Starting phenix.real_space_refine on Wed May 6 08:04:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vj8_65106/05_2026/9vj8_65106.map" } resolution = 3.9 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= 0.008 sd= 0.049 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: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 118 5.16 5 C 23823 2.51 5 N 6132 2.21 5 O 6910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36995 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "B" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "C" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "D" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "E" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "F" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "G" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "I" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2347 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain: "J" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "K" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2347 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain: "L" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "N" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "P" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2347 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain: "R" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "V" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1828 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 3, 'TRANS': 216} Chain: "T" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1828 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 3, 'TRANS': 216} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.05, per 1000 atoms: 0.22 Number of scatterers: 36995 At special positions: 0 Unit cell: (209, 143, 196.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 118 16.00 O 6910 8.00 N 6132 7.00 C 23823 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: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 47 sheets defined 50.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 90 through 113 removed outlier: 3.651A pdb=" N LYS A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.746A pdb=" N LYS A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.842A pdb=" N GLN B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.746A pdb=" N TYR B 68 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.932A pdb=" N LYS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 114 removed outlier: 4.410A pdb=" N LYS B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N MET B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.599A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.628A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.770A pdb=" N TYR C 68 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 90 removed outlier: 3.708A pdb=" N ASP C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 113 removed outlier: 4.129A pdb=" N GLU C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.699A pdb=" N GLY C 134 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 175 through 189 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.593A pdb=" N GLN D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.833A pdb=" N LEU D 59 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.983A pdb=" N TYR D 68 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.802A pdb=" N LEU D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 removed outlier: 4.160A pdb=" N LYS D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 144 through 158 removed outlier: 4.096A pdb=" N ARG D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.990A pdb=" N LEU E 59 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 Processing helix chain 'E' and resid 90 through 113 removed outlier: 3.635A pdb=" N LYS E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 143 through 158 removed outlier: 3.745A pdb=" N LYS E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 172 removed outlier: 4.092A pdb=" N TYR E 172 " --> pdb=" O ALA E 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 169 through 172' Processing helix chain 'E' and resid 175 through 188 Processing helix chain 'F' and resid 25 through 37 removed outlier: 4.024A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.534A pdb=" N GLY F 67 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR F 68 " --> pdb=" O ILE F 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 68' Processing helix chain 'F' and resid 72 through 90 removed outlier: 4.133A pdb=" N LYS F 90 " --> pdb=" O GLN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 114 removed outlier: 4.297A pdb=" N LYS F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER F 95 " --> pdb=" O PRO F 91 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N MET F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.703A pdb=" N ARG F 156 " --> pdb=" O THR F 152 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR F 157 " --> pdb=" O GLN F 153 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 187 Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.535A pdb=" N GLN G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.553A pdb=" N LEU G 59 " --> pdb=" O PRO G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 removed outlier: 3.752A pdb=" N TYR G 68 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 90 removed outlier: 3.697A pdb=" N ASP G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 113 removed outlier: 4.159A pdb=" N GLU G 98 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.705A pdb=" N GLY G 134 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 158 removed outlier: 3.503A pdb=" N LYS G 147 " --> pdb=" O THR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 189 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.756A pdb=" N LEU H 59 " --> pdb=" O PRO H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 removed outlier: 3.981A pdb=" N TYR H 68 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 90 removed outlier: 3.720A pdb=" N LEU H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 115 removed outlier: 3.979A pdb=" N LYS H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 143 through 158 removed outlier: 4.108A pdb=" N ARG H 156 " --> pdb=" O THR H 152 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR H 157 " --> pdb=" O GLN H 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 158 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 187 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 51 through 60 removed outlier: 3.672A pdb=" N GLU I 60 " --> pdb=" O ARG I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.143A pdb=" N THR I 91 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 123 removed outlier: 3.898A pdb=" N ARG I 123 " --> pdb=" O HIS I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 137 removed outlier: 4.104A pdb=" N ALA I 130 " --> pdb=" O GLY I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 160 removed outlier: 3.759A pdb=" N HIS I 150 " --> pdb=" O ASN I 146 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 159 " --> pdb=" O TYR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 195 removed outlier: 3.698A pdb=" N ALA I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY I 195 " --> pdb=" O LEU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 218 Processing helix chain 'I' and resid 221 through 231 removed outlier: 3.931A pdb=" N VAL I 225 " --> pdb=" O PHE I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 244 removed outlier: 3.732A pdb=" N ARG I 242 " --> pdb=" O PRO I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 249 Processing helix chain 'I' and resid 260 through 277 Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 88 through 95 Processing helix chain 'J' and resid 97 through 122 Processing helix chain 'J' and resid 125 through 137 Processing helix chain 'J' and resid 146 through 161 Processing helix chain 'J' and resid 170 through 195 removed outlier: 3.714A pdb=" N ALA J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 218 removed outlier: 3.687A pdb=" N MET J 218 " --> pdb=" O ALA J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 232 removed outlier: 4.185A pdb=" N VAL J 225 " --> pdb=" O PHE J 221 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN J 232 " --> pdb=" O ILE J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 248 removed outlier: 3.996A pdb=" N MET J 240 " --> pdb=" O ALA J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 277 Processing helix chain 'K' and resid 35 through 37 No H-bonds generated for 'chain 'K' and resid 35 through 37' Processing helix chain 'K' and resid 51 through 60 removed outlier: 3.710A pdb=" N GLU K 60 " --> pdb=" O ARG K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 93 removed outlier: 3.894A pdb=" N THR K 91 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG K 92 " --> pdb=" O LEU K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 123 removed outlier: 3.555A pdb=" N LYS K 101 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG K 123 " --> pdb=" O HIS K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 138 removed outlier: 3.726A pdb=" N GLU K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 160 removed outlier: 3.817A pdb=" N HIS K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 195 removed outlier: 3.744A pdb=" N ALA K 174 " --> pdb=" O ASN K 170 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 218 Processing helix chain 'K' and resid 221 through 231 removed outlier: 3.953A pdb=" N VAL K 225 " --> pdb=" O PHE K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 244 removed outlier: 3.837A pdb=" N