Starting phenix.real_space_refine on Mon Apr 6 07:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7k_63685/04_2026/9m7k_63685.map" } resolution = 3.44 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= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 80 5.16 5 C 10475 2.51 5 N 2817 2.21 5 O 3199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16599 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2308 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2292 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2334 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2347 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2344 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "E" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2342 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2328 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.09, per 1000 atoms: 0.25 Number of scatterers: 16599 At special positions: 0 Unit cell: (117.67, 132.43, 136.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 21 15.00 Mg 7 11.99 O 3199 8.00 N 2817 7.00 C 10475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 735.3 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 64.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.968A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 113 removed outlier: 5.179A pdb=" N TYR G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 113 through 118 removed outlier: 3.656A pdb=" N TYR G 117 " --> pdb=" O MET G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 158 through 163 removed outlier: 4.115A pdb=" N ILE G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET G 163 " --> pdb=" O MET G 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 158 through 163' Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.091A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 226 removed outlier: 3.653A pdb=" N GLY G 222 " --> pdb=" O THR G 218 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 224 " --> pdb=" O TRP G 220 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN G 225 " --> pdb=" O ASP G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 247 Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 3.590A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 310 Processing helix chain 'G' and resid 310 through 318 Processing helix chain 'G' and resid 340 through 346 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.585A pdb=" N ALA A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.552A pdb=" N LEU A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 4.332A pdb=" N ASN A 119 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 120 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.563A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.575A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 294 through 319 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.564A pdb=" N ILE B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 113 removed outlier: 5.369A pdb=" N TYR B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix removed outlier: 3.529A pdb=" N MET B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.991A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 6.898A pdb=" N LEU B 122 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.642A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.820A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.504A pdb=" N ASP B 240 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.523A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 347 removed outlier: 3.595A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.579A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 119 through 124 removed outlier: 6.951A pdb=" N LEU C 122 " --> pdb=" O ASN C 119 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.650A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.854A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.051A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.565A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 5.704A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.891A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.566A pdb=" N ALA D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 66' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.630A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 116 through 124 removed outlier: 4.173A pdb=" N ASN D 119 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 120 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Proline residue: D 121 - end of helix removed outlier: 3.846A pdb=" N GLN D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 124' Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.875A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.656A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.003A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 294 through 319 removed outlier: 5.341A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 66 Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 113 removed outlier: 5.471A pdb=" N TYR E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.601A pdb=" N TYR E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 4.046A pdb=" N GLN E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.055A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.995A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 319 Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.775A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 113 removed outlier: 5.652A pdb=" N TYR F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.895A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 6.683A pdb=" N LEU F 122 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.954A pdb=" N GLY F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.074A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.610A pdb=" N THR F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.921A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 80 through 81 removed outlier: 4.007A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN G 153 