211 " --> pdb=" O ALA e 207 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE e 212 " --> pdb=" O GLN e 208 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU e 213 " --> pdb=" O ARG e 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL e 214 " --> pdb=" O ALA e 210 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU e 215 " --> pdb=" O GLN e 211 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN e 219 " --> pdb=" O GLU e 215 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET e 237 " --> pdb=" O GLU e 233 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS e 244 " --> pdb=" O GLU e 240 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN e 245 " --> pdb=" O ALA e 241 " (cutoff:3.500A) Processing helix chain 'e' and resid 246 through 266 removed outlier: 3.738A pdb=" N LYS e 250 " --> pdb=" O PRO e 246 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR e 266 " --> pdb=" O LYS e 262 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 279 Processing helix chain 'e' and resid 284 through 287 Processing helix chain 'e' and resid 288 through 293 Processing helix chain 'f' and resid 34 through 39 Processing helix chain 'f' and resid 116 through 124 Processing helix chain 'f' and resid 127 through 146 Proline residue: f 134 - end of helix removed outlier: 4.493A pdb=" N ASN f 138 " --> pdb=" O PRO f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 149 through 156 Processing helix chain 'f' and resid 156 through 174 removed outlier: 4.169A pdb=" N ASP f 174 " --> pdb=" O GLU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 190 through 245 removed outlier: 3.832A pdb=" N GLN f 211 " --> pdb=" O ALA f 207 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE f 212 " --> pdb=" O GLN f 208 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU f 213 " --> pdb=" O ARG f 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL f 214 " --> pdb=" O ALA f 210 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU f 215 " --> pdb=" O GLN f 211 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN f 219 " --> pdb=" O GLU f 215 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET f 237 " --> pdb=" O GLU f 233 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS f 244 " --> pdb=" O GLU f 240 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN f 245 " --> pdb=" O ALA f 241 " (cutoff:3.500A) Processing helix chain 'f' and resid 246 through 266 removed outlier: 3.816A pdb=" N LYS f 250 " --> pdb=" O PRO f 246 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR f 266 " --> pdb=" O LYS f 262 " (cutoff:3.500A) Processing helix chain 'f' and resid 276 through 279 Processing helix chain 'f' and resid 284 through 287 Processing helix chain 'f' and resid 288 through 293 Processing helix chain 'g' and resid 34 through 38 removed outlier: 3.520A pdb=" N GLU g 38 " --> pdb=" O TYR g 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 34 through 38' Processing helix chain 'g' and resid 116 through 124 Processing helix chain 'g' and resid 127 through 146 Proline residue: g 134 - end of helix removed outlier: 4.488A pdb=" N ASN g 138 " --> pdb=" O PRO g 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA g 146 " --> pdb=" O LYS g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 156 Processing helix chain 'g' and resid 156 through 174 removed outlier: 4.123A pdb=" N ASP g 174 " --> pdb=" O GLU g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 245 removed outlier: 3.842A pdb=" N GLN g 211 " --> pdb=" O ALA g 207 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE g 212 " --> pdb=" O GLN g 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU g 213 " --> pdb=" O ARG g 209 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL g 214 " --> pdb=" O ALA g 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU g 215 " --> pdb=" O GLN g 211 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN g 219 " --> pdb=" O GLU g 215 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET g 237 " --> pdb=" O GLU g 233 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS g 244 " --> pdb=" O GLU g 240 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'g' and resid 246 through 266 removed outlier: 3.706A pdb=" N LYS g 250 " --> pdb=" O PRO g 246 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR g 266 " --> pdb=" O LYS g 262 " (cutoff:3.500A) Processing helix chain 'g' and resid 276 through 279 Processing helix chain 'g' and resid 288 through 293 Processing helix chain 'h' and resid 34 through 39 Processing helix chain 'h' and resid 116 through 124 Processing helix chain 'h' and resid 127 through 146 Proline residue: h 134 - end of helix removed outlier: 4.544A pdb=" N ASN h 138 " --> pdb=" O PRO h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 149 through 156 Processing helix chain 'h' and resid 156 through 174 removed outlier: 4.151A pdb=" N ASP h 174 " --> pdb=" O GLU h 170 " (cutoff:3.500A) Processing helix chain 'h' and resid 190 through 243 removed outlier: 3.802A pdb=" N GLN h 211 " --> pdb=" O ALA h 207 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE h 212 " --> pdb=" O GLN h 208 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU h 213 " --> pdb=" O ARG h 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL h 214 " --> pdb=" O ALA h 210 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU h 215 " --> pdb=" O GLN h 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN h 219 " --> pdb=" O GLU h 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 246 through 266 removed outlier: 3.831A pdb=" N LYS h 250 " --> pdb=" O PRO h 246 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR h 266 " --> pdb=" O LYS h 262 " (cutoff:3.500A) Processing helix chain 'h' and resid 276 through 279 Processing helix chain 'h' and resid 284 through 287 Processing helix chain 'h' and resid 288 through 293 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 116 through 124 Processing helix chain 'i' and resid 127 through 146 Proline residue: i 134 - end of helix removed outlier: 4.505A pdb=" N ASN i 138 " --> pdb=" O PRO i 134 " (cutoff:3.500A) Processing helix chain 'i' and resid 149 through 156 Processing helix chain 'i' and resid 156 through 174 removed outlier: 4.169A pdb=" N ASP i 174 " --> pdb=" O GLU i 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 190 through 245 removed outlier: 3.846A pdb=" N GLN i 211 " --> pdb=" O ALA i 207 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE i 212 " --> pdb=" O GLN i 208 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU i 213 " --> pdb=" O ARG i 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL i 214 " --> pdb=" O ALA i 210 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU i 215 " --> pdb=" O GLN i 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN i 219 " --> pdb=" O GLU i 215 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET i 237 " --> pdb=" O GLU i 233 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU i 240 " --> pdb=" O LYS i 236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS i 244 " --> pdb=" O GLU i 240 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN i 245 " --> pdb=" O ALA i 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 246 through 266 removed outlier: 3.693A pdb=" N LYS i 250 " --> pdb=" O PRO i 246 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR i 266 " --> pdb=" O LYS i 262 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 279 Processing helix chain 'i' and resid 288 through 293 Processing helix chain 'j' and resid 35 through 39 Processing helix chain 'j' and resid 116 through 124 Processing helix chain 'j' and resid 127 through 146 Proline residue: j 134 - end of helix removed outlier: 4.486A pdb=" N ASN j 138 " --> pdb=" O PRO j 134 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 156 Processing helix chain 'j' and resid 156 through 174 removed outlier: 4.148A pdb=" N ASP j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 190 through 245 removed outlier: 3.822A pdb=" N GLN j 211 " --> pdb=" O ALA j 207 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE j 212 " --> pdb=" O GLN j 208 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU j 213 " --> pdb=" O ARG j 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL j 214 " --> pdb=" O ALA j 210 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU j 215 " --> pdb=" O GLN j 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN j 219 " --> pdb=" O GLU j 215 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET j 237 " --> pdb=" O GLU j 233 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS j 244 " --> pdb=" O GLU j 240 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN j 245 " --> pdb=" O ALA j 241 " (cutoff:3.500A) Processing helix chain 'j' and resid 246 through 266 removed outlier: 3.804A pdb=" N LYS j 250 " --> pdb=" O PRO j 246 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR j 266 " --> pdb=" O LYS j 262 " (cutoff:3.500A) Processing helix chain 'j' and resid 276 through 279 Processing helix chain 'j' and resid 284 through 287 Processing helix chain 'j' and resid 288 through 293 Processing helix chain 'k' and resid 34 through 39 Processing helix chain 'k' and resid 116 through 124 Processing helix chain 'k' and resid 127 through 146 Proline residue: k 134 - end of helix removed outlier: 4.424A pdb=" N ASN k 138 " --> pdb=" O PRO k 134 " (cutoff:3.500A) Processing helix chain 'k' and resid 149 through 156 Processing helix chain 'k' and resid 156 through 174 removed outlier: 4.110A pdb=" N ASP k 174 " --> pdb=" O GLU k 170 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 245 removed outlier: 3.818A pdb=" N GLN k 211 " --> pdb=" O ALA k 207 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE k 212 " --> pdb=" O GLN k 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU k 213 " --> pdb=" O ARG k 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL k 214 " --> pdb=" O ALA k 210 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU k 215 " --> pdb=" O GLN k 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN k 219 " --> pdb=" O GLU k 215 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET k 237 " --> pdb=" O GLU k 233 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS k 244 " --> pdb=" O GLU k 240 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN k 245 " --> pdb=" O ALA k 241 " (cutoff:3.500A) Processing helix chain 'k' and resid 246 through 266 removed outlier: 3.824A pdb=" N LYS k 250 " --> pdb=" O PRO k 246 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR k 266 " --> pdb=" O LYS k 262 " (cutoff:3.500A) Processing helix chain 'k' and resid 276 through 279 Processing helix chain 'k' and resid 284 through 287 Processing helix chain 'k' and resid 288 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 50 removed outlier: 5.198A pdb=" N ILE A 38 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 48 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 50 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N HIS A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 81 removed outlier: 7.370A pdb=" N ASN A 87 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR A 174 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN A 89 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS A 172 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 91 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 170 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG A 93 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 168 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 95 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.160A pdb=" N THR C 258 " --> pdb=" O LEU b 273 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR G 258 " --> pdb=" O LEU f 273 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR H 258 " --> pdb=" O LEU g 273 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR A 258 " --> pdb=" O LEU k 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 50 removed outlier: 5.098A pdb=" N ILE B 38 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 48 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL B 50 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N HIS B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 81 removed outlier: 7.345A pdb=" N ASN B 87 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B 174 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 89 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS B 172 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 91 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU B 170 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG B 93 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 168 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 95 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 50 removed outlier: 5.065A pdb=" N ILE C 38 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE C 48 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 50 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N HIS C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 81 removed outlier: 7.374A pdb=" N ASN C 87 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR C 174 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C 89 " --> pdb=" O HIS C 172 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 172 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 91 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 170 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG C 93 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 168 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 95 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 30 Processing sheet with id=AB3, first strand: chain 'D' and resid 44 through 50 removed outlier: 4.975A pdb=" N ILE D 38 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE D 48 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL D 50 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 72 through 81 removed outlier: 