ARG K 242 " --> pdb=" O PRO K 238 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS K 243 " --> pdb=" O ILE K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 249 Processing helix chain 'K' and resid 260 through 277 removed outlier: 3.530A pdb=" N ASN K 277 " --> pdb=" O VAL K 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 61 Processing helix chain 'L' and resid 88 through 95 Processing helix chain 'L' and resid 97 through 123 Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 146 through 161 Processing helix chain 'L' and resid 170 through 195 removed outlier: 3.633A pdb=" N ALA L 174 " --> pdb=" O ASN L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 218 removed outlier: 3.513A pdb=" N MET L 218 " --> pdb=" O ALA L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 232 removed outlier: 4.115A pdb=" N VAL L 225 " --> pdb=" O PHE L 221 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN L 232 " --> pdb=" O ILE L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 248 removed outlier: 3.651A pdb=" N MET L 240 " --> pdb=" O ALA L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 277 Processing helix chain 'O' and resid 51 through 60 Processing helix chain 'O' and resid 86 through 93 Processing helix chain 'O' and resid 97 through 122 removed outlier: 3.511A pdb=" N LYS O 101 " --> pdb=" O THR O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 137 removed outlier: 3.952A pdb=" N ALA O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 161 Processing helix chain 'O' and resid 170 through 195 removed outlier: 3.979A pdb=" N ALA O 174 " --> pdb=" O ASN O 170 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY O 195 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 217 Processing helix chain 'O' and resid 218 through 220 No H-bonds generated for 'chain 'O' and resid 218 through 220' Processing helix chain 'O' and resid 221 through 232 removed outlier: 4.438A pdb=" N ASN O 232 " --> pdb=" O ILE O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 244 Processing helix chain 'O' and resid 245 through 250 Processing helix chain 'O' and resid 260 through 277 removed outlier: 3.729A pdb=" N ILE O 264 " --> pdb=" O PHE O 260 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 60 removed outlier: 3.584A pdb=" N GLU P 60 " --> pdb=" O ARG P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 95 removed outlier: 3.887A pdb=" N THR P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA P 95 " --> pdb=" O THR P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 122 removed outlier: 3.587A pdb=" N LYS P 101 " --> pdb=" O THR P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 137 Processing helix chain 'P' and resid 146 through 161 removed outlier: 3.762A pdb=" N HIS P 150 " --> pdb=" O ASN P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 195 removed outlier: 4.066A pdb=" N ALA P 174 " --> pdb=" O ASN P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 219 removed outlier: 3.729A pdb=" N GLU P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 232 removed outlier: 4.184A pdb=" N VAL P 225 " --> pdb=" O PHE P 221 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN P 232 " --> pdb=" O ILE P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 248 Processing helix chain 'P' and resid 260 through 277 Processing helix chain 'Q' and resid 35 through 37 No H-bonds generated for 'chain 'Q' and resid 35 through 37' Processing helix chain 'Q' and resid 51 through 60 Processing helix chain 'Q' and resid 86 through 93 Processing helix chain 'Q' and resid 97 through 122 removed outlier: 3.528A pdb=" N LYS Q 101 " --> pdb=" O THR Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 137 removed outlier: 4.185A pdb=" N ALA Q 130 " --> pdb=" O GLY Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 161 removed outlier: 3.534A pdb=" N LEU Q 159 " --> pdb=" O TYR Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 195 removed outlier: 4.112A pdb=" N ALA Q 174 " --> pdb=" O ASN Q 170 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY Q 195 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 218 Processing helix chain 'Q' and resid 221 through 231 removed outlier: 3.603A pdb=" N VAL Q 225 " --> pdb=" O PHE Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 244 Processing helix chain 'Q' and resid 245 through 249 Processing helix chain 'Q' and resid 260 through 277 removed outlier: 3.896A pdb=" N ILE Q 264 " --> pdb=" O PHE Q 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN Q 277 " --> pdb=" O VAL Q 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.626A pdb=" N GLU R 60 " --> pdb=" O ARG R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 94 removed outlier: 3.994A pdb=" N THR R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 122 Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 146 through 161 removed outlier: 3.838A pdb=" N HIS R 150 " --> pdb=" O ASN R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 195 removed outlier: 3.582A pdb=" N ALA R 174 " --> pdb=" O ASN R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 219 removed outlier: 3.649A pdb=" N GLU R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 232 removed outlier: 4.233A pdb=" N VAL R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN R 232 " --> pdb=" O ILE R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 248 Processing helix chain 'R' and resid 260 through 277 Processing helix chain 'S' and resid 521 through 534 Processing helix chain 'S' and resid 549 through 561 Processing helix chain 'S' and resid 568 through 581 removed outlier: 3.585A pdb=" N ILE S 572 " --> pdb=" O LYS S 568 " (cutoff:3.500A) Processing helix chain 'S' and resid 600 through 607 Processing helix chain 'S' and resid 611 through 617 Processing helix chain 'S' and resid 620 through 634 removed outlier: 3.589A pdb=" N PHE S 634 " --> pdb=" O ILE S 630 " (cutoff:3.500A) Processing helix chain 'S' and resid 637 through 645 Processing helix chain 'S' and resid 652 through 660 Processing helix chain 'S' and resid 686 through 693 Processing helix chain 'S' and resid 704 through 710 Processing helix chain 'S' and resid 716 through 725 removed outlier: 4.006A pdb=" N ILE S 720 " --> pdb=" O PHE S 716 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN S 721 " --> pdb=" O LYS S 717 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS S 722 " --> pdb=" O ASN S 718 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA S 723 " --> pdb=" O ALA S 719 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER S 725 " --> pdb=" O GLN S 721 " (cutoff:3.500A) Processing helix chain 'T' and resid 521 through 534 Processing helix chain 'T' and resid 549 through 561 Processing helix chain 'T' and resid 568 through 581 Processing helix chain 'T' and resid 600 through 607 Processing helix chain 'T' and resid 611 through 617 Processing helix chain 'T' and resid 620 through 634 removed outlier: 3.898A pdb=" N PHE T 634 " --> pdb=" O ILE T 630 " (cutoff:3.500A) Processing helix chain 'T' and resid 637 through 645 Processing helix chain 'T' and resid 646 through 648 No H-bonds generated for 'chain 'T' and resid 646 through 648' Processing helix chain 'T' and resid 652 through 660 Processing helix chain 'T' and resid 671 through 676 Processing helix chain 'T' and resid 686 through 693 Processing helix chain 'T' and resid 704 through 710 Processing helix chain 'T' and resid 717 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.060A pdb=" N ILE A 165 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 167 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 164 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 195 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 166 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 22 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N ALA A 17 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N TYR A 206 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 19 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU A 208 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 21 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 203 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 219 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 205 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 217 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 207 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.481A pdb=" N PHE B 60 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE B 167 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 62 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 18 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLU B 196 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 20 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 205 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 217 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.833A pdb=" N ILE C 167 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 18 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU C 196 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 20 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N PHE C 204 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE C 19 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG C 203 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA C 219 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.886A pdb=" N PHE D 60 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE D 167 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL D 62 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 18 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU D 196 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 