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE G 190 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE G 155 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP G 192 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET G 230 " --> pdb=" O CYS G 187 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL G 129 " --> pdb=" O GLY G 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 251 " --> pdb=" O GLY G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 5.786A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 233 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.826A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.995A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 157 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS C 187 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE C 232 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 189 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA C 234 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE C 191 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.703A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE D 157 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS D 187 " --> pdb=" O MET D 230 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE D 232 " --> pdb=" O CYS D 187 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE D 189 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA D 234 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 191 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 129 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR D 235 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 131 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.070A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE E 157 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS E 187 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE E 232 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 189 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA E 234 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE E 191 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.150A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 157 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 234 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2292 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: 2.51 Time building geometry restraints manager: 1.78 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: 5182 1.34 - 1.46: 2747 1.46 - 1.58: 8779 1.58 - 1.70: 20 1.70 - 1.82: 139 Bond restraints: 16867 Sorted by residual: bond pdb=" C PRO G 338 " pdb=" N LEU G 339 " ideal model delta sigma weight residual 1.330 1.386 -0.056 1.32e-02 5.74e+03 1.77e+01 bond pdb=" C LEU G 339 " pdb=" N LYS G 340 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.37e-02 5.33e+03 8.96e+00 bond pdb=" CA SER C 156 " pdb=" C SER C 156 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.27e-02 6.20e+03 8.35e+00 bond pdb=" CG LEU A 198 " pdb=" CD1 LEU A 198 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.91e+00 bond pdb=" CA ILE C 157 " pdb=" C ILE C 157 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.28e-02 6.10e+03 6.51e+00 ... (remaining 16862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 22225 2.33 - 4.65: 438 4.65 - 6.98: 79 6.98 - 9.30: 25 9.30 - 11.63: 11 Bond angle restraints: 22778 Sorted by residual: angle pdb=" N LEU E 146 " pdb=" CA LEU E 146 " pdb=" C LEU E 146 " ideal model delta sigma weight residual 111.07 105.81 5.26 1.07e+00 8.73e-01 2.42e+01 angle pdb=" N TYR E 264 " pdb=" CA TYR E 264 " pdb=" C TYR E 264 " ideal model delta sigma weight residual 111.07 105.85 5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" N GLU G 149 " pdb=" CA GLU G 149 " pdb=" C GLU G 149 " ideal model delta sigma weight residual 111.28 116.26 -4.98 1.09e+00 8.42e-01 2.09e+01 angle pdb=" N ASN F 153 " pdb=" CA ASN F 153 " pdb=" C ASN F 153 " ideal model delta sigma weight residual 110.10 103.69 6.41 1.49e+00 4.50e-01 1.85e+01 angle pdb=" C SER C 156 " pdb=" N ILE C 157 " pdb=" CA ILE C 157 " ideal model delta sigma weight residual 122.43 114.71 7.72 1.81e+00 3.05e-01 1.82e+01 ... (remaining 22773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8813 17.96 - 35.92: 1323 35.92 - 53.89: 361 53.89 - 71.85: 75 71.85 - 89.81: 31 Dihedral angle restraints: 10603 sinusoidal: 4534 harmonic: 6069 Sorted by residual: dihedral pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" N PHE B 154 " pdb=" CA PHE B 154 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ILE B 157 " pdb=" C ILE B 157 " pdb=" N ARG B 158 " pdb=" CA ARG B 158 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" N ILE C 157 " pdb=" C ILE C 157 " pdb=" CA ILE C 157 " pdb=" CB ILE C 157 " ideal model delta harmonic sigma weight residual 123.40 133.55 -10.15 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 10600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2346 0.085 - 0.170: 242 0.170 - 0.255: 12 0.255 - 0.340: 2 0.340 - 0.425: 1 Chirality restraints: 2603 Sorted by residual: chirality pdb=" CA ILE C 157 " pdb=" N ILE C 157 " pdb=" C ILE C 157 " pdb=" CB ILE C 157 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA GLU F 149 " pdb=" N GLU F 149 " pdb=" C GLU F 149 " pdb=" CB GLU F 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ASP G 343 " pdb=" N ASP G 343 " pdb=" C ASP G 343 " pdb=" CB ASP G 343 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2600 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 167 " -0.020 2.00e-02 2.50e+03 1.75e-02 6.10e+00 pdb=" CG TYR B 167 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B 167 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 167 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 167 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 167 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 167 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 167 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 148 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C LYS F 148 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS F 148 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU F 149 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 104 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C HIS A 104 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 104 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 105 " -0.014 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 141 2.54 - 3.13: 12639 3.13 - 3.72: 28239 3.72 - 4.31: 37457 4.31 - 4.90: 62031 Nonbonded interactions: 140507 Sorted by model distance: nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 403 " model vdw 1.955 2.170 nonbonded pdb=" O1B ATP G 401 " pdb="MG MG F 401 " model vdw 2.014 2.170 nonbonded pdb=" O1G ATP C 401 " pdb="MG MG C 402 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.029 2.170 nonbonded pdb="MG MG A 403 " pdb=" O1B ATP B 401 " model vdw 2.032 2.170 ... (remaining 140502 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' and resid 43 through 349) selection = (chain 'B' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'C' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'D' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'E' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'F' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'G' and (resid 43 through 319 or resid 337 through 349)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.020 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.080 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16867 Z= 0.223 Angle : 0.837 11.627 22778 Z= 0.429 Chirality : 0.050 0.425 2603 Planarity : 0.005 0.049 2858 Dihedral : 18.752 89.810 6649 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.55 % Allowed : 28.23 % Favored : 71.22 % 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: -0.07 (0.18), residues: 2037 helix: 0.20 (0.15), residues: 1097 sheet: -0.04 (0.46), residues: 137 loop : -0.18 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 252 TYR 0.042 0.002 TYR B 167 PHE 0.014 0.002 PHE C 154 TRP 0.016 0.001 TRP A 220 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00474 (16867) covalent geometry : angle 0.83708 (22778) hydrogen bonds : bond 0.16227 ( 799) hydrogen bonds : angle 6.06434 ( 2292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 381 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 CYS cc_start: 0.8161 (m) cc_final: 0.7929 (m) REVERT: G 313 TYR cc_start: 0.7921 (t80) cc_final: 0.7259 (t80) REVERT: A 88 ILE cc_start: 0.7727 (mm) cc_final: 0.7513 (mt) REVERT: A 139 LYS cc_start: 0.6750 (mtpt) cc_final: 0.5894 (mptp) REVERT: B 163 MET cc_start: 0.8438 (mmt) cc_final: 0.8139 (mmt) REVERT: B 243 ASP cc_start: 0.8303 (t70) cc_final: 0.7888 (m-30) REVERT: B 264 TYR cc_start: 0.8402 (t80) cc_final: 0.8188 (t80) REVERT: B 342 LYS cc_start: 0.8966 (tttt) cc_final: 0.8573 (tptt) REVERT: F 156 SER cc_start: 0.8466 (t) cc_final: 0.8217 (p) REVERT: F 248 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8369 (mtt90) REVERT: F 347 LYS cc_start: 0.8710 (tppt) cc_final: 0.8408 (mttp) outliers start: 10 outliers final: 4 residues processed: 386 average time/residue: 0.1225 time to fit residues: 73.3344 Evaluate side-chains 345 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 341 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain E residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN G 206 HIS A 50 GLN B 236 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 236 ASN D 262 GLN E 236 ASN F 50 GLN F 236 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.152237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119693 restraints weight = 27080.809| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.62 r_work: 0.3322 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16867 Z= 0.128 Angle : 0.574 9.988 22778 Z= 0.283 Chirality : 0.040 0.136 2603 Planarity : 0.004 0.039 2858 Dihedral : 11.947 89.627 2473 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.51 % Allowed : 27.29 % Favored : 69.19 % 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: 0.76 (0.18), residues: 2037 helix: 0.92 (0.16), residues: 1125 sheet: -0.26 (0.46), residues: 142 loop : 0.25 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 263 TYR 0.019 0.001 TYR C 313 PHE 0.017 0.001 PHE A 154 TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS F 206 Details of bonding type rmsd covalent geometry : bond 0.00291 (16867) covalent geometry : angle 0.57392 (22778) hydrogen bonds : bond 0.03882 ( 799) hydrogen bonds : angle 4.73748 ( 2292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 356 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 192 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: G 275 LYS cc_start: 0.8416 (tptt) cc_final: 0.7572 (mtmt) REVERT: G 311 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8496 (pttp) REVERT: G 313 TYR cc_start: 0.7955 (t80) cc_final: 0.7263 (t80) REVERT: A 47 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7490 (mppt) REVERT: A 88 ILE cc_start: 0.7867 (mm) cc_final: 0.7634 (mt) REVERT: A 124 GLN cc_start: 0.8313 (mt0) cc_final: 0.7669 (mm-40) REVERT: A 139 LYS cc_start: 0.7009 (mtpt) cc_final: 0.6588 (mttp) REVERT: A 219 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 224 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6489 (mm) REVERT: B 342 LYS cc_start: 0.8856 (tttt) cc_final: 0.8445 (tptt) REVERT: D 289 ASN cc_start: 0.8693 (m-40) cc_final: 0.8386 (m-40) REVERT: F 273 ASP cc_start: 0.7477 (t0) cc_final: 0.7199 (t0) REVERT: F 347 LYS cc_start: 0.8614 (tppt) cc_final: 0.8395 (mttp) outliers start: 64 outliers final: 30 residues processed: 391 average time/residue: 0.1196 time to fit residues: 73.0428 Evaluate side-chains 363 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 330 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 192 ASP Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN D 262 GLN D 284 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112483 restraints weight = 27238.331| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.66 r_work: 0.3266 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16867 Z= 0.171 Angle : 0.574 9.013 22778 Z= 0.281 Chirality : 0.041 0.266 2603 Planarity : 0.004 0.