7.357A pdb=" N ASN D 87 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR D 174 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN D 89 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS D 172 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR D 91 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU D 170 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG D 93 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL D 168 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 95 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 50 removed outlier: 5.001A pdb=" N ILE E 38 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE E 48 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL E 50 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 72 through 81 removed outlier: 7.389A pdb=" N ASN E 87 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR E 174 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN E 89 " --> pdb=" O HIS E 172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS E 172 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR E 91 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU E 170 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG E 93 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL E 168 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU E 95 " --> pdb=" O ASP E 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'F' and resid 44 through 50 removed outlier: 5.023A pdb=" N ILE F 38 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE F 48 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL F 50 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N HIS F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 72 through 81 removed outlier: 7.339A pdb=" N ASN F 87 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR F 174 " --> pdb=" O ASN F 87 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN F 89 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS F 172 " --> pdb=" O ASN F 89 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 91 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU F 170 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG F 93 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL F 168 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU F 95 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'G' and resid 44 through 50 removed outlier: 5.070A pdb=" N ILE G 38 " --> pdb=" O GLN G 46 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE G 48 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL G 50 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HIS G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 72 through 81 removed outlier: 7.384A pdb=" N ASN G 87 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR G 174 " --> pdb=" O ASN G 87 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN G 89 " --> pdb=" O HIS G 172 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS G 172 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR G 91 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU G 170 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG G 93 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL G 168 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU G 95 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'H' and resid 44 through 50 removed outlier: 4.968A pdb=" N ILE H 38 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE H 48 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL H 50 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 72 through 81 removed outlier: 7.336A pdb=" N ASN H 87 " --> pdb=" O THR H 174 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR H 174 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN H 89 " --> pdb=" O HIS H 172 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS H 172 " --> pdb=" O ASN H 89 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR H 91 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU H 170 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG H 93 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL H 168 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU H 95 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 27 through 30 Processing sheet with id=AC9, first strand: chain 'I' and resid 44 through 50 removed outlier: 4.983A pdb=" N ILE I 38 " --> pdb=" O GLN I 46 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE I 48 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL I 50 " --> pdb=" O HIS I 34 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N HIS I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 72 through 81 removed outlier: 7.358A pdb=" N ASN I 87 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR I 174 " --> pdb=" O ASN I 87 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN I 89 " --> pdb=" O HIS I 172 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS I 172 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR I 91 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU I 170 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG I 93 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL I 168 " --> pdb=" O ARG I 93 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU I 95 " --> pdb=" O ASP I 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 27 through 30 Processing sheet with id=AD3, first strand: chain 'J' and resid 44 through 50 removed outlier: 5.050A pdb=" N ILE J 38 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE J 48 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL J 50 " --> pdb=" O HIS J 34 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N HIS J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 72 through 81 removed outlier: 7.360A pdb=" N ASN J 87 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR J 174 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN J 89 " --> pdb=" O HIS J 172 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS J 172 " --> pdb=" O ASN J 89 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR J 91 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU J 170 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG J 93 " --> pdb=" O VAL J 168 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL J 168 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU J 95 " --> pdb=" O ASP J 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 27 through 30 Processing sheet with id=AD6, first strand: chain 'K' and resid 44 through 50 removed outlier: 5.001A pdb=" N ILE K 38 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE K 48 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL K 50 " --> pdb=" O HIS K 34 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 72 through 81 removed outlier: 7.412A pdb=" N ASN K 87 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR K 174 " --> pdb=" O ASN K 87 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN K 89 " --> pdb=" O HIS K 172 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS K 172 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR K 91 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU K 170 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG K 93 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL K 168 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU K 95 " --> pdb=" O ASP K 166 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a' and resid 40 through 43 Processing sheet with id=AD9, first strand: chain 'a' and resid 57 through 64 removed outlier: 9.198A pdb=" N GLN a 60 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ASN a 53 " --> pdb=" O GLN a 60 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR a 62 " --> pdb=" O PHE a 51 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE a 51 " --> pdb=" O THR a 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 86 through 95 removed outlier: 7.274A pdb=" N MET a 101 " --> pdb=" O SER a 188 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER a 188 " --> pdb=" O MET a 101 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN a 103 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU a 186 " --> pdb=" O ASN a 103 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER a 105 " --> pdb=" O ILE a 184 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE a 184 " --> pdb=" O SER a 105 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG a 107 " --> pdb=" O VAL a 182 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL a 182 " --> pdb=" O ARG a 107 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU a 109 " --> pdb=" O ASP a 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 40 through 43 Processing sheet with id=AE3, first strand: chain 'b' and resid 57 through 64 removed outlier: 5.223A pdb=" N PHE b 51 " --> pdb=" O GLN b 59 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ASP b 61 " --> pdb=" O ALA b 49 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N ALA b 49 " --> pdb=" O ASP b 61 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N ILE b 63 " --> pdb=" O HIS b 47 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N HIS b 47 " --> pdb=" O ILE b 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 86 through 95 removed outlier: 7.347A pdb=" N MET b 101 " --> pdb=" O SER b 188 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER b 188 " --> pdb=" O MET b 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN b 103 " --> pdb=" O GLU b 186 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU b 186 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER b 105 " --> pdb=" O ILE b 184 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE b 184 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG b 107 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL b 182 " --> pdb=" O ARG b 107 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU b 109 " --> pdb=" O ASP b 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 40 through 43 Processing sheet with id=AE6, first strand: chain 'c' and resid 57 through 64 removed outlier: 5.349A pdb=" N PHE c 51 " --> pdb=" O GLN c 59 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASP c 61 " --> pdb=" O ALA c 49 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ALA c 49 " --> pdb=" O ASP c 61 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ILE c 63 " --> pdb=" O HIS c 47 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N HIS c 47 " --> pdb=" O ILE c 63 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 86 through 95 removed outlier: 7.215A pdb=" N MET c 101 " --> pdb=" O SER c 188 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER c 188 " --> pdb=" O MET c 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN c 103 " --> pdb=" O GLU c 186 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU c 186 " --> pdb=" O ASN c 103 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER c 105 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE c 184 " --> pdb=" O SER c 105 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG c 107 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL c 182 " --> pdb=" O ARG c 107 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU c 109 " --> pdb=" O ASP c 180 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 57 through 64 removed outlier: 5.282A pdb=" N PHE d 51 " --> pdb=" O GLN d 59 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ASP d 61 " --> pdb=" O ALA d 49 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N ALA d 49 " --> pdb=" O ASP d 61 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ILE d 63 " --> pdb=" O HIS d 47 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N HIS d 47 " --> pdb=" O ILE d 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 86 through 95 removed outlier: 7.244A pdb=" N MET d 101 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER d 188 " --> pdb=" O MET d 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN d 103 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU d 186 " --> pdb=" O ASN d 103 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER d 105 " --> pdb=" O ILE d 184 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE d 184 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG d 107 " --> pdb=" O VAL d 182 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL d 182 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU d 109 " --> pdb=" O ASP d 180 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 57 through 64 removed outlier: 5.250A pdb=" N PHE e 51 " --> pdb=" O GLN e 59 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ASP e 61 " --> pdb=" O ALA e 49 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N ALA e 49 " --> pdb=" O ASP e 61 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N ILE e 63 " --> pdb=" O HIS e 47 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N HIS e 47 " --> pdb=" O ILE e 63 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'e' and resid 86 through 95 removed outlier: 7.212A pdb=" N MET e 101 " --> pdb=" O SER e 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER e 188 " --> pdb=" O MET e 101 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN e 103 " --> pdb=" O GLU e 186 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU e 186 " --> pdb=" O ASN e 103 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER e 105 " --> pdb=" O ILE e 184 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE e 184 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG e 107 " --> pdb=" O VAL e 182 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL e 182 " --> pdb=" O ARG e 107 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU e 109 " --> pdb=" O ASP e 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 40 through 43 Processing sheet with id=AF4, first strand: chain 'f' and resid 57 through 64 removed outlier: 5.409A pdb=" N PHE f 51 " --> pdb=" O GLN f 59 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ASP f 61 " --> pdb=" O ALA f 49 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N ALA f 49 " --> pdb=" O ASP f 61 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE f 63 " --> pdb=" O HIS f 47 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N HIS f 47 " --> pdb=" O ILE f 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 86 through 95 removed outlier: 7.244A pdb=" N MET f 101 " --> pdb=" O SER f 188 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER f 188 " --> pdb=" O MET f 101 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN f 103 " --> pdb=" O GLU f 186 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU f 186 " --> pdb=" O ASN f 103 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER f 105 " --> pdb=" O ILE f 184 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE f 184 " --> pdb=" O SER f 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG f 107 " --> pdb=" O VAL f 182 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL f 182 " --> pdb=" O ARG f 107 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU f 109 " --> pdb=" O ASP f 180 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 57 through 64 removed outlier: 5.239A pdb=" N PHE g 51 " --> pdb=" O GLN g 59 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASP g 61 " --> pdb=" O ALA g 49 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ALA g 49 " --> pdb=" O ASP g 61 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ILE g 63 " --> pdb=" O HIS g 47 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N HIS g 47 " --> pdb=" O ILE g 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 86 through 95 removed outlier: 7.223A pdb=" N MET g 101 " --> pdb=" O SER g 188 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER g 188 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN g 103 " --> pdb=" O GLU g 186 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU g 186 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER g 105 " --> pdb=" O ILE g 184 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE g 184 " --> pdb=" O SER g 105 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG g 107 " --> pdb=" O VAL g 182 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL g 182 " --> pdb=" O ARG g 107 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU g 109 " --> pdb=" O ASP g 180 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 40 through 43 Processing sheet with id=AF9, first strand: chain 'h' and resid 57 through 58 Processing sheet with id=AG1, first strand: chain 'h' and resid 86 through 95 removed outlier: 7.246A pdb=" N MET h 101 " --> pdb=" O SER h 188 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER h 188 " --> pdb=" O MET h 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN h 103 " --> pdb=" O GLU h 186 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU h 186 " --> pdb=" O ASN h 103 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER h 105 " --> pdb=" O ILE h 184 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE h 184 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG h 107 " --> pdb=" O VAL h 182 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL h 182 " --> pdb=" O ARG h 107 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU h 109 " --> pdb=" O ASP h 180 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'i' and resid 40 through 43 Processing sheet with id=AG3, first strand: chain 'i' and resid 57 through 64 removed outlier: 5.282A pdb=" N PHE i 51 " --> pdb=" O GLN i 59 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N ASP i 61 " --> pdb=" O ALA i 49 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N ALA i 49 " --> pdb=" O ASP i 61 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ILE i 63 " --> pdb=" O HIS i 47 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N HIS i 47 " --> pdb=" O ILE i 63 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 86 through 95 removed outlier: 7.223A pdb=" N MET i 101 " --> pdb=" O SER i 188 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER i 188 " --> pdb=" O MET i 101 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN i 103 " --> pdb=" O GLU i 186 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU i 186 " --> pdb=" O ASN i 103 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER i 105 " --> pdb=" O ILE i 184 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE i 184 " --> pdb=" O SER i 105 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG i 107 " --> pdb=" O VAL i 182 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL i 182 " --> pdb=" O ARG i 107 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU i 109 " --> pdb=" O ASP i 180 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 40 through 43 Processing sheet with id=AG6, first strand: chain 'j' and resid 57 through 64 removed outlier: 9.189A pdb=" N GLN j 60 " --> pdb=" O ASN j 53 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N ASN j 53 " --> pdb=" O GLN j 60 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR j 62 " --> pdb=" O PHE j 51 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE j 51 " --> pdb=" O THR j 62 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'j' and resid 86 through 95 removed outlier: 7.220A pdb=" N MET j 101 " --> pdb=" O SER j 188 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER j 188 " --> pdb=" O MET j 101 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN j 103 " --> pdb=" O GLU j 186 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU j 186 " --> pdb=" O ASN j 103 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER j 105 " --> pdb=" O ILE j 184 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE j 184 " --> pdb=" O SER j 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG j 107 " --> pdb=" O VAL j 182 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL j 182 " --> pdb=" O ARG j 107 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU j 109 " --> pdb=" O ASP j 180 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 40 through 43 Processing sheet with id=AG9, first strand: chain 'k' and resid 57 through 58 Processing sheet with id=AH1, first strand: chain 'k' and resid 86 through 95 removed outlier: 7.312A pdb=" N MET k 101 " --> pdb=" O SER k 188 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER k 188 " --> pdb=" O MET k 101 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN k 103 " --> pdb=" O GLU k 186 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU k 186 " --> pdb=" O ASN k 103 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER k 105 " --> pdb=" O ILE k 184 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE k 184 " --> pdb=" O SER k 105 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG k 107 " --> pdb=" O VAL k 182 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL k 182 " --> pdb=" O ARG k 107 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU k 109 " --> pdb=" O ASP k 180 " (cutoff:3.500A) 2785 hydrogen bonds defined for protein. 8079 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: 9.77 Time building geometry restraints manager: 5.06 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: 15036 1.34 - 1.46: 7771 1.46 - 1.58: 21468 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 44352 Sorted by residual: bond pdb=" CG1 ILE j 271 " pdb=" CD1 ILE j 271 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CA ILE k 184 " pdb=" CB ILE k 184 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.99e-01 bond pdb=" CA ILE d 184 " pdb=" CB ILE d 184 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.65e-01 bond pdb=" CA ILE h 184 " pdb=" CB ILE h 184 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.64e-01 bond pdb=" CA ILE a 184 " pdb=" CB ILE a 184 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.46e-01 ... (remaining 44347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 55708 0.83 - 1.67: 3511 1.67 - 2.50: 461 2.50 - 3.34: 199 3.34 - 4.17: 60 Bond angle restraints: 59939 Sorted by residual: angle pdb=" N SER c 92 " pdb=" CA SER c 92 " pdb=" C SER c 92 " ideal model delta sigma weight residual 108.11 111.67 -3.56 1.29e+00 6.01e-01 7.63e+00 angle pdb=" CB GLN J 102 " pdb=" CG GLN J 102 " pdb=" CD GLN J 102 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.70e+00 3.46e-01 6.02e+00 angle pdb=" N ILE H 110 " pdb=" CA ILE H 110 " pdb=" C ILE H 110 " ideal model delta sigma weight residual 111.48 109.30 2.18 9.40e-01 1.13e+00 5.40e+00 angle pdb=" N SER j 92 " pdb=" CA SER j 92 " pdb=" C SER j 92 " ideal model delta sigma weight residual 108.11 110.76 -2.65 1.29e+00 6.01e-01 4.23e+00 angle pdb=" N SER h 92 " pdb=" CA SER h 92 " pdb=" C SER h 92 " ideal model delta sigma weight residual 108.11 110.76 -2.65 1.29e+00 6.01e-01 4.22e+00 ... (remaining 59934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 23994 17.96 - 35.92: 2484 35.92 - 53.87: 637 53.87 - 71.83: 202 71.83 - 89.79: 51 Dihedral angle restraints: 27368 sinusoidal: 11176 harmonic: 16192 Sorted by residual: dihedral pdb=" CA LEU d 68 " pdb=" C LEU d 68 " pdb=" N HIS d 69 " pdb=" CA HIS d 69 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE a 51 " pdb=" C PHE a 51 " pdb=" N PHE a 52 " pdb=" CA PHE a 52 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ILE d 72 " pdb=" C ILE d 72 " pdb=" N PRO d 73 " pdb=" CA PRO d 73 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 27365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4208 0.029 - 0.059: 1817 0.059 - 0.088: 558 0.088 - 0.117: 209 0.117 - 0.146: 160 Chirality restraints: 6952 Sorted by residual: chirality pdb=" CA VAL K 88 " pdb=" N VAL K 88 " pdb=" C VAL K 88 " pdb=" CB VAL K 88 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE F 65 " pdb=" N ILE F 65 " pdb=" C ILE F 65 " pdb=" CB ILE F 65 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE K 58 " pdb=" N ILE K 58 " pdb=" C ILE K 58 " pdb=" CB ILE K 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 6949 not shown) Planarity restraints: 7843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 102 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" CD GLN J 102 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN J 102 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN J 102 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER h 92 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO h 93 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO h 93 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO h 93 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER j 92 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO j 93 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO j 93 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO j 93 " 0.023 5.00e-02 4.00e+02 ... (remaining 7840 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 231 2.52 - 3.11: 32892 3.11 - 3.71: 69565 3.71 - 4.30: 103062 4.30 - 4.90: 173934 Nonbonded interactions: 379684 Sorted by model distance: nonbonded pdb=" OG SER H 71 " pdb=" OD2 ASP H 166 " model vdw 1.922 3.040 nonbonded pdb=" OG SER G 71 " pdb=" OD2 ASP G 166 " model vdw 1.925 3.040 nonbonded pdb=" OG SER I 71 " pdb=" OD2 ASP I 166 " model vdw 1.930 3.040 nonbonded pdb=" OG SER D 71 " pdb=" OD2 ASP D 166 " model vdw 1.936 3.040 nonbonded pdb=" OG SER C 71 " pdb=" OD2 ASP C 166 " model vdw 1.940 3.040 ... (remaining 379679 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' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 40.330 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44352 Z= 0.188 Angle : 0.482 4.171 59939 Z= 0.269 Chirality : 0.041 0.146 6952 Planarity : 0.005 0.064 7843 Dihedral : 16.585 89.788 16830 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.96 % Allowed : 15.90 % Favored : 83.14 % 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: 0.79 (0.11), residues: 5500 helix: 1.15 (0.09), residues: 2662 sheet: -0.03 (0.17), residues: 902 loop : 0.11 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 255 TYR 0.015 0.001 TYR E 249 PHE 0.007 0.001 PHE F 56 TRP 0.005 0.001 TRP A 60 HIS 0.003 0.001 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00409 (44352) covalent geometry : angle 0.48233 (59939) hydrogen bonds : bond 0.10947 ( 2785) hydrogen bonds : angle 5.94090 ( 8079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 530 time to evaluate : 1.693 Fit side-chains REVERT: A 144 GLU cc_start: 0.7492 (mp0) cc_final: 0.7197 (mp0) REVERT: C 31 ASP cc_start: 0.8026 (m-30) cc_final: 0.7537 (t0) REVERT: C 148 ARG cc_start: 0.8187 (tpp-160) cc_final: 0.7710 (ttp-110) REVERT: D 46 GLN cc_start: 0.8395 (mm110) cc_final: 0.7830 (mm-40) REVERT: D 148 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7702 (ttp-110) REVERT: D 255 ARG cc_start: 0.8349 (mtt-85) cc_final: 0.7979 (mtt90) REVERT: E 31 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7603 (t0) REVERT: E 46 GLN cc_start: 0.8374 (mm110) cc_final: 0.8040 (mm110) REVERT: F 31 ASP cc_start: 0.8049 (m-30) cc_final: 0.7713 (t0) REVERT: F 46 GLN cc_start: 0.8335 (mm110) cc_final: 0.7712 (mm-40) REVERT: F 255 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8065 (mtt90) REVERT: G 31 ASP cc_start: 0.7972 (m-30) cc_final: 0.7554 (t0) REVERT: H 46 GLN cc_start: 0.8280 (mm110) cc_final: 0.7712 (mm-40) REVERT: H 102 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8063 (mm-40) REVERT: H 148 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7654 (ttp-110) REVERT: I 31 ASP cc_start: 0.8047 (m-30) cc_final: 0.7573 (t0) REVERT: I 43 ARG cc_start: 0.7709 (mpp80) cc_final: 0.7508 (mpp80) REVERT: I 46 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7985 (mm-40) REVERT: I 255 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8040 (mtt90) REVERT: J 31 ASP cc_start: 0.8021 (m-30) cc_final: 0.7548 (t0) REVERT: J 102 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8240 (mm-40) REVERT: J 125 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: J 144 GLU cc_start: 0.7624 (mp0) cc_final: 0.7349 (mp0) REVERT: J 148 ARG cc_start: 0.8070 (tpt170) cc_final: 0.7618 (ttp-110) REVERT: K 31 ASP cc_start: 0.8019 (m-30) cc_final: 0.7541 (t0) REVERT: K 43 