20 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N PHE D 204 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE D 19 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 217 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 207 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 215 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'E' and resid 61 through 62 removed outlier: 3.529A pdb=" N ILE E 167 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 164 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 195 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE E 166 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR E 18 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLU E 196 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 20 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 119 through 120 removed outlier: 3.957A pdb=" N LYS H 136 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 136 through 137 removed outlier: 3.888A pdb=" N LYS E 136 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 120 " --> pdb=" O LYS E 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB5, first strand: chain 'F' and resid 60 through 62 removed outlier: 6.386A pdb=" N PHE F 60 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE F 167 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL F 62 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR F 18 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU F 196 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 20 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N PHE F 204 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N PHE F 19 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG F 203 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA F 219 " --> pdb=" O ARG F 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN F 205 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 217 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 137 removed outlier: 3.959A pdb=" N LYS F 136 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AB8, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.721A pdb=" N ILE G 167 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU G 164 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU G 195 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE G 166 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR G 18 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU G 196 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU G 20 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE G 204 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE G 19 " --> pdb=" O PHE G 204 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG G 203 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA G 219 " --> pdb=" O ARG G 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 2 through 3 Processing sheet with id=AC1, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.904A pdb=" N PHE H 60 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE H 167 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL H 62 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR H 18 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLU H 196 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU H 20 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N ALA H 17 " --> pdb=" O PHE H 204 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N TYR H 206 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE H 19 " --> pdb=" O TYR H 206 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU H 208 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR H 21 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG H 203 " --> pdb=" O ALA H 219 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 219 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 217 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 207 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 30 through 33 removed outlier: 3.952A pdb=" N GLU I 30 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE I 23 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE I 32 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL I 22 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER I 15 " --> pdb=" O VAL I 22 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER I 12 " --> pdb=" O SER I 48 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N THR I 50 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU I 14 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 39 through 42 removed outlier: 7.633A pdb=" N VAL I 64 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS I 76 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE I 66 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS J 76 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'J' and resid 63 through 65 removed outlier: 3.545A pdb=" N VAL J 8 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR J 5 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU M 106 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL J 7 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.801A pdb=" N PHE J 23 " --> pdb=" O GLU J 30 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA J 25 " --> pdb=" O HIS J 28 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS J 28 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.754A pdb=" N TYR J 252 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET J 259 " --> pdb=" O TYR J 252 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 7 through 8 Processing sheet with id=AC9, first strand: chain 'K' and resid 13 through 16 removed outlier: 3.575A pdb=" N SER K 15 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 22 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE K 32 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE K 23 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU K 30 " --> pdb=" O PHE K 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.579A pdb=" N LEU L 49 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 76 through 79 removed outlier: 3.531A pdb=" N LYS K 76 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS L 76 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 252 through 254 Processing sheet with id=AD4, first strand: chain 'L' and resid 63 through 65 removed outlier: 3.622A pdb=" N VAL L 39 " --> pdb=" O ARG L 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL L 8 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR L 5 " --> pdb=" O VAL N 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 13 through 16 removed outlier: 3.720A pdb=" N HIS L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 252 through 254 removed outlier: 3.666A pdb=" N TYR L 252 " --> pdb=" O MET L 259 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET L 259 " --> pdb=" O TYR L 252 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 4 through 7 removed outlier: 7.134A pdb=" N ARG O 4 " --> pdb=" O ASP O 38 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU O 40 " --> pdb=" O ARG O 4 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL O 6 " --> pdb=" O LEU O 40 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU O 63 " --> pdb=" O ASP O 38 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL O 64 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS O 76 " --> pdb=" O VAL O 64 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE O 66 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS O 76 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU P 78 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 31 through 33 removed outlier: 3.573A pdb=" N VAL O 22 " --> pdb=" O SER O 15 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER O 15 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR O 50 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR O 16 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 252 through 254 removed outlier: 3.639A pdb=" N TYR O 252 " --> pdb=" O MET O 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET O 259 " --> pdb=" O TYR O 252 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 63 through 65 removed outlier: 3.978A pdb=" N LEU P 63 " --> pdb=" O ASP P 38 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ARG P 4 " --> pdb=" O ASP P 38 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU P 40 " --> pdb=" O ARG P 4 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL P 6 " --> pdb=" O LEU P 40 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU P 42 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL P 8 " --> pdb=" O LEU P 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL U 104 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL P 7 " --> pdb=" O VAL U 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 20 through 25 removed outlier: 3.931A pdb=" N PHE P 23 " --> pdb=" O GLU P 30 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS P 28 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 252 through 254 Processing sheet with id=AE4, first strand: chain 'Q' and resid 32 through 33 removed outlier: 7.085A pdb=" N SER Q 12 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N THR Q 50 " --> pdb=" O SER Q 12 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU Q 14 " --> pdb=" O THR Q 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 39 through 41 removed outlier: 7.245A pdb=" N VAL Q 64 " --> pdb=" O LYS Q 76 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS Q 76 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE Q 66 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS Q 76 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU R 78 " --> pdb=" O LYS Q 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU Q 78 " --> pdb=" O LYS R 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS R 76 " --> pdb=" O LEU Q 78 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 252 through 254 removed outlier: 3.916A pdb=" N TYR Q 252 " --> pdb=" O MET Q 259 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET Q 259 " --> pdb=" O TYR Q 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 63 through 65 removed outlier: 4.106A pdb=" N LEU R 63 " --> pdb=" O ASP R 38 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG R 4 " --> pdb=" O ASP R 38 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU R 40 " --> pdb=" O ARG R 4 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL R 6 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU R 42 " --> pdb=" O VAL R 6 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL R 8 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL V 104 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 7 " --> pdb=" O VAL V 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 13 through 16 removed outlier: 4.157A pdb=" N SER R 15 " --> pdb=" O VAL R 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL R 22 " --> pdb=" O SER R 15 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE R 23 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS R 28 " --> pdb=" O ALA R 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 252 through 254 Processing sheet with id=AF1, first strand: chain 'S' and resid 545 through 546 removed outlier: 4.457A pdb=" N THR S 586 " --> pdb=" O THR S 539 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 537 through 539 removed outlier: 3.646A pdb=" N THR T 539 " --> pdb=" O THR T 586 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR T 586 " --> pdb=" O THR T 539 " (cutoff:3.500A) 1673 hydrogen bonds defined for protein. 4851 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: 6.68 Time building geometry restraints manager: 3.77 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: 11967 1.34 - 1.46: 6813 1.46 - 1.58: 18659 1.58 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 37649 Sorted by residual: bond pdb=" C GLU K 219 " pdb=" N PRO K 220 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.57e+00 bond pdb=" C GLU Q 219 " pdb=" N PRO Q 220 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" N LYS L 256 " pdb=" CA LYS L 256 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.56e+00 bond pdb=" C ASN I 157 " pdb=" N THR I 158 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.79e-02 3.12e+03 1.16e+00 bond pdb=" CA MET B 117 " pdb=" C MET B 117 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.05e+00 ... (remaining 37644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 49779 1.66 - 3.33: 856 3.33 - 4.99: 118 4.99 - 6.65: 42 6.65 - 8.31: 9 Bond angle restraints: 50804 Sorted by residual: angle pdb=" C SER J 87 " pdb=" CA SER J 87 " pdb=" CB SER J 87 " ideal model delta sigma weight residual 116.63 110.32 6.31 1.16e+00 7.43e-01 2.96e+01 angle pdb=" C GLN J 278 " pdb=" CA GLN J 278 " pdb=" CB GLN J 278 " ideal model delta sigma weight residual 115.89 110.60 5.29 1.32e+00 5.74e-01 1.60e+01 angle pdb=" C MET H 117 " pdb=" CA MET H 117 " pdb=" CB MET H 117 " ideal model delta sigma weight residual 115.89 110.78 5.11 1.32e+00 5.74e-01 1.50e+01 angle pdb=" CA SER J 87 " pdb=" C SER J 87 " pdb=" N LEU J 88 " ideal model delta sigma weight residual 119.63 116.67 2.96 8.10e-01 1.52e+00 1.34e+01 angle pdb=" N SER O 86 " pdb=" CA SER O 86 " pdb=" C SER O 86 " ideal model delta sigma weight residual 114.04 109.54 4.50 1.24e+00 6.50e-01 1.32e+01 ... (remaining 50799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 21030 17.95 - 35.90: 1366 35.90 - 53.85: 324 53.85 - 71.80: 44 71.80 - 89.75: 24 Dihedral angle restraints: 22788 sinusoidal: 9466 harmonic: 13322 Sorted by residual: dihedral pdb=" CA GLY O 195 " pdb=" C GLY O 195 " pdb=" N CYS O 196 " pdb=" CA CYS O 196 " ideal model delta harmonic sigma weight residual 180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA THR D 143 " pdb=" C THR D 143 " pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLY Q 195 " pdb=" C GLY Q 195 " pdb=" N CYS Q 196 " pdb=" CA CYS Q 196 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 22785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4443 0.045 - 0.091: 1058 0.091 - 0.136: 287 0.136 - 0.182: 6 0.182 - 0.227: 1 Chirality restraints: 5795 Sorted by residual: chirality pdb=" CB ILE B 137 " pdb=" CA ILE B 137 " pdb=" CG1 ILE B 137 " pdb=" CG2 ILE B 137 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU Q 219 " pdb=" N GLU Q 219 " pdb=" C GLU Q 219 " pdb=" CB GLU Q 219 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA PRO D 91 " pdb=" N PRO D 91 " pdb=" C PRO D 91 " pdb=" CB PRO D 91 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 5792 not shown) Planarity restraints: 6452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU S 517 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO S 518 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO S 518 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 518 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 114 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C GLU D 114 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU D 114 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS D 115 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 115 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C HIS D 115 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS D 115 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU D 116 " -0.010 2.00e-02 2.50e+03 ... (remaining 6449 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 92 2.36 - 3.00: 19403 3.00 - 3.63: 53735 3.63 - 4.27: 75151 4.27 - 4.90: 124285 Nonbonded interactions: 272666 Sorted by model distance: nonbonded pdb=" CD GLU B 138 " pdb="CA CA B 302 " model vdw 1.726 2.740 nonbonded pdb=" OE2 GLU B 138 " pdb="CA CA B 302 " model vdw 1.908 2.510 nonbonded pdb=" OG1 THR I 251 " pdb=" OE1 GLN I 258 " model vdw 2.176 3.040 nonbonded pdb=" O LEU P 200 " pdb=" ND2 ASN P 212 " model vdw 2.193 3.120 nonbonded pdb=" O LEU P 191 " pdb=" OG1 THR P 194 " model vdw 2.204 3.040 ... (remaining 272661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 301) selection = chain 'C' selection = (chain 'D' and resid 1 through 301) selection = chain 'E' selection = (chain 'F' and resid 1 through 301) selection = chain 'G' selection = (chain 'H' and resid 1 through 301) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 3 through 288) selection = chain 'K' selection = (chain 'L' and resid 3 through 288) selection = (chain 'O' and resid 3 through 288) selection = (chain 'P' and resid 3 through 288) selection = chain 'Q' selection = (chain 'R' and resid 3 through 288) } ncs_group { reference = chain 'M' selection = (chain 'N' and resid 102 through 107) selection = (chain 'U' and resid 102 through 107) selection = (chain 'V' and resid 102 through 107) } ncs_group { reference = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.440 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.003 0.037 37649 Z= 0.147 Angle : 0.574 8.313 50804 Z= 0.321 Chirality : 0.041 0.227 5795 Planarity : 0.003 0.049 6452 Dihedral : 12.897 89.749 14146 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.21 % Favored : 91.50 % Rotamer: Outliers : 4.08 % Allowed : 9.36 % Favored : 86.57 % 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: -0.33 (0.13), residues: 4468 helix: 1.50 (0.12), residues: 2043 sheet: -0.37 (0.27), residues: 438 loop : -2.13 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 233 TYR 0.018 0.001 TYR L 155 PHE 0.021 0.001 PHE A 60 TRP 0.012 0.001 TRP R 96 HIS 0.004 0.001 HIS G 155 Details of bonding type rmsd covalent geometry : bond 0.00298 (37649) covalent geometry : angle 0.57351 (50804) hydrogen bonds : bond 0.16616 ( 1673) hydrogen bonds : angle 5.12266 ( 4851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 572 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 LEU cc_start: 0.9207 (tp) cc_final: 0.8986 (tt) REVERT: C 213 TYR cc_start: 0.8232 (m-10) cc_final: 0.7940 (m-10) REVERT: D 115 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7922 (t70) REVERT: E 1 MET cc_start: 0.8141 (ttt) cc_final: 0.7790 (ttm) REVERT: F 138 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6123 (pt0) REVERT: G 88 ASN cc_start: 0.8706 (t0) cc_final: 0.8503 (t0) REVERT: G 213 TYR cc_start: 0.8212 (m-10) cc_final: 0.7942 (m-10) REVERT: I 213 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9002 (tp) REVERT: J 133 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8813 (mt) REVERT: L 247 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8414 (tp) REVERT: O 198 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7664 (p) REVERT: S 551 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7853 (ptpp) REVERT: T 551 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7687 (ptpp) outliers start: 166 outliers final: 43 residues processed: 727 average time/residue: 0.2215 time to fit residues: 256.6070 Evaluate side-chains 308 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 138 GLU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 191 ASP Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 248 PHE Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 193 GLN Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 701 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 86 GLN B 188 ASN B 201 GLN C 155 HIS C 201 GLN D 42 ASN D 180 GLN E 42 ASN E 86 GLN E 115 HIS E 179 GLN F 179 GLN G 155 HIS H 42 ASN H 50 GLN H 202 ASN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN J 150 HIS J 271 HIS K 212 ASN K 227 GLN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 GLN ** L 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 ASN O 119 HIS ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 232 ASN O 277 ASN O 278 GLN P 11 HIS P 157 ASN Q 193 GLN R 116 GLN R 122 GLN ** R 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 GLN R 258 GLN S 596 ASN T 581 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.042212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029490 restraints weight = 285504.