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7204 (mmm-85) REVERT: K 46 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7795 (mm-40) REVERT: K 148 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7729 (ttp-110) REVERT: K 255 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8071 (mtt90) REVERT: b 34 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4541 (t80) REVERT: b 60 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: c 166 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7055 (ttm110) REVERT: d 270 ARG cc_start: 0.8593 (mmm160) cc_final: 0.8106 (mmm-85) REVERT: e 38 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7037 (tt0) REVERT: e 60 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: e 181 ASP cc_start: 0.8824 (t70) cc_final: 0.8469 (t70) REVERT: g 60 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7662 (mp-120) REVERT: h 115 GLN cc_start: 0.8523 (mt0) cc_final: 0.8256 (mm110) REVERT: i 115 GLN cc_start: 0.8498 (mt0) cc_final: 0.8208 (mm110) REVERT: j 143 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (m) REVERT: j 285 GLU cc_start: 0.8137 (tp30) cc_final: 0.7796 (tp30) REVERT: k 284 ASP cc_start: 0.8605 (t0) cc_final: 0.8342 (t0) outliers start: 45 outliers final: 35 residues processed: 564 average time/residue: 1.1238 time to fit residues: 733.3508 Evaluate side-chains 560 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 518 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 227 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 69 CYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 69 CYS Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 213 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 119 SER Chi-restraints excluded: chain k residue 129 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.3980 chunk 223 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN G 102 GLN H 89 ASN k 59 GLN k 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091052 restraints weight = 56980.855| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.49 r_work: 0.2949 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 44352 Z= 0.174 Angle : 0.514 7.530 59939 Z= 0.279 Chirality : 0.043 0.212 6952 Planarity : 0.005 0.046 7843 Dihedral : 5.690 76.444 6170 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.68 % Allowed : 14.65 % Favored : 82.67 % 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: 1.05 (0.11), residues: 5500 helix: 1.49 (0.09), residues: 2728 sheet: 0.18 (0.17), residues: 847 loop : -0.09 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.015 0.001 TYR H 249 PHE 0.006 0.001 PHE D 56 TRP 0.006 0.001 TRP A 60 HIS 0.003 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00385 (44352) covalent geometry : angle 0.51377 (59939) hydrogen bonds : bond 0.05952 ( 2785) hydrogen bonds : angle 4.97240 ( 8079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 578 time to evaluate : 1.912 Fit side-chains REVERT: A 48 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8015 (mp) REVERT: A 125 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: A 144 GLU cc_start: 0.7556 (mp0) cc_final: 0.7212 (mp0) REVERT: C 31 ASP cc_start: 0.7876 (m-30) cc_final: 0.7384 (t0) REVERT: C 102 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8211 (mm-40) REVERT: C 148 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7514 (ttp-110) REVERT: C 253 ARG cc_start: 0.8557 (mpp-170) cc_final: 0.8127 (mpp-170) REVERT: D 46 GLN cc_start: 0.8357 (mm110) cc_final: 0.7729 (mm-40) REVERT: D 148 ARG cc_start: 0.8130 (tpt170) cc_final: 0.7505 (ttp-110) REVERT: D 253 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7996 (mtp-110) REVERT: D 255 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.8012 (mtt90) REVERT: E 31 ASP cc_start: 0.7836 (m-30) cc_final: 0.7390 (t0) REVERT: E 46 GLN cc_start: 0.8366 (mm110) cc_final: 0.7916 (mm-40) REVERT: F 31 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (t0) REVERT: F 46 GLN cc_start: 0.8348 (mm110) cc_final: 0.7683 (mm-40) REVERT: F 125 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: F 255 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8058 (mtt90) REVERT: G 31 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7473 (t0) REVERT: G 48 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8104 (mp) REVERT: G 125 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: G 213 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8711 (t) REVERT: H 46 GLN cc_start: 0.8243 (mm110) cc_final: 0.7642 (mm-40) REVERT: H 148 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7479 (ttp-110) REVERT: H 215 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: I 31 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7447 (t0) REVERT: I 46 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7922 (mm-40) REVERT: I 102 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8158 (mm110) REVERT: I 165 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8036 (mp) REVERT: I 213 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (t) REVERT: I 215 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: J 31 ASP cc_start: 0.7911 (m-30) cc_final: 0.7381 (t0) REVERT: J 125 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: J 144 GLU cc_start: 0.7646 (mp0) cc_final: 0.7300 (mp0) REVERT: J 148 ARG cc_start: 0.8011 (tpt170) cc_final: 0.7448 (ttp-110) REVERT: K 31 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7377 (t0) REVERT: K 43 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7042 (mmm-85) REVERT: K 46 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7769 (mm-40) REVERT: K 125 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: K 148 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7591 (ttp-110) REVERT: K 215 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: K 253 ARG cc_start: 0.8564 (mpp-170) cc_final: 0.8132 (mpp-170) REVERT: a 216 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8428 (tttm) REVERT: b 60 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: b 101 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8119 (tmm) REVERT: b 139 GLU cc_start: 0.8582 (tt0) cc_final: 0.8381 (tt0) REVERT: c 101 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8256 (tmm) REVERT: c 166 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7061 (ttm110) REVERT: c 216 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8383 (tttm) REVERT: d 60 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: d 139 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: e 38 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: e 60 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: e 181 ASP cc_start: 0.8829 (t70) cc_final: 0.8445 (t70) REVERT: f 181 ASP cc_start: 0.8798 (t70) cc_final: 0.8559 (t70) REVERT: f 216 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8458 (tttm) REVERT: g 60 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7586 (mp-120) REVERT: g 291 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8451 (m) REVERT: h 36 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7306 (p) REVERT: h 115 GLN cc_start: 0.8573 (mt0) cc_final: 0.8226 (mm110) REVERT: h 213 LEU cc_start: 0.8687 (mp) cc_final: 0.8469 (mm) REVERT: i 60 GLN cc_start: 0.7950 (mm110) cc_final: 0.7654 (mm110) REVERT: i 143 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8270 (m) REVERT: j 70 PHE cc_start: 0.7202 (m-80) cc_final: 0.6473 (t80) REVERT: j 159 GLN cc_start: 0.8474 (mp10) cc_final: 0.8183 (mp10) REVERT: j 166 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7297 (ttm110) REVERT: j 291 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8476 (m) REVERT: k 143 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8340 (m) REVERT: k 159 GLN cc_start: 0.8346 (mp10) cc_final: 0.7985 (mp10) outliers start: 126 outliers final: 58 residues processed: 662 average time/residue: 1.0576 time to fit residues: 819.0131 Evaluate side-chains 638 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 546 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 101 MET Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 139 GLU Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 161 SER Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 291 SER Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 435 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 492 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN J 102 GLN b 259 ASN c 259 ASN d 259 ASN f 259 ASN h 259 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090575 restraints weight = 57208.709| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.50 r_work: 0.2959 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44352 Z= 0.147 Angle : 0.478 7.010 59939 Z= 0.259 Chirality : 0.042 0.185 6952 Planarity : 0.004 0.046 7843 Dihedral : 5.228 73.830 6147 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 15.09 % Favored : 82.18 % 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: 1.26 (0.11), residues: 5500 helix: 1.66 (0.09), residues: 2728 sheet: 0.30 (0.17), residues: 825 loop : 0.02 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 255 TYR 0.013 0.001 TYR H 249 PHE 0.006 0.001 PHE D 56 TRP 0.004 0.001 TRP J 60 HIS 0.002 0.000 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00313 (44352) covalent geometry : angle 0.47753 (59939) hydrogen bonds : bond 0.05568 ( 2785) hydrogen bonds : angle 4.79151 ( 8079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 604 time to evaluate : 1.858 Fit side-chains REVERT: A 48 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 144 GLU cc_start: 0.7542 (mp0) cc_final: 0.7184 (mp0) REVERT: A 213 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8599 (t) REVERT: A 215 GLU cc_start: 0.8445 (tt0) cc_final: 0.8134 (tp30) REVERT: B 47 ASP cc_start: 0.8027 (m-30) cc_final: 0.7502 (t70) REVERT: B 215 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: C 31 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7360 (t0) REVERT: C 102 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 148 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7469 (ttp-110) REVERT: C 213 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8636 (t) REVERT: C 253 ARG cc_start: 0.8510 (mpp-170) cc_final: 0.8023 (mpp-170) REVERT: D 46 GLN cc_start: 0.8333 (mm110) cc_final: 0.7638 (mm-40) REVERT: D 148 ARG cc_start: 0.8066 (tpt170) cc_final: 0.7448 (ttp-110) REVERT: D 255 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.7997 (mtt90) REVERT: E 31 ASP cc_start: 0.7817 (m-30) cc_final: 0.7406 (t0) REVERT: E 46 GLN cc_start: 0.8360 (mm110) cc_final: 0.7931 (mm110) REVERT: F 31 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7513 (t0) REVERT: F 46 GLN cc_start: 0.8429 (mm110) cc_final: 0.7737 (mm-40) REVERT: F 125 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: F 255 ARG cc_start: 0.8463 (mtt-85) cc_final: 0.8030 (mtt90) REVERT: G 31 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7473 (t0) REVERT: G 125 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: G 213 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8653 (t) REVERT: H 46 GLN cc_start: 0.8280 (mm110) cc_final: 0.7646 (mm-40) REVERT: H 148 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7457 (ttp-110) REVERT: I 31 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7422 (t0) REVERT: I 46 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7978 (mm-40) REVERT: I 102 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8130 (mm110) REVERT: I 165 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8058 (mp) REVERT: I 213 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8557 (t) REVERT: I 215 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: J 31 ASP cc_start: 0.7881 (m-30) cc_final: 0.7359 (t0) REVERT: J 125 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: J 144 GLU cc_start: 0.7694 (mp0) cc_final: 0.7311 (mp0) REVERT: J 148 ARG cc_start: 0.7969 (tpt170) cc_final: 0.7385 (ttp-110) REVERT: K 31 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7362 (t0) REVERT: K 43 ARG cc_start: 0.7727 (mtm180) cc_final: 0.6935 (mmm-85) REVERT: K 46 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7721 (mm-40) REVERT: K 125 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: K 148 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7543 (ttp-110) REVERT: a 181 ASP cc_start: 0.8853 (t70) cc_final: 0.8317 (t70) REVERT: a 213 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8453 (mm) REVERT: a 216 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: b 120 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: b 270 ARG cc_start: 0.8469 (mmm160) cc_final: 0.7932 (mmm-85) REVERT: c 161 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8744 (t) REVERT: c 166 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.7079 (ttm110) REVERT: c 216 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8336 (tttm) REVERT: d 60 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: d 101 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8258 (tmm) REVERT: d 139 GLU cc_start: 0.8402 (tt0) cc_final: 0.8118 (tt0) REVERT: d 163 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8168 (mp) REVERT: e 38 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: e 139 GLU cc_start: 0.8525 (tt0) cc_final: 0.8304 (tt0) REVERT: e 166 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7196 (mtm110) REVERT: e 181 ASP cc_start: 0.8787 (t70) cc_final: 0.8404 (t70) REVERT: f 115 GLN cc_start: 0.8565 (mt0) cc_final: 0.8150 (mm110) REVERT: f 181 ASP cc_start: 0.8805 (t70) cc_final: 0.8572 (t70) REVERT: f 216 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8397 (tttm) REVERT: g 291 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8409 (m) REVERT: h 38 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7135 (mt-10) REVERT: h 139 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: i 120 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8342 (ttp) REVERT: i 143 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8224 (m) REVERT: j 70 PHE cc_start: 0.7182 (m-80) cc_final: 