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.030453 restraints weight = 167738.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.031112 restraints weight = 118082.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.031566 restraints weight = 91815.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.031850 restraints weight = 76661.741| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 37649 Z= 0.248 Angle : 0.725 12.753 50804 Z= 0.374 Chirality : 0.042 0.234 5795 Planarity : 0.004 0.074 6452 Dihedral : 6.043 70.443 4951 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.50 % Favored : 91.20 % Rotamer: Outliers : 2.95 % Allowed : 14.73 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.04 (0.13), residues: 4468 helix: 1.76 (0.12), residues: 2083 sheet: 0.23 (0.28), residues: 388 loop : -2.18 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 140 TYR 0.018 0.001 TYR D 172 PHE 0.027 0.001 PHE C 47 TRP 0.026 0.002 TRP L 105 HIS 0.005 0.001 HIS L 119 Details of bonding type rmsd covalent geometry : bond 0.00533 (37649) covalent geometry : angle 0.72472 (50804) hydrogen bonds : bond 0.04743 ( 1673) hydrogen bonds : angle 4.57972 ( 4851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 255 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8920 (pt0) cc_final: 0.8660 (pm20) REVERT: B 1 MET cc_start: 0.7988 (mmm) cc_final: 0.7688 (ttm) REVERT: D 115 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8597 (t70) REVERT: D 116 GLU cc_start: 0.8778 (pm20) cc_final: 0.8316 (pm20) REVERT: D 117 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7950 (mpp) REVERT: E 1 MET cc_start: 0.8013 (ttt) cc_final: 0.7691 (tpp) REVERT: G 2 ARG cc_start: 0.9006 (mtp180) cc_final: 0.8717 (mtp-110) REVERT: G 108 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9234 (tp) REVERT: I 240 MET cc_start: 0.8976 (ptp) cc_final: 0.8741 (mtt) REVERT: J 125 TYR cc_start: 0.8726 (m-10) cc_final: 0.8415 (m-10) REVERT: J 133 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9309 (pp) REVERT: J 248 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.9003 (t80) REVERT: K 28 HIS cc_start: 0.8543 (m-70) cc_final: 0.8021 (m-70) REVERT: K 139 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8141 (mm) REVERT: L 259 MET cc_start: 0.8334 (mtm) cc_final: 0.7711 (mpp) REVERT: O 27 ASP cc_start: 0.9130 (p0) cc_final: 0.8919 (p0) REVERT: P 249 MET cc_start: 0.8873 (tpp) cc_final: 0.8542 (tpt) REVERT: R 252 TYR cc_start: 0.9036 (m-80) cc_final: 0.8751 (m-80) REVERT: R 259 MET cc_start: 0.8662 (mtp) cc_final: 0.8314 (ptp) REVERT: S 574 GLN cc_start: 0.9526 (mm-40) cc_final: 0.9305 (mm-40) REVERT: T 574 GLN cc_start: 0.9610 (mm-40) cc_final: 0.9280 (mm-40) REVERT: T 594 GLN cc_start: 0.8939 (pm20) cc_final: 0.8627 (pm20) outliers start: 120 outliers final: 62 residues processed: 360 average time/residue: 0.2020 time to fit residues: 123.2651 Evaluate side-chains 286 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 218 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 248 PHE Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 242 ARG Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 186 ILE Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 596 ASN Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 596 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 175 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 356 optimal weight: 0.0170 chunk 258 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN H 42 ASN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 GLN J 119 HIS K 18 ASN L 93 GLN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 HIS ** R 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 707 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.029251 restraints weight = 293517.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.030241 restraints weight = 172386.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030913 restraints weight = 120687.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.031401 restraints weight = 93643.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.031723 restraints weight = 77896.799| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37649 Z= 0.159 Angle : 0.607 10.209 50804 Z= 0.315 Chirality : 0.041 0.274 5795 Planarity : 0.003 0.036 6452 Dihedral : 5.526 70.186 4919 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.14 % Favored : 92.59 % Rotamer: Outliers : 2.85 % Allowed : 15.35 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.04 (0.13), residues: 4468 helix: 1.81 (0.12), residues: 2092 sheet: 0.26 (0.28), residues: 390 loop : -2.12 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 140 TYR 0.016 0.001 TYR O 178 PHE 0.013 0.001 PHE O 221 TRP 0.035 0.002 TRP J 3 HIS 0.005 0.001 HIS L 119 Details of bonding type rmsd covalent geometry : bond 0.00346 (37649) covalent geometry : angle 0.60664 (50804) hydrogen bonds : bond 0.04131 ( 1673) hydrogen bonds : angle 4.30160 ( 4851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 232 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 GLU cc_start: 0.8801 (pm20) cc_final: 0.8578 (pm20) REVERT: D 117 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8163 (mpp) REVERT: G 2 ARG cc_start: 0.9020 (mtp180) cc_final: 0.8727 (mtp-110) REVERT: G 117 MET cc_start: 0.9067 (mpp) cc_final: 0.8816 (mpp) REVERT: H 86 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: H 117 MET cc_start: 0.8757 (mpp) cc_final: 0.8344 (mpp) REVERT: H 213 TYR cc_start: 0.8356 (m-10) cc_final: 0.8068 (m-10) REVERT: J 125 TYR cc_start: 0.8708 (m-10) cc_final: 0.8339 (m-10) REVERT: K 139 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (mm) REVERT: L 196 CYS cc_start: 0.7903 (t) cc_final: 0.7699 (t) REVERT: O 218 MET cc_start: 0.8791 (ptt) cc_final: 0.8515 (ptt) REVERT: O 285 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: P 249 MET cc_start: 0.8868 (tpp) cc_final: 0.8490 (tpt) REVERT: Q 196 CYS cc_start: 0.7974 (t) cc_final: 0.7646 (t) REVERT: R 183 LEU cc_start: 0.9645 (tt) cc_final: 0.9290 (tp) REVERT: R 218 MET cc_start: 0.9091 (ptp) cc_final: 0.8777 (mtp) REVERT: R 252 TYR cc_start: 0.9089 (m-80) cc_final: 0.8747 (m-80) REVERT: R 261 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8979 (mp) REVERT: S 574 GLN cc_start: 0.9572 (mm-40) cc_final: 0.9300 (mm-40) REVERT: S 593 ASP cc_start: 0.9325 (m-30) cc_final: 0.8992 (t0) REVERT: T 574 GLN cc_start: 0.9619 (mm-40) cc_final: 0.9274 (mm-40) REVERT: T 594 GLN cc_start: 0.8861 (pm20) cc_final: 0.8618 (pm20) REVERT: T 673 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9271 (tppt) outliers start: 116 outliers final: 75 residues processed: 332 average time/residue: 0.1951 time to fit residues: 110.9435 Evaluate side-chains 299 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 186 ILE Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 200 LEU Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 596 ASN Chi-restraints excluded: chain T residue 596 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 278 optimal weight: 20.0000 chunk 378 optimal weight: 0.4980 chunk 161 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 chunk 398 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.0050 overall best weight: 3.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.029219 restraints weight = 292756.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.030209 restraints weight = 171584.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030859 restraints weight = 120077.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.031338 restraints weight = 94384.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031679 restraints weight = 78131.006| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37649 Z= 0.135 Angle : 0.587 12.841 50804 Z= 0.302 Chirality : 0.040 0.302 5795 Planarity : 0.003 0.033 6452 Dihedral : 5.239 71.141 4909 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 2.95 % Allowed : 15.67 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.12 (0.13), residues: 4468 helix: 1.85 (0.12), residues: 2091 sheet: 0.33 (0.28), residues: 390 loop : -2.05 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 661 TYR 0.020 0.001 TYR Q 178 PHE 0.011 0.001 PHE O 221 TRP 0.019 0.001 TRP I 96 HIS 0.004 0.001 HIS L 119 Details of bonding type rmsd covalent geometry : bond 0.00294 (37649) covalent geometry : angle 0.58665 (50804) hydrogen bonds : bond 0.03821 ( 1673) hydrogen bonds : angle 4.19545 ( 4851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 225 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8261 (mmt90) REVERT: D 117 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8163 (mpp) REVERT: G 2 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8723 (mtp-110) REVERT: H 86 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: H 213 TYR cc_start: 0.8476 (m-10) cc_final: 0.8226 (m-10) REVERT: I 28 HIS cc_start: 0.9163 (m90) cc_final: 0.8742 (m-70) REVERT: J 125 TYR cc_start: 0.8737 (m-10) cc_final: 0.8381 (m-10) REVERT: K 28 HIS cc_start: 0.8396 (m-70) cc_final: 0.7746 (m-70) REVERT: K 139 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8279 (mm) REVERT: L 196 CYS cc_start: 0.7794 (t) cc_final: 0.7517 (t) REVERT: L 240 MET cc_start: 0.9211 (ppp) cc_final: 0.8659 (pmm) REVERT: O 203 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8515 (mmmm) REVERT: O 218 MET cc_start: 0.8806 (ptt) cc_final: 0.8499 (ptt) REVERT: O 285 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: P 218 MET cc_start: 0.8166 (ppp) cc_final: 0.7895 (ppp) REVERT: P 249 MET cc_start: 0.8830 (tpp) cc_final: 0.8440 (tpt) REVERT: P 252 TYR cc_start: 0.8562 (m-80) cc_final: 0.8095 (m-80) REVERT: Q 178 TYR cc_start: 0.9178 (m-80) cc_final: 0.8920 (m-80) REVERT: Q 196 CYS cc_start: 0.7972 (t) cc_final: 0.7600 (t) REVERT: R 52 MET cc_start: 0.8707 (tpp) cc_final: 0.8487 (tpp) REVERT: R 183 LEU cc_start: 0.9640 (tt) cc_final: 0.9271 (tp) REVERT: R 218 MET cc_start: 0.9044 (ptp) cc_final: 0.8690 (mtp) REVERT: R 252 TYR cc_start: 0.9123 (m-80) cc_final: 0.8259 (m-10) REVERT: R 261 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8237 (mm) REVERT: S 574 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9274 (mm-40) REVERT: S 593 ASP cc_start: 0.9291 (m-30) cc_final: 0.8965 (t0) REVERT: T 574 GLN cc_start: 0.9622 (mm-40) cc_final: 0.9278 (mm-40) outliers start: 120 outliers final: 84 residues processed: 329 average time/residue: 0.1933 time to fit residues: 109.5090 Evaluate side-chains 298 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 208 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 186 ILE Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 193 GLN Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 624 LEU Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 278 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 68 optimal weight: 0.0070 chunk 267 optimal weight: 20.0000 overall best weight: 8.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 211 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN H 42 ASN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 HIS ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN Q 84 HIS ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.040459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.027982 restraints weight = 302673.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.028922 restraints weight = 177617.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.029541 restraints weight = 124661.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.029987 restraints weight = 98335.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.030270 restraints weight = 82194.904| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 37649 Z= 0.263 Angle : 0.672 10.047 50804 Z= 0.345 Chirality : 0.041 0.306 5795 Planarity : 0.003 0.031 6452 Dihedral : 5.330 72.920 4905 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.26 % Favored : 91.52 % Rotamer: Outliers : 3.73 % Allowed : 15.99 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.09 (0.13), residues: 4468 helix: 1.67 (0.12), residues: 2099 sheet: -0.06 (0.27), residues: 414 loop : -2.12 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 641 TYR 0.016 0.001 TYR D 172 PHE 0.016 0.001 PHE P 211 TRP 0.019 0.001 TRP I 96 HIS 0.009 0.001 HIS H 115 Details of bonding type rmsd covalent geometry : bond 0.00564 (37649) covalent geometry : angle 0.67217 (50804) hydrogen bonds : bond 0.04187 ( 1673) hydrogen bonds : angle 4.45473 ( 4851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 198 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8404 (tpp) cc_final: 0.7408 (tpp) REVERT: D 117 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8447 (mpp) REVERT: G 2 ARG cc_start: 0.9056 (mtp180) cc_final: 0.8730 (mtp-110) REVERT: G 150 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8685 (tm-30) REVERT: I 28 HIS cc_start: 0.9236 (m90) cc_final: 0.8948 (m90) REVERT: J 125 TYR cc_start: 0.8889 (m-10) cc_final: 0.8535 (m-10) REVERT: K 28 HIS cc_start: 0.8574 (m-70) cc_final: 0.7962 (m-70) REVERT: K 139 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8532 (mm) REVERT: L 196 CYS cc_start: 0.7812 (t) cc_final: 0.7576 (t) REVERT: L 212 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7484 (p0) REVERT: O 203 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (mmmm) REVERT: O 218 MET cc_start: 0.8962 (ptt) cc_final: 0.8676 (ptt) REVERT: P 249 MET cc_start: 0.8812 (tpp) cc_final: 0.8361 (tpt) REVERT: P 259 MET cc_start: 0.9222 (mtm) cc_final: 0.8881 (pmm) REVERT: Q 178 TYR cc_start: 0.9256 (m-80) cc_final: 0.9013 (m-80) REVERT: Q 196 CYS cc_start: 0.8031 (t) cc_final: 0.7803 (t) REVERT: R 140 ARG cc_start: 0.9610 (OUTLIER) cc_final: 0.9330 (ttp-110) REVERT: R 183 LEU cc_start: 0.9648 (tt) cc_final: 0.9240 (tp) REVERT: R 218 MET cc_start: 0.8998 (ptp) cc_final: 0.8611 (mtp) REVERT: R 252 TYR cc_start: 0.9118 (m-80) cc_final: 0.8374 (m-80) REVERT: R 261 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8179 (mm) REVERT: S 574 GLN cc_start: 0.9614 (mm-40) cc_final: 0.9271 (mm-40) REVERT: S 593 ASP cc_start: 0.9346 (m-30) cc_final: 0.8966 (t0) REVERT: T 574 GLN cc_start: 0.9636 (mm-40) cc_final: 0.9256 (mm-40) REVERT: T 673 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9213 (tppt) outliers start: 152 outliers final: 100 residues processed: 331 average time/residue: 0.1894 time to fit residues: 108.5938 Evaluate side-chains 299 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 193 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 186 ILE Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 624 LEU Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 412 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN R 18 ASN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.040640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.028192 restraints weight = 301435.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.029149 restraints weight = 176946.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.029805 restraints weight = 124743.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.030227 restraints weight = 96943.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030570 restraints weight = 81729.624| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37649 Z= 0.171 Angle : 0.617 10.834 50804 Z= 0.315 Chirality : 0.041 0.313 5795 Planarity : 0.003 0.044 6452 Dihedral : 5.264 72.852 4905 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer: Outliers : 3.24 % Allowed : 16.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.01 (0.13), residues: 4468 helix: 1.75 (0.11), residues: 2099 sheet: -0.07 (0.27), residues: 414 loop : -2.08 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 147 TYR 0.020 0.001 TYR O 178 PHE 0.011 0.001 PHE P 211 TRP 0.029 0.001 TRP I 96 HIS 0.004 0.001 HIS H 115 Details of bonding type rmsd covalent geometry : bond 0.00372 (37649) covalent geometry : angle 0.61677 (50804) hydrogen bonds : bond 0.03863 ( 1673) hydrogen bonds : angle 4.26741 ( 4851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 202 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8488 (mpp) REVERT: F 177 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9043 (mt-10) REVERT: G 2 ARG cc_start: 0.9016 (mtp180) cc_final: 0.8724 (mtp-110) REVERT: G 146 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8668 (pt0) REVERT: G 150 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8679 (tm-30) REVERT: H 42 ASN cc_start: 0.7618 (p0) cc_final: 0.7110 (p0) REVERT: J 125 TYR cc_start: 0.8852 (m-10) cc_final: 0.8469 (m-10) REVERT: K 139 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8595 (mm) REVERT: L 240 MET cc_start: 0.9244 (ppp) cc_final: 0.8652 (pmm) REVERT: O 218 MET cc_start: 0.8972 (ptt) cc_final: 0.8647 (ptt) REVERT: P 249 MET cc_start: 0.8750 (tpp) cc_final: 0.8297 (tpt) REVERT: P 259 MET cc_start: 0.9202 (mtm) cc_final: 0.8953 (ptp) REVERT: Q 178 TYR cc_start: 0.9242 (m-80) cc_final: 0.8937 (m-80) REVERT: Q 196 CYS cc_start: 0.8012 (t) cc_final: 0.7722 (t) REVERT: R 140 ARG cc_start: 0.9600 (OUTLIER) cc_final: 0.9331 (ttp-110) REVERT: R 183 LEU cc_start: 0.9651 (tt) cc_final: 0.9186 (tp) REVERT: R 218 MET cc_start: 0.9002 (ptp) cc_final: 0.8583 (mtp) REVERT: R 252 TYR cc_start: 0.9122 (m-80) cc_final: 0.8412 (m-10) REVERT: R 261 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8332 (mm) REVERT: S 574 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9263 (mm-40) REVERT: S 593 ASP cc_start: 0.9319 (m-30) cc_final: 0.8929 (t0) REVERT: T 528 MET cc_start: 0.9045 (mmm) cc_final: 0.8691 (mmm) REVERT: T 574 GLN cc_start: 0.9637 (mm-40) cc_final: 0.9239 (mm-40) REVERT: T 673 LYS cc_start: 0.9669 (mmmt) cc_final: 0.9240 (tppt) outliers start: 132 outliers final: 104 residues processed: 319 average time/residue: 0.1953 time to fit residues: 107.6167 Evaluate side-chains 307 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 198 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 186 ILE Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 222 ARG Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 624 LEU Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Chi-restraints excluded: chain T residue 655 VAL Chi-restraints excluded: chain T residue 701 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 332 optimal weight: 5.9990 chunk 359 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 365 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 387 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 ASN ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 HIS ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN P 278 GLN ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.028855 restraints weight = 295714.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029823 restraints weight = 171257.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.030484 restraints weight = 119095.