0.6449 (t80) REVERT: j 159 GLN cc_start: 0.8424 (mp10) cc_final: 0.8115 (mp10) REVERT: k 143 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8287 (m) REVERT: k 159 GLN cc_start: 0.8334 (mp10) cc_final: 0.7960 (mp10) outliers start: 128 outliers final: 58 residues processed: 684 average time/residue: 1.0314 time to fit residues: 824.6973 Evaluate side-chains 662 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 572 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 213 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 237 MET Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 120 MET Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 161 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 239 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 508 optimal weight: 0.9980 chunk 479 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 333 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 392 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 89 ASN G 89 ASN G 102 GLN H 89 ASN d 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089913 restraints weight = 57128.635| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.48 r_work: 0.2945 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 44352 Z= 0.167 Angle : 0.495 10.723 59939 Z= 0.267 Chirality : 0.042 0.202 6952 Planarity : 0.004 0.048 7843 Dihedral : 4.897 73.295 6136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.17 % Allowed : 14.92 % Favored : 81.90 % 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: 1.18 (0.11), residues: 5500 helix: 1.61 (0.09), residues: 2728 sheet: 0.27 (0.17), residues: 825 loop : -0.05 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 105 TYR 0.014 0.001 TYR J 249 PHE 0.006 0.001 PHE F 56 TRP 0.004 0.001 TRP J 60 HIS 0.002 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00368 (44352) covalent geometry : angle 0.49483 (59939) hydrogen bonds : bond 0.05785 ( 2785) hydrogen bonds : angle 4.80370 ( 8079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 579 time to evaluate : 1.868 Fit side-chains REVERT: A 48 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8032 (mp) REVERT: A 144 GLU cc_start: 0.7558 (mp0) cc_final: 0.7197 (mp0) REVERT: A 213 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 215 GLU cc_start: 0.8442 (tt0) cc_final: 0.8125 (tp30) REVERT: B 47 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7525 (t70) REVERT: B 215 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: C 31 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7370 (t0) REVERT: C 102 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8191 (mm-40) REVERT: C 148 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7503 (ttp-110) REVERT: C 213 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8652 (t) REVERT: C 253 ARG cc_start: 0.8514 (mpp-170) cc_final: 0.8026 (mpp-170) REVERT: D 46 GLN cc_start: 0.8351 (mm110) cc_final: 0.7645 (mm-40) REVERT: D 148 ARG cc_start: 0.8080 (tpt170) cc_final: 0.7466 (ttp-110) REVERT: D 255 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8013 (mtt90) REVERT: E 31 ASP cc_start: 0.7822 (m-30) cc_final: 0.7407 (t0) REVERT: E 46 GLN cc_start: 0.8380 (mm110) cc_final: 0.7958 (mm110) REVERT: E 213 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8656 (t) REVERT: F 31 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (t0) REVERT: F 46 GLN cc_start: 0.8473 (mm110) cc_final: 0.7753 (mm-40) REVERT: F 125 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: F 255 ARG cc_start: 0.8491 (mtt-85) cc_final: 0.8051 (mtt90) REVERT: G 31 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7456 (t0) REVERT: G 125 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: G 213 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8663 (t) REVERT: H 46 GLN cc_start: 0.8310 (mm110) cc_final: 0.7683 (mm-40) REVERT: H 148 ARG cc_start: 0.8124 (tpt170) cc_final: 0.7471 (ttp-110) REVERT: H 215 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: I 31 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7409 (t0) REVERT: I 43 ARG cc_start: 0.7648 (mpp80) cc_final: 0.7435 (mpp80) REVERT: I 46 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7988 (mm-40) REVERT: I 102 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8134 (mm110) REVERT: I 165 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8116 (mp) REVERT: I 213 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8582 (t) REVERT: I 215 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: J 31 ASP cc_start: 0.7896 (m-30) cc_final: 0.7368 (t0) REVERT: J 125 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: J 144 GLU cc_start: 0.7677 (mp0) cc_final: 0.7306 (mp0) REVERT: J 148 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7386 (ttp-110) REVERT: K 31 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7360 (t0) REVERT: K 43 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7043 (mmm-85) REVERT: K 46 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7810 (mm-40) REVERT: K 125 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: K 148 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.7553 (ttp-110) REVERT: K 213 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8558 (t) REVERT: K 253 ARG cc_start: 0.8546 (mpp-170) cc_final: 0.8076 (mpp-170) REVERT: a 163 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8232 (mp) REVERT: a 181 ASP cc_start: 0.8868 (t70) cc_final: 0.8298 (t70) REVERT: a 213 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (mm) REVERT: a 216 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8389 (tttm) REVERT: b 270 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7932 (mmm-85) REVERT: c 120 MET cc_start: 0.8404 (ttt) cc_final: 0.8075 (ttp) REVERT: c 166 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7086 (ttm110) REVERT: c 216 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8329 (tttm) REVERT: c 270 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8147 (tpt90) REVERT: d 60 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: d 101 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8243 (tmm) REVERT: d 163 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8192 (mp) REVERT: e 38 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7219 (tt0) REVERT: e 139 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: e 181 ASP cc_start: 0.8753 (t70) cc_final: 0.8377 (t70) REVERT: f 115 GLN cc_start: 0.8575 (mt0) cc_final: 0.8152 (mm110) REVERT: f 181 ASP cc_start: 0.8801 (t70) cc_final: 0.8554 (t70) REVERT: f 216 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8411 (tttm) REVERT: g 291 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8431 (m) REVERT: h 38 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7143 (mt-10) REVERT: h 139 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: h 270 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8044 (tpt90) REVERT: i 143 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8244 (m) REVERT: i 213 LEU cc_start: 0.8700 (mp) cc_final: 0.8465 (mm) REVERT: i 270 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7977 (mmm160) REVERT: j 70 PHE cc_start: 0.7159 (m-80) cc_final: 0.6410 (t80) REVERT: j 159 GLN cc_start: 0.8397 (mp10) cc_final: 0.8093 (mp10) REVERT: k 115 GLN cc_start: 0.8435 (mt0) cc_final: 0.8058 (mm110) REVERT: k 143 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8306 (m) outliers start: 149 outliers final: 77 residues processed: 677 average time/residue: 1.0110 time to fit residues: 800.8976 Evaluate side-chains 678 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 563 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 213 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain c residue 270 ARG Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 101 MET Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 237 MET Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 130 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 416 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN a 60 GLN a 122 GLN c 159 GLN c 259 ASN d 159 GLN h 259 ASN k 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087422 restraints weight = 57341.833| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.49 r_work: 0.2911 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 44352 Z= 0.252 Angle : 0.554 10.830 59939 Z= 0.298 Chirality : 0.046 0.234 6952 Planarity : 0.005 0.051 7843 Dihedral : 5.114 72.161 6136 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.79 % Allowed : 14.92 % Favored : 81.29 % 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: 0.89 (0.11), residues: 5500 helix: 1.36 (0.09), residues: 2728 sheet: 0.21 (0.17), residues: 825 loop : -0.22 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 86 TYR 0.018 0.002 TYR J 249 PHE 0.009 0.001 PHE D 56 TRP 0.005 0.001 TRP H 60 HIS 0.002 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00586 (44352) covalent geometry : angle 0.55354 (59939) hydrogen bonds : bond 0.06593 ( 2785) hydrogen bonds : angle 4.99212 ( 8079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 555 time to evaluate : 1.788 Fit side-chains REVERT: A 48 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 144 GLU cc_start: 0.7597 (mp0) cc_final: 0.7213 (mp0) REVERT: A 213 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8566 (t) REVERT: B 215 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 31 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7404 (t0) REVERT: C 47 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: C 102 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8234 (mm-40) REVERT: C 125 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: C 148 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7438 (ttp-110) REVERT: C 213 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8664 (t) REVERT: D 46 GLN cc_start: 0.8347 (mm110) cc_final: 0.7684 (mm-40) REVERT: D 125 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: D 148 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7477 (ttp-110) REVERT: D 253 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8025 (mtp-110) REVERT: D 255 ARG cc_start: 0.8515 (mtt-85) cc_final: 0.8052 (mtt90) REVERT: E 31 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7395 (t0) REVERT: E 46 GLN cc_start: 0.8422 (mm110) cc_final: 0.7940 (mm110) REVERT: E 48 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8034 (mp) REVERT: E 213 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8695 (t) REVERT: F 31 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7550 (t0) REVERT: F 46 GLN cc_start: 0.8431 (mm110) cc_final: 0.7715 (mm-40) REVERT: F 253 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: F 255 ARG cc_start: 0.8519 (mtt-85) cc_final: 0.8058 (mtt90) REVERT: G 31 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7456 (t0) REVERT: G 90 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8929 (tt) REVERT: G 125 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: G 213 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (t) REVERT: H 46 GLN cc_start: 0.8307 (mm110) cc_final: 0.7820 (mm-40) REVERT: H 148 ARG cc_start: 0.8146 (tpt170) cc_final: 0.7488 (ttp-110) REVERT: H 215 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: I 31 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7429 (t0) REVERT: I 43 ARG cc_start: 0.7605 (mpp80) cc_final: 0.7387 (mpp80) REVERT: I 46 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8017 (mm-40) REVERT: I 102 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8104 (mm110) REVERT: I 165 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8026 (mp) REVERT: I 213 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8603 (t) REVERT: I 215 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: J 31 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7375 (t0) REVERT: J 102 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: J 125 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: J 144 GLU cc_start: 0.7651 (mp0) cc_final: 0.7349 (mp0) REVERT: J 148 ARG cc_start: 0.7994 (tpt170) cc_final: 0.7390 (ttp-110) REVERT: J 215 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: K 31 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7339 (t0) REVERT: K 43 ARG cc_start: 0.7665 (mtm180) cc_final: 0.6941 (mmm-85) REVERT: K 46 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7849 (mm-40) REVERT: K 125 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: K 148 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7560 (ttp-110) REVERT: K 213 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8576 (t) REVERT: K 215 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: K 253 ARG cc_start: 0.8573 (mpp-170) cc_final: 0.8122 (mpp-170) REVERT: a 216 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: b 60 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: b 270 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7977 (mmm-85) REVERT: c 101 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8243 (tmm) REVERT: c 120 MET cc_start: 0.8430 (ttt) cc_final: 0.8065 (ttp) REVERT: c 166 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7078 (ttm110) REVERT: c 216 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8495 (ttpm) REVERT: d 60 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: d 86 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7410 (ttp-110) REVERT: d 191 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.8176 (ttp-110) REVERT: e 38 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7184 (tt0) REVERT: e 60 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: e 120 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8230 (ttp) REVERT: e 139 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: e 181 ASP cc_start: 0.8762 (t70) cc_final: 0.8333 (t70) REVERT: f 115 GLN cc_start: 0.8575 (mt0) cc_final: 0.8170 (mm110) REVERT: f 181 ASP cc_start: 0.8827 (t70) cc_final: 0.8554 (t70) REVERT: f 216 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: g 60 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: g 291 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (m) REVERT: h 38 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7128 (mt-10) REVERT: h 139 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: h 270 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7983 (mmm-85) REVERT: i 60 GLN cc_start: 0.7952 (mm110) cc_final: 0.7712 (mm-40) REVERT: i 143 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8281 (m) REVERT: i 270 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8020 (mmm160) REVERT: j 143 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (m) REVERT: j 159 GLN cc_start: 0.8404 (mp10) cc_final: 0.8174 (mp10) REVERT: j 291 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8440 (m) REVERT: k 115 GLN cc_start: 0.8430 (mt0) cc_final: 0.8052 (mm110) REVERT: k 143 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8335 (m) REVERT: k 159 GLN cc_start: 0.8271 (mp-120) cc_final: 0.7992 (mp10) outliers start: 178 outliers final: 81 residues processed: 672 average time/residue: 0.9243 time to fit residues: 726.4854 Evaluate side-chains 675 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 543 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 139 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain j residue 161 SER Chi-restraints excluded: chain j residue 173 LYS Chi-restraints excluded: chain j residue 291 SER Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 86 optimal weight: 4.9990 chunk 431 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 439 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 442 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 457 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: B 102 GLN G 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088380 restraints weight = 57345.386| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.47 r_work: 0.2926 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 44352 Z= 0.203 Angle : 0.522 10.277 59939 Z= 0.282 Chirality : 0.044 0.222 6952 Planarity : 0.004 0.050 7843 Dihedral : 4.995 70.729 6136 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.56 % Allowed : 15.12 % Favored : 81.33 % 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: 0.92 (0.11), residues: 5500 helix: 1.38 (0.09), residues: 2717 sheet: 0.21 (0.17), residues: 825 loop : -0.17 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 191 TYR 0.017 0.001 TYR H 249 PHE 0.007 0.001 PHE D 56 TRP 0.005 0.001 TRP J 60 HIS 0.003 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00461 (44352) covalent geometry : angle 0.52165 (59939) hydrogen bonds : bond 0.06203 ( 2785) hydrogen bonds : angle 4.91527 ( 8079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 567 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8022 (mp) REVERT: A 144 GLU cc_start: 0.7607 (mp0) cc_final: 0.7226 (mp0) REVERT: A 213 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 47 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7570 (t70) REVERT: B 215 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: C 31 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7404 (t0) REVERT: C 47 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: C 102 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8203 (mm-40) REVERT: C 125 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: C 148 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.7474 (ttp-110) REVERT: D 46 GLN cc_start: 0.8346 (mm110) cc_final: 0.7698 (mm-40) REVERT: D 148 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7487 (ttp-110) REVERT: D 253 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8009 (mtp-110) REVERT: D 255 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8055 (mtt90) REVERT: E 31 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7393 (t0) REVERT: E 46 GLN cc_start: 0.8398 (mm110) cc_final: 0.7959 (mm110) REVERT: E 48 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8048 (mp) REVERT: E 213 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8681 (t) REVERT: F 31 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7555 (t0) REVERT: F 46 GLN cc_start: 0.8476 (mm110) cc_final: 0.7734 (mm-40) REVERT: F 255 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8081 (mtt90) REVERT: G 31 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7462 (t0) REVERT: G 90 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8923 (tt) REVERT: G 125 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: G 213 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (t) REVERT: H 46 GLN cc_start: 0.8328 (mm110) cc_final: 0.7685 (mm-40) REVERT: H 215 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: I 31 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7412 (t0) REVERT: I 43 ARG cc_start: 0.7588 (mpp80) cc_final: 0.7339 (mpp80) REVERT: I 46 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8035 (mm-40) REVERT: I 102 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8119 (mm110) REVERT: I 165 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8010 (mp) REVERT: I 213 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8601 (t) REVERT: I 215 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: J 31 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7367 (t0) REVERT: J 125 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: J 144 GLU cc_start: 0.7671 (mp0) cc_final: 0.7371 (mp0) REVERT: J 148 ARG cc_start: 0.7988 (tpt170) cc_final: 0.7400 (ttp-110) REVERT: J 215 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: K 31 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7351 (t0) REVERT: K 43 ARG cc_start: 0.7661 (mtm180) cc_final: 0.6960 (mmm-85) REVERT: K 46 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7858 (mm-40) REVERT: K 125 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: K 148 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7567 (ttp-110) REVERT: K 213 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8577 (t) REVERT: K 215 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: K 253 ARG cc_start: 0.8514 (mpp-170) cc_final: 0.8057 (mpp-170) REVERT: a 216 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: b 270 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7949 (mmm-85) REVERT: c 101 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: c 120 MET cc_start: 0.8409 (ttt) cc_final: 0.8047 (ttp) REVERT: c 166 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7066 (ttm110) REVERT: c 216 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8341 (tttm) REVERT: d 60 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: d 86 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7389 (ttp-110) REVERT: d 163 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8207 (mp) REVERT: e 38 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: e 60 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: e 120 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: e 181 ASP cc_start: 0.8762 (t70) cc_final: 0.8353 (t70) REVERT: f 115 GLN cc_start: 0.8578 (mt0) cc_final: 0.8163 (mm110) REVERT: f 181 ASP cc_start: 0.8833 (t70) cc_final: 0.8569 (t70) REVERT: f 216 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8419 (tttm) REVERT: g 60 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: g 291 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8442 (m) REVERT: h 36 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7215 (p) REVERT: h 38 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7144 (mt-10) REVERT: h 270 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7978 (mmm-85) REVERT: i 60 GLN cc_start: 0.7952 (mm110) cc_final: 0.7670 (mm-40) REVERT: i 143 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8269 (m) REVERT: i 213 LEU cc_start: 0.8744 (mp) cc_final: 0.8506 (mm) REVERT: j 143 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8313 (m) REVERT: j 159 GLN cc_start: 0.8401 (mp10) cc_final: 0.8172 (mp10) REVERT: k 115 GLN cc_start: 0.8441 (mt0) cc_final: 0.8050 (mm110) REVERT: k 143 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8326 (m) REVERT: k 151 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8494 (t) REVERT: k 159 GLN cc_start: 0.8298 (mp-120) cc_final: 0.8050 (mp10) outliers start: 167 outliers final: 81 residues processed: 680 average time/residue: 0.9189 time to fit residues: 733.0240 Evaluate side-chains 678 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 550 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 43 VAL Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain j residue 173 LYS Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 151 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 421 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 481 optimal weight: 0.0050 chunk 404 optimal weight: 0.9990 chunk 526 optimal weight: 7.9990 chunk 452 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN c 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091589 restraints weight = 56740.974| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.51 r_work: 0.2959 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 44352 Z= 0.156 Angle : 0.491 11.546 59939 Z= 0.265 Chirality : 0.042 0.246 6952 Planarity : 0.004 0.049 7843 Dihedral : 4.763 67.696 6134 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.04 % Allowed : 15.84 % Favored : 81.12 % 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: 1.06 (0.11), residues: 5500 helix: 1.53 (0.09), residues: 2728 sheet: 0.06 (0.17), residues: 891 loop : -0.06 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG k 191 TYR 0.014 0.001 TYR H 249 PHE 0.006 0.001 PHE F 56 TRP 0.006 0.001 TRP K 60 HIS 0.002 0.000 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00337 (44352) covalent geometry : angle 0.49123 (59939) hydrogen bonds : bond 0.05668 ( 2785) hydrogen bonds : angle 4.77940 ( 8079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 578 time to evaluate : 1.670 Fit side-chains REVERT: A 48 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 144 GLU cc_start: 0.7598 (mp0) cc_final: 0.7300 (mp0) REVERT: A 213 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (t) REVERT: A 215 GLU cc_start: 0.8471 (tt0) cc_final: 0.8135 (tp30) REVERT: B 47 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7532 (t70) REVERT: B 215 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: B 253 ARG cc_start: 0.8482 (mpp-170) cc_final: 0.8280 (mpp-170) REVERT: C 31 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7389 (t0) REVERT: C 102 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8235 (mm-40) REVERT: C 148 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7555 (ttp-110) REVERT: C 213 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (t) REVERT: C 253 ARG cc_start: 0.8522 (mpp-170) cc_final: 0.8060 (mpp-170) REVERT: D 46 GLN cc_start: 0.8421 (mm110) cc_final: 0.7772 (mm-40) REVERT: D 148 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7538 (ttp-110) REVERT: D 255 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8058 (mtt90) REVERT: E 31 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7465 (t0) REVERT: E 46 GLN cc_start: 0.8428 (mm110) cc_final: 0.7946 (mm110) REVERT: E 213 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8672 (t) REVERT: F 31 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7567 (t0) REVERT: F 43 ARG cc_start: 0.7847 (mpp80) cc_final: 0.7561 (mpp80) REVERT: F 46 GLN cc_start: 0.8513 (mm110) cc_final: 0.7819 (mm-40) REVERT: F 255 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8126 (mtt90) REVERT: G 31 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7468 (t0) REVERT: G 90 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8944 (tt) REVERT: G 213 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (t) REVERT: H 46 GLN cc_start: 0.8350 (mm110) cc_final: 0.7739 (mm-40) REVERT: H 148 ARG cc_start: 0.8164 (tpt170) cc_final: 0.7555 (ttp-110) REVERT: H 215 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: I 31 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7418 (t0) REVERT: I 43 ARG cc_start: 0.7597 (mpp80) cc_final: 0.7343 (mpp80) REVERT: I 46 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8103 (mm-40) REVERT: I 102 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8145 (mm110) REVERT: I 165 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8140 (mp) REVERT: I 213 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8632 (t) REVERT: I 215 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: J 31 ASP cc_start: 0.7953 (m-30) cc_final: 0.7377 (t0) REVERT: J 125 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: J 144 GLU cc_start: 0.7701 (mp0) cc_final: 0.7342 (mp0) REVERT: J 148 ARG cc_start: 0.7991 (tpt170) cc_final: 0.7425 (ttp-110) REVERT: J 215 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: K 31 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7406 (t0) REVERT: K 43 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7010 (mmm-85) REVERT: K 46 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7769 (mm-40) REVERT: K 125 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: K 148 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.7608 (ttp-110) REVERT: K 213 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8596 (t) REVERT: K 215 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: K 253 ARG cc_start: 0.8516 (mpp-170) cc_final: 0.8039 (mpp-170) REVERT: a 143 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8313 (m) REVERT: a 163 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8255 (mp) REVERT: a 213 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (mm) REVERT: a 216 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8410 (tttm) REVERT: b 270 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7819 (mmm-85) REVERT: c 101 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: c 120 MET cc_start: 0.8406 (ttt) cc_final: 0.8080 (ttp) REVERT: c 166 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7051 (ttm110) REVERT: c 216 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8377 (tttm) REVERT: d 60 