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030948 restraints weight = 91975.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031269 restraints weight = 76278.732| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37649 Z= 0.114 Angle : 0.589 12.736 50804 Z= 0.300 Chirality : 0.040 0.243 5795 Planarity : 0.003 0.037 6452 Dihedral : 5.118 72.236 4905 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.25 % Favored : 92.52 % Rotamer: Outliers : 3.17 % Allowed : 17.14 % Favored : 79.69 % 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: 0.13 (0.13), residues: 4468 helix: 1.86 (0.12), residues: 2096 sheet: 0.02 (0.26), residues: 431 loop : -2.01 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 147 TYR 0.017 0.001 TYR O 178 PHE 0.011 0.001 PHE H 145 TRP 0.048 0.001 TRP I 96 HIS 0.004 0.001 HIS L 119 Details of bonding type rmsd covalent geometry : bond 0.00248 (37649) covalent geometry : angle 0.58853 (50804) hydrogen bonds : bond 0.03537 ( 1673) hydrogen bonds : angle 4.08987 ( 4851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 210 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8545 (mpp) REVERT: F 177 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.9010 (mt-10) REVERT: G 2 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8696 (mtp-110) REVERT: G 146 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8620 (pt0) REVERT: G 150 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8660 (tm-30) REVERT: I 28 HIS cc_start: 0.9131 (m90) cc_final: 0.8843 (m-70) REVERT: I 52 MET cc_start: 0.8981 (mmm) cc_final: 0.8619 (tpt) REVERT: I 259 MET cc_start: 0.8094 (pmm) cc_final: 0.7739 (pmm) REVERT: J 125 TYR cc_start: 0.8807 (m-10) cc_final: 0.8408 (m-10) REVERT: J 259 MET cc_start: 0.6966 (pmm) cc_final: 0.6561 (pmm) REVERT: K 139 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8565 (mm) REVERT: L 212 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7720 (p0) REVERT: O 27 ASP cc_start: 0.8993 (p0) cc_final: 0.8773 (p0) REVERT: O 218 MET cc_start: 0.8960 (ptt) cc_final: 0.8633 (ptt) REVERT: P 249 MET cc_start: 0.8729 (tpp) cc_final: 0.8291 (tpt) REVERT: P 259 MET cc_start: 0.9168 (mtm) cc_final: 0.8966 (ptp) REVERT: Q 135 MET cc_start: 0.7338 (ppp) cc_final: 0.6576 (ppp) REVERT: Q 178 TYR cc_start: 0.9252 (m-80) cc_final: 0.8943 (m-80) REVERT: Q 196 CYS cc_start: 0.7871 (t) cc_final: 0.7598 (t) REVERT: Q 240 MET cc_start: 0.9409 (ptp) cc_final: 0.8922 (ptp) REVERT: R 60 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: R 140 ARG cc_start: 0.9580 (OUTLIER) cc_final: 0.9354 (ttp-110) REVERT: R 183 LEU cc_start: 0.9674 (tt) cc_final: 0.9211 (tp) REVERT: R 218 MET cc_start: 0.8968 (ptp) cc_final: 0.8566 (mtp) REVERT: R 252 TYR cc_start: 0.9129 (m-80) cc_final: 0.8412 (m-10) REVERT: R 261 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8360 (mm) REVERT: S 574 GLN cc_start: 0.9571 (mm-40) cc_final: 0.9223 (mm-40) REVERT: S 593 ASP cc_start: 0.9223 (m-30) cc_final: 0.8871 (t0) REVERT: T 528 MET cc_start: 0.9053 (mmm) cc_final: 0.8683 (mmm) REVERT: T 574 GLN cc_start: 0.9617 (mm-40) cc_final: 0.9201 (mm-40) outliers start: 129 outliers final: 95 residues processed: 323 average time/residue: 0.1946 time to fit residues: 108.8934 Evaluate side-chains 302 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 200 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 193 GLN Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain S residue 586 THR Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 655 VAL Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Chi-restraints excluded: chain T residue 655 VAL Chi-restraints excluded: chain T residue 701 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 271 optimal weight: 0.1980 chunk 422 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 268 optimal weight: 0.2980 chunk 41 optimal weight: 20.0000 chunk 409 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 363 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 93 GLN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.040805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028665 restraints weight = 295388.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029609 restraints weight = 172233.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030256 restraints weight = 120531.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030715 restraints weight = 93735.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031043 restraints weight = 77471.148| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37649 Z= 0.133 Angle : 0.602 11.509 50804 Z= 0.305 Chirality : 0.040 0.265 5795 Planarity : 0.003 0.040 6452 Dihedral : 5.025 72.788 4901 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.63 % Favored : 92.17 % Rotamer: Outliers : 3.05 % Allowed : 17.51 % Favored : 79.44 % 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: 0.14 (0.13), residues: 4468 helix: 1.85 (0.12), residues: 2096 sheet: -0.07 (0.26), residues: 439 loop : -1.98 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 147 TYR 0.024 0.001 TYR D 110 PHE 0.010 0.001 PHE H 145 TRP 0.055 0.001 TRP I 96 HIS 0.003 0.001 HIS H 115 Details of bonding type rmsd covalent geometry : bond 0.00290 (37649) covalent geometry : angle 0.60159 (50804) hydrogen bonds : bond 0.03557 ( 1673) hydrogen bonds : angle 4.09883 ( 4851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 203 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8551 (mpp) REVERT: F 177 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9018 (mt-10) REVERT: G 2 ARG cc_start: 0.8952 (mtp180) cc_final: 0.8696 (mtp-110) REVERT: G 146 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8618 (pt0) REVERT: G 150 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8670 (tm-30) REVERT: I 28 HIS cc_start: 0.9160 (m90) cc_final: 0.8892 (m-70) REVERT: I 52 MET cc_start: 0.9013 (mmm) cc_final: 0.8642 (tpt) REVERT: J 125 TYR cc_start: 0.8890 (m-10) cc_final: 0.8481 (m-10) REVERT: J 233 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8700 (mtm180) REVERT: J 259 MET cc_start: 0.6782 (pmm) cc_final: 0.6464 (pmm) REVERT: K 139 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8648 (mm) REVERT: L 105 TRP cc_start: 0.9541 (OUTLIER) cc_final: 0.9320 (t-100) REVERT: P 249 MET cc_start: 0.8728 (tpp) cc_final: 0.8286 (tpt) REVERT: P 259 MET cc_start: 0.9156 (mtm) cc_final: 0.8901 (ptp) REVERT: Q 178 TYR cc_start: 0.9230 (m-80) cc_final: 0.8848 (m-80) REVERT: Q 196 CYS cc_start: 0.7878 (t) cc_final: 0.7608 (t) REVERT: R 52 MET cc_start: 0.8790 (tpp) cc_final: 0.8537 (tpp) REVERT: R 140 ARG cc_start: 0.9576 (OUTLIER) cc_final: 0.9345 (ttp-110) REVERT: R 183 LEU cc_start: 0.9674 (tt) cc_final: 0.9188 (tp) REVERT: R 218 MET cc_start: 0.8962 (ptp) cc_final: 0.8522 (mtp) REVERT: R 252 TYR cc_start: 0.9135 (m-80) cc_final: 0.8394 (m-10) REVERT: R 261 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8333 (mm) REVERT: S 574 GLN cc_start: 0.9583 (mm-40) cc_final: 0.9230 (mm-40) REVERT: S 593 ASP cc_start: 0.9236 (m-30) cc_final: 0.8866 (t0) REVERT: T 528 MET cc_start: 0.9105 (mmm) cc_final: 0.8892 (mmm) REVERT: T 574 GLN cc_start: 0.9635 (mm-40) cc_final: 0.9237 (mm-40) REVERT: T 625 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8788 (tm-30) outliers start: 124 outliers final: 100 residues processed: 312 average time/residue: 0.1934 time to fit residues: 105.2944 Evaluate side-chains 304 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 197 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 TRP Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 222 ARG Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 193 GLN Chi-restraints excluded: chain R residue 212 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 263 ASN Chi-restraints excluded: chain S residue 586 THR Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 655 VAL Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Chi-restraints excluded: chain T residue 655 VAL Chi-restraints excluded: chain T residue 701 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 226 optimal weight: 0.0470 chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 GLN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.028304 restraints weight = 303535.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029233 restraints weight = 177333.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029878 restraints weight = 124054.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030326 restraints weight = 96297.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030596 restraints weight = 80088.230| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37649 Z= 0.167 Angle : 0.626 11.789 50804 Z= 0.317 Chirality : 0.041 0.275 5795 Planarity : 0.003 0.032 6452 Dihedral : 5.024 73.037 4899 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.06 % Favored : 91.74 % Rotamer: Outliers : 3.29 % Allowed : 17.49 % Favored : 79.22 % 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: 0.12 (0.13), residues: 4468 helix: 1.82 (0.12), residues: 2100 sheet: 0.04 (0.27), residues: 414 loop : -1.98 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 147 TYR 0.020 0.001 TYR O 178 PHE 0.011 0.001 PHE L 23 TRP 0.060 0.002 TRP I 96 HIS 0.004 0.001 HIS H 115 Details of bonding type rmsd covalent geometry : bond 0.00365 (37649) covalent geometry : angle 0.62646 (50804) hydrogen bonds : bond 0.03721 ( 1673) hydrogen bonds : angle 4.19704 ( 4851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 202 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9481 (tp) REVERT: D 117 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8566 (mpp) REVERT: F 177 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9076 (mt-10) REVERT: G 2 ARG cc_start: 0.8995 (mtp180) cc_final: 0.8714 (mtp-110) REVERT: G 146 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8694 (pt0) REVERT: G 150 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8705 (tm-30) REVERT: I 28 HIS cc_start: 0.9224 (m90) cc_final: 0.8996 (m-70) REVERT: I 259 MET cc_start: 0.8028 (pmm) cc_final: 0.7684 (pmm) REVERT: J 125 TYR cc_start: 0.8952 (m-10) cc_final: 0.8564 (m-10) REVERT: J 233 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8698 (mtm180) REVERT: K 139 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (mm) REVERT: L 105 TRP cc_start: 0.9567 (OUTLIER) cc_final: 0.9344 (t-100) REVERT: L 212 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7597 (p0) REVERT: O 240 MET cc_start: 0.9543 (ptt) cc_final: 0.9290 (ptp) REVERT: P 249 MET cc_start: 0.8722 (tpp) cc_final: 0.8278 (tpt) REVERT: P 259 MET cc_start: 0.9186 (mtm) cc_final: 0.8904 (pmm) REVERT: Q 135 MET cc_start: 0.6623 (ppp) cc_final: 0.5995 (ppp) REVERT: Q 178 TYR cc_start: 0.9253 (m-80) cc_final: 0.8862 (m-80) REVERT: Q 196 CYS cc_start: 0.7933 (t) cc_final: 0.7644 (t) REVERT: Q 253 MET cc_start: 0.9513 (tpp) cc_final: 0.9169 (tpp) REVERT: R 52 MET cc_start: 0.8844 (tpp) cc_final: 0.8585 (tpp) REVERT: R 60 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: R 140 ARG cc_start: 0.9602 (OUTLIER) cc_final: 0.9354 (ttp-110) REVERT: R 252 TYR cc_start: 0.9148 (m-80) cc_final: 0.8419 (m-10) REVERT: R 259 MET cc_start: 0.9039 (ptp) cc_final: 0.8749 (pmm) REVERT: R 261 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8368 (mm) REVERT: S 574 GLN cc_start: 0.9605 (mm-40) cc_final: 0.9236 (mm-40) REVERT: S 593 ASP cc_start: 0.9292 (m-30) cc_final: 0.8880 (t0) REVERT: T 528 MET cc_start: 0.9122 (mmm) cc_final: 0.8890 (mmm) REVERT: T 574 GLN cc_start: 0.9644 (mm-40) cc_final: 0.9214 (mm-40) REVERT: T 625 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8815 (tm-30) outliers start: 134 outliers final: 105 residues processed: 320 average time/residue: 0.1907 time to fit residues: 105.4810 Evaluate side-chains 308 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 177 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 TRP Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 204 HIS Chi-restraints excluded: chain O residue 233 ARG Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain U residue 106 LEU Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 193 GLN Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 586 THR Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 655 VAL Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Chi-restraints excluded: chain T residue 655 VAL Chi-restraints excluded: chain T residue 701 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 264 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 313 optimal weight: 1.9990 chunk 412 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028526 restraints weight = 297590.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029481 restraints weight = 172893.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030132 restraints weight = 120141.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030588 restraints weight = 92925.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030906 restraints weight = 77054.483| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37649 Z= 0.131 Angle : 0.647 15.391 50804 Z= 0.323 Chirality : 0.041 0.331 5795 Planarity : 0.003 0.050 6452 Dihedral : 4.988 72.632 4899 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 2.85 % Allowed : 18.15 % Favored : 79.00 % 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: 0.15 (0.13), residues: 4468 helix: 1.83 (0.12), residues: 2095 sheet: 0.07 (0.27), residues: 432 loop : -1.95 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 222 TYR 0.020 0.001 TYR G 157 PHE 0.012 0.001 PHE H 145 TRP 0.060 0.001 TRP I 96 HIS 0.002 0.001 HIS L 84 Details of bonding type rmsd covalent geometry : bond 0.00286 (37649) covalent geometry : angle 0.64724 (50804) hydrogen bonds : bond 0.03601 ( 1673) hydrogen bonds : angle 4.13500 ( 4851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8936 Ramachandran restraints generated. 4468 Oldfield, 0 Emsley, 4468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 201 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9481 (tp) REVERT: D 117 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: G 2 ARG cc_start: 0.8928 (mtp180) cc_final: 0.8670 (mtp-110) REVERT: G 146 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8620 (pt0) REVERT: G 150 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8676 (tm-30) REVERT: I 28 HIS cc_start: 0.9181 (m90) cc_final: 0.8958 (m-70) REVERT: I 240 MET cc_start: 0.9359 (mtm) cc_final: 0.9085 (mpp) REVERT: I 259 MET cc_start: 0.7993 (pmm) cc_final: 0.7690 (pmm) REVERT: J 125 TYR cc_start: 0.8918 (m-10) cc_final: 0.8525 (m-10) REVERT: J 233 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8691 (mtm180) REVERT: K 139 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (mm) REVERT: L 105 TRP cc_start: 0.9535 (OUTLIER) cc_final: 0.9313 (t-100) REVERT: L 212 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7601 (p0) REVERT: O 27 ASP cc_start: 0.8956 (p0) cc_final: 0.8699 (p0) REVERT: P 249 MET cc_start: 0.8721 (tpp) cc_final: 0.8286 (tpt) REVERT: P 259 MET cc_start: 0.9148 (mtm) cc_final: 0.8865 (ptp) REVERT: Q 135 MET cc_start: 0.6795 (ppp) cc_final: 0.6335 (ppp) REVERT: Q 178 TYR cc_start: 0.9275 (m-80) cc_final: 0.8908 (m-80) REVERT: Q 196 CYS cc_start: 0.7943 (t) cc_final: 0.7619 (t) REVERT: Q 253 MET cc_start: 0.9494 (tpp) cc_final: 0.9166 (tpp) REVERT: R 52 MET cc_start: 0.8808 (tpp) cc_final: 0.8548 (tpp) REVERT: R 60 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8768 (tm-30) REVERT: R 183 LEU cc_start: 0.9669 (tp) cc_final: 0.9466 (tt) REVERT: R 252 TYR cc_start: 0.9131 (m-80) cc_final: 0.8410 (m-10) REVERT: R 259 MET cc_start: 0.8908 (ptp) cc_final: 0.8490 (pmm) REVERT: R 261 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8513 (mm) REVERT: S 574 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9215 (mm-40) REVERT: S 593 ASP cc_start: 0.9217 (m-30) cc_final: 0.8870 (t0) REVERT: T 528 MET cc_start: 0.9139 (mmm) cc_final: 0.8910 (mmm) REVERT: T 574 GLN cc_start: 0.9626 (mm-40) cc_final: 0.9194 (mm-40) REVERT: T 625 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8794 (tm-30) outliers start: 116 outliers final: 100 residues processed: 301 average time/residue: 0.1832 time to fit residues: 95.5152 Evaluate side-chains 302 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 194 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain E residue 36 TYR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 81 TYR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain I residue 204 HIS Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 233 ARG Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 283 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 81 TYR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 187 PHE Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 263 ASN Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 TRP Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 212 ASN Chi-restraints excluded: chain L residue 231 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 81 TYR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 233 ARG Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain O residue 285 GLU Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 38 ASP Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 202 LEU Chi-restraints excluded: chain P residue 213 LEU Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 253 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 193 GLN Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 586 THR Chi-restraints excluded: chain S residue 610 LEU Chi-restraints excluded: chain S residue 655 VAL Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain T residue 530 PHE Chi-restraints excluded: chain T residue 596 ASN Chi-restraints excluded: chain T residue 610 LEU Chi-restraints excluded: chain T residue 655 VAL Chi-restraints excluded: chain T residue 701 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 383 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 380 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.028494 restraints weight = 299705.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029447 restraints weight = 173899.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030111 restraints weight = 120857.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030560 restraints weight = 93153.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030880 restraints weight = 77260.339| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37649 Z= 0.132 Angle : 0.635 12.667 50804 Z= 0.320 Chirality : 0.041 0.319 5795 Planarity : 0.003 0.038 6452 Dihedral : 4.978 72.665 4898 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.68 % Favored : 92.10 % Rotamer: Outliers : 2.85 % Allowed : 18.27 % Favored : 78.88 % 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: 0.18 (0.13), residues: 4468 helix: 1.85 (0.12), residues: 2091 sheet: 0.07 (0.27), residues: 432 loop : -1.92 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 222 TYR 0.027 0.001 TYR O 178 PHE 0.012 0.001 PHE H 145 TRP 0.058 0.001 TRP I 96 HIS 0.005 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00288 (37649) covalent geometry : angle 0.63461 (50804) hydrogen bonds : bond 0.03553 ( 1673) hydrogen bonds : angle 4.13050 ( 4851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.10 seconds wall clock time: 98 minutes 6.53 seconds (5886.53 seconds total)