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: d 86 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7388 (ttp-110) REVERT: d 163 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8237 (mp) REVERT: e 38 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: e 60 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: e 120 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: e 166 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7251 (mtm110) REVERT: e 181 ASP cc_start: 0.8736 (t70) cc_final: 0.8348 (t70) REVERT: f 115 GLN cc_start: 0.8611 (mt0) cc_final: 0.8192 (mm110) REVERT: f 181 ASP cc_start: 0.8834 (t70) cc_final: 0.8586 (t70) REVERT: f 213 LEU cc_start: 0.8712 (mp) cc_final: 0.8474 (mm) REVERT: f 216 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8456 (tttm) REVERT: g 60 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: g 291 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8459 (m) REVERT: h 38 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7190 (mt-10) REVERT: h 270 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8061 (tpt90) REVERT: i 143 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8275 (m) REVERT: i 213 LEU cc_start: 0.8681 (mp) cc_final: 0.8462 (mm) REVERT: i 270 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7970 (mmm160) REVERT: j 70 PHE cc_start: 0.7198 (m-80) cc_final: 0.6473 (t80) REVERT: j 159 GLN cc_start: 0.8457 (mp10) cc_final: 0.8220 (mp10) REVERT: k 115 GLN cc_start: 0.8466 (mt0) cc_final: 0.8079 (mm110) REVERT: k 143 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8321 (m) REVERT: k 159 GLN cc_start: 0.8359 (mp-120) cc_final: 0.8092 (mp10) outliers start: 143 outliers final: 73 residues processed: 672 average time/residue: 0.9562 time to fit residues: 753.6185 Evaluate side-chains 672 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 556 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 213 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 270 ARG Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 270 ARG Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 161 SER Chi-restraints excluded: chain j residue 173 LYS Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 274 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 508 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 525 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN H 89 ASN c 259 ASN d 259 ASN f 259 ASN h 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091372 restraints weight = 57029.965| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.51 r_work: 0.2955 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 44352 Z= 0.165 Angle : 0.501 10.822 59939 Z= 0.270 Chirality : 0.042 0.215 6952 Planarity : 0.004 0.049 7843 Dihedral : 4.672 64.421 6129 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.15 % Allowed : 16.07 % Favored : 80.77 % 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: 1.06 (0.11), residues: 5500 helix: 1.53 (0.09), residues: 2728 sheet: 0.07 (0.17), residues: 891 loop : -0.07 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.014 0.001 TYR E 249 PHE 0.006 0.001 PHE F 56 TRP 0.005 0.001 TRP K 60 HIS 0.002 0.000 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00363 (44352) covalent geometry : angle 0.50058 (59939) hydrogen bonds : bond 0.05787 ( 2785) hydrogen bonds : angle 4.78533 ( 8079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 565 time to evaluate : 1.801 Fit side-chains REVERT: A 48 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 144 GLU cc_start: 0.7619 (mp0) cc_final: 0.7318 (mp0) REVERT: A 213 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8568 (t) REVERT: A 253 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8247 (mpp-170) REVERT: B 47 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7508 (t70) REVERT: B 215 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: C 31 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7386 (t0) REVERT: C 102 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8234 (mm-40) REVERT: C 148 ARG cc_start: 0.8233 (tpp-160) cc_final: 0.7548 (ttp-110) REVERT: C 213 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8666 (t) REVERT: C 215 GLU cc_start: 0.8475 (tt0) cc_final: 0.8168 (tp30) REVERT: D 43 ARG cc_start: 0.7822 (mpp80) cc_final: 0.7525 (mpp80) REVERT: D 46 GLN cc_start: 0.8433 (mm110) cc_final: 0.7779 (mm-40) REVERT: D 148 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7541 (ttp-110) REVERT: D 255 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.8016 (mtt90) REVERT: E 31 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7463 (t0) REVERT: E 46 GLN cc_start: 0.8431 (mm110) cc_final: 0.7960 (mm110) REVERT: E 213 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8682 (t) REVERT: F 31 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7574 (t0) REVERT: F 46 GLN cc_start: 0.8517 (mm110) cc_final: 0.7837 (mm-40) REVERT: F 255 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8097 (mtt90) REVERT: G 31 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7487 (t0) REVERT: G 213 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8711 (t) REVERT: H 46 GLN cc_start: 0.8368 (mm110) cc_final: 0.7768 (mm-40) REVERT: H 148 ARG cc_start: 0.8152 (tpt170) cc_final: 0.7553 (ttp-110) REVERT: I 31 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7425 (t0) REVERT: I 46 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8107 (mm-40) REVERT: I 102 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8170 (mm110) REVERT: I 165 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8173 (mp) REVERT: I 213 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (t) REVERT: I 215 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: J 31 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7394 (t0) REVERT: J 125 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: J 144 GLU cc_start: 0.7700 (mp0) cc_final: 0.7341 (mp0) REVERT: J 148 ARG cc_start: 0.7973 (tpt170) cc_final: 0.7418 (ttp-110) REVERT: K 31 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7412 (t0) REVERT: K 43 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6988 (mmm-85) REVERT: K 46 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7821 (mm-40) REVERT: K 90 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8919 (tt) REVERT: K 125 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: K 148 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.7611 (ttp-110) REVERT: K 213 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8607 (t) REVERT: K 215 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: K 253 ARG cc_start: 0.8525 (mpp-170) cc_final: 0.8046 (mpp-170) REVERT: a 143 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8320 (m) REVERT: a 163 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8232 (mp) REVERT: a 181 ASP cc_start: 0.8861 (t70) cc_final: 0.8263 (t70) REVERT: a 213 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (mm) REVERT: a 216 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: b 60 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: b 139 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: c 101 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8260 (tmm) REVERT: c 120 MET cc_start: 0.8418 (ttt) cc_final: 0.8085 (ttp) REVERT: c 166 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7055 (ttm110) REVERT: c 216 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8376 (tttm) REVERT: d 60 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: d 86 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7401 (ttp-110) REVERT: d 163 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8245 (mp) REVERT: e 38 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: e 60 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: e 120 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: e 166 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7278 (mtm110) REVERT: e 181 ASP cc_start: 0.8763 (t70) cc_final: 0.8370 (t70) REVERT: f 115 GLN cc_start: 0.8607 (mt0) cc_final: 0.8201 (mm110) REVERT: f 181 ASP cc_start: 0.8825 (t70) cc_final: 0.8577 (t70) REVERT: f 216 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8447 (tttm) REVERT: g 60 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: g 291 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (m) REVERT: h 38 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7151 (mt-10) REVERT: h 115 GLN cc_start: 0.8642 (mt0) cc_final: 0.8239 (mm-40) REVERT: h 270 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8063 (tpt90) REVERT: i 143 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8285 (m) REVERT: i 213 LEU cc_start: 0.8679 (mp) cc_final: 0.8457 (mm) REVERT: i 270 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7977 (mmm160) REVERT: j 70 PHE cc_start: 0.7161 (m-80) cc_final: 0.6466 (t80) REVERT: j 159 GLN cc_start: 0.8434 (mp10) cc_final: 0.8205 (mp10) REVERT: k 115 GLN cc_start: 0.8453 (mt0) cc_final: 0.8072 (mm110) REVERT: k 143 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8329 (m) REVERT: k 151 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8525 (t) REVERT: k 159 GLN cc_start: 0.8342 (mp-120) cc_final: 0.8067 (mp10) outliers start: 148 outliers final: 78 residues processed: 660 average time/residue: 0.6330 time to fit residues: 494.1279 Evaluate side-chains 676 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 553 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 213 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 270 ARG Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 237 MET Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 161 SER Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 151 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 505 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 533 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 447 optimal weight: 7.9990 chunk 332 optimal weight: 0.7980 chunk 449 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 102 GLN c 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.088995 restraints weight = 57457.212| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.48 r_work: 0.2937 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 44352 Z= 0.190 Angle : 0.520 10.438 59939 Z= 0.280 Chirality : 0.043 0.221 6952 Planarity : 0.004 0.050 7843 Dihedral : 4.730 60.440 6129 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.02 % Allowed : 16.14 % Favored : 80.84 % 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: 1.00 (0.11), residues: 5500 helix: 1.46 (0.09), residues: 2717 sheet: 0.25 (0.17), residues: 825 loop : -0.16 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.015 0.001 TYR H 249 PHE 0.007 0.001 PHE F 56 TRP 0.004 0.001 TRP B 60 HIS 0.003 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00426 (44352) covalent geometry : angle 0.51951 (59939) hydrogen bonds : bond 0.06053 ( 2785) hydrogen bonds : angle 4.84385 ( 8079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 554 time to evaluate : 1.094 Fit side-chains REVERT: A 48 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 144 GLU cc_start: 0.7629 (mp0) cc_final: 0.7317 (mp0) REVERT: A 213 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8559 (t) REVERT: B 47 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7490 (t70) REVERT: B 215 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: C 31 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7377 (t0) REVERT: C 102 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8211 (mm-40) REVERT: C 125 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: C 148 ARG cc_start: 0.8204 (tpp-160) cc_final: 0.7501 (ttp-110) REVERT: C 213 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8644 (t) REVERT: C 215 GLU cc_start: 0.8484 (tt0) cc_final: 0.8175 (tp30) REVERT: D 46 GLN cc_start: 0.8400 (mm110) cc_final: 0.7727 (mm-40) REVERT: D 125 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: D 148 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7486 (ttp-110) REVERT: D 253 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7765 (mtp-110) REVERT: D 255 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.8009 (mtt90) REVERT: E 31 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7401 (t0) REVERT: E 43 ARG cc_start: 0.7692 (mpp80) cc_final: 0.7442 (mpp80) REVERT: E 46 GLN cc_start: 0.8407 (mm110) cc_final: 0.7894 (mm110) REVERT: E 213 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8680 (t) REVERT: F 31 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7540 (t0) REVERT: F 43 ARG cc_start: 0.7699 (mpp80) cc_final: 0.7445 (mpp80) REVERT: F 46 GLN cc_start: 0.8491 (mm110) cc_final: 0.7796 (mm-40) REVERT: F 255 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8099 (mtt90) REVERT: G 31 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7439 (t0) REVERT: G 213 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8692 (t) REVERT: H 46 GLN cc_start: 0.8353 (mm110) cc_final: 0.7738 (mm-40) REVERT: H 148 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7531 (ttp-110) REVERT: H 213 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (t) REVERT: I 31 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7380 (t0) REVERT: I 46 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8069 (mm-40) REVERT: I 102 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8129 (mm110) REVERT: I 165 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8045 (mp) REVERT: I 213 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8583 (t) REVERT: I 215 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: J 31 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7381 (t0) REVERT: J 125 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: J 144 GLU cc_start: 0.7677 (mp0) cc_final: 0.7371 (mp0) REVERT: J 148 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7381 (ttp-110) REVERT: K 31 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7361 (t0) REVERT: K 43 ARG cc_start: 0.7596 (mtm180) cc_final: 0.6933 (mmm-85) REVERT: K 46 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7946 (mm-40) REVERT: K 90 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8917 (tt) REVERT: K 125 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: K 148 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.7568 (ttp-110) REVERT: K 213 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8557 (t) REVERT: K 215 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: K 253 ARG cc_start: 0.8534 (mpp-170) cc_final: 0.8056 (mpp-170) REVERT: a 143 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8272 (m) REVERT: a 163 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8182 (mp) REVERT: a 216 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8376 (tttm) REVERT: b 60 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: b 139 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: c 101 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (tmm) REVERT: c 120 MET cc_start: 0.8399 (ttt) cc_final: 0.8040 (ttp) REVERT: c 166 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7048 (ttm110) REVERT: c 216 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8317 (tttm) REVERT: d 60 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: d 86 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7409 (ttp-110) REVERT: d 163 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8197 (mp) REVERT: e 38 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: e 60 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: e 120 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8222 (ttp) REVERT: e 181 ASP cc_start: 0.8769 (t70) cc_final: 0.8371 (t70) REVERT: e 216 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8328 (tttm) REVERT: f 115 GLN cc_start: 0.8579 (mt0) cc_final: 0.8177 (mm110) REVERT: f 181 ASP cc_start: 0.8841 (t70) cc_final: 0.8581 (t70) REVERT: f 216 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: g 60 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: g 291 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8423 (m) REVERT: h 38 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7128 (mt-10) REVERT: h 115 GLN cc_start: 0.8627 (mt0) cc_final: 0.8219 (mm-40) REVERT: h 270 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8023 (tpt90) REVERT: i 115 GLN cc_start: 0.8601 (mt0) cc_final: 0.8106 (mm110) REVERT: i 143 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8264 (m) REVERT: i 213 LEU cc_start: 0.8681 (mp) cc_final: 0.8453 (mm) REVERT: i 270 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7981 (mmm160) REVERT: j 143 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (m) REVERT: j 159 GLN cc_start: 0.8385 (mp10) cc_final: 0.8147 (mp10) REVERT: k 115 GLN cc_start: 0.8432 (mt0) cc_final: 0.8055 (mm110) REVERT: k 143 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8315 (m) REVERT: k 151 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8495 (t) REVERT: k 159 GLN cc_start: 0.8295 (mp-120) cc_final: 0.8015 (mp10) outliers start: 142 outliers final: 77 residues processed: 646 average time/residue: 0.6220 time to fit residues: 473.7220 Evaluate side-chains 675 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 549 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain j residue 161 SER Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 151 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 482 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 405 optimal weight: 3.9990 chunk 469 optimal weight: 4.9990 chunk 392 optimal weight: 0.0970 chunk 48 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 516 optimal weight: 0.9990 chunk 472 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 524 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN G 102 GLN H 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090265 restraints weight = 57151.124| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.51 r_work: 0.2937 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 44352 Z= 0.205 Angle : 0.533 10.894 59939 Z= 0.287 Chirality : 0.044 0.219 6952 Planarity : 0.005 0.053 7843 Dihedral : 4.778 56.714 6129 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 16.35 % Favored : 80.86 % 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: 0.94 (0.11), residues: 5500 helix: 1.40 (0.09), residues: 2717 sheet: 0.23 (0.17), residues: 825 loop : -0.18 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 191 TYR 0.017 0.001 TYR H 249 PHE 0.007 0.001 PHE g 189 TRP 0.004 0.001 TRP B 60 HIS 0.002 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00466 (44352) covalent geometry : angle 0.53293 (59939) hydrogen bonds : bond 0.06206 ( 2785) hydrogen bonds : angle 4.88683 ( 8079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 546 time to evaluate : 0.985 Fit side-chains REVERT: A 48 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 144 GLU cc_start: 0.7648 (mp0) cc_final: 0.7272 (mp0) REVERT: A 213 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 47 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7531 (t70) REVERT: B 215 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: C 31 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7412 (t0) REVERT: C 102 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8249 (mm-40) REVERT: C 125 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: C 148 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7513 (ttp-110) REVERT: C 213 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8659 (t) REVERT: C 215 GLU cc_start: 0.8523 (tt0) cc_final: 0.8228 (tp30) REVERT: D 46 GLN cc_start: 0.8422 (mm110) cc_final: 0.7762 (mm-40) REVERT: D 125 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: D 148 ARG cc_start: 0.8146 (tpt170) cc_final: 0.7550 (ttp-110) REVERT: D 253 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7730 (mtp-110) REVERT: D 255 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8041 (mtt90) REVERT: E 31 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7453 (t0) REVERT: E 43 ARG cc_start: 0.7675 (mpp80) cc_final: 0.7447 (mpp80) REVERT: E 46 GLN cc_start: 0.8424 (mm110) cc_final: 0.8007 (mm110) REVERT: E 213 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (t) REVERT: F 31 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7595 (t0) REVERT: F 43 ARG cc_start: 0.7701 (mpp80) cc_final: 0.7455 (mpp80) REVERT: F 46 GLN cc_start: 0.8509 (mm110) cc_final: 0.7817 (mm-40) REVERT: F 255 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8119 (mtt90) REVERT: G 31 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7469 (t0) REVERT: G 90 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8937 (tt) REVERT: G 213 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (t) REVERT: H 46 GLN cc_start: 0.8367 (mm110) cc_final: 0.7750 (mm-40) REVERT: H 148 ARG cc_start: 0.8169 (tpt170) cc_final: 0.7557 (ttp-110) REVERT: I 31 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7437 (t0) REVERT: I 46 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8116 (mm-40) REVERT: I 102 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8151 (mm110) REVERT: I 165 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8058 (mp) REVERT: I 213 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8630 (t) REVERT: I 215 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: J 31 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7388 (t0) REVERT: J 144 GLU cc_start: 0.7692 (mp0) cc_final: 0.7399 (mp0) REVERT: J 148 ARG cc_start: 0.8001 (tpt170) cc_final: 0.7427 (ttp-110) REVERT: K 31 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7404 (t0) REVERT: K 43 ARG cc_start: 0.7647 (mtm180) cc_final: 0.6980 (mmm-85) REVERT: K 46 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7965 (mm-40) REVERT: K 90 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8931 (tt) REVERT: K 125 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: K 148 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.7626 (ttp-110) REVERT: K 213 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8604 (t) REVERT: K 215 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: a 163 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8238 (mp) REVERT: a 216 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8425 (tttm) REVERT: b 60 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: b 139 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: c 101 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8271 (tmm) REVERT: c 166 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.7076 (ttm110) REVERT: c 216 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: d 60 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: d 86 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7483 (ttp-110) REVERT: d 163 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8243 (mp) REVERT: e 38 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7231 (tt0) REVERT: e 60 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: e 120 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: e 181 ASP cc_start: 0.8776 (t70) cc_final: 0.8378 (t70) REVERT: f 115 GLN cc_start: 0.8606 (mt0) cc_final: 0.8203 (mm110) REVERT: f 181 ASP cc_start: 0.8860 (t70) cc_final: 0.8630 (t70) REVERT: f 216 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8449 (tttm) REVERT: g 60 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: g 291 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (m) REVERT: h 38 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7165 (mt-10) REVERT: h 115 GLN cc_start: 0.8633 (mt0) cc_final: 0.8243 (mm-40) REVERT: h 270 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8019 (mmm-85) REVERT: i 60 GLN cc_start: 0.7977 (mm110) cc_final: 0.7749 (mm-40) REVERT: i 115 GLN cc_start: 0.8632 (mt0) cc_final: 0.8132 (mm110) REVERT: i 143 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8312 (m) REVERT: i 213 LEU cc_start: 0.8741 (mp) cc_final: 0.8506 (mm) REVERT: i 270 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8014 (mmm160) REVERT: j 143 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8343 (m) REVERT: j 159 GLN cc_start: 0.8447 (mp10) cc_final: 0.8214 (mp10) REVERT: k 115 GLN cc_start: 0.8447 (mt0) cc_final: 0.8067 (mm110) REVERT: k 143 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8355 (m) REVERT: k 151 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8536 (t) REVERT: k 159 GLN cc_start: 0.8335 (mp-120) cc_final: 0.8061 (mp10) outliers start: 131 outliers final: 81 residues processed: 634 average time/residue: 0.5819 time to fit residues: 435.2344 Evaluate side-chains 668 residues out of total 4697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 542 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 213 SER Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 213 SER Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 256 ASN Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 41 ARG Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 213 SER Chi-restraints excluded: chain K residue 215 GLU Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 129 GLU Chi-restraints excluded: chain a residue 143 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 91 SER Chi-restraints excluded: chain b residue 102 VAL Chi-restraints excluded: chain b residue 129 GLU Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain c residue 101 MET Chi-restraints excluded: chain c residue 129 GLU Chi-restraints excluded: chain c residue 143 SER Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 163 LEU Chi-restraints excluded: chain c residue 173 LYS Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 237 MET Chi-restraints excluded: chain d residue 43 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 86 ARG Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 163 LEU Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 68 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 237 MET Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 129 GLU Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 216 LYS Chi-restraints excluded: chain f residue 291 SER Chi-restraints excluded: chain g residue 60 GLN Chi-restraints excluded: chain g residue 91 SER Chi-restraints excluded: chain g residue 143 SER Chi-restraints excluded: chain g residue 237 MET Chi-restraints excluded: chain g residue 291 SER Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 161 SER Chi-restraints excluded: chain h residue 270 ARG Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 270 ARG Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain j residue 161 SER Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 129 GLU Chi-restraints excluded: chain k residue 143 SER Chi-restraints excluded: chain k residue 151 SER Chi-restraints excluded: chain k residue 161 SER Chi-restraints excluded: chain k residue 237 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 523 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 530 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 497 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088533 restraints weight = 57647.894| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.49 r_work: 0.2930 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 44352 Z= 0.203 Angle : 0.531 10.147 59939 Z= 0.286 Chirality : 0.044 0.221 6952 Planarity : 0.005 0.051 7843 Dihedral : 4.771 54.269 6129 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.85 % Allowed : 16.46 % Favored : 80.69 % 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: 0.93 (0.11), residues: 5500 helix: 1.40 (0.09), residues: 2717 sheet: 0.22 (0.17), residues: 825 loop : -0.18 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 191 TYR 0.018 0.001 TYR K 249 PHE 0.008 0.001 PHE F 56 TRP 0.005 0.001 TRP K 60 HIS 0.002 0.001 HIS d 69 Details of bonding type rmsd covalent geometry : bond 0.00462 (44352) covalent geometry : angle 0.53121 (59939) hydrogen bonds : bond 0.06176 ( 2785) hydrogen bonds : angle 4.88271 ( 8079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16746.44 seconds wall clock time: 284 minutes 52.97 seconds (17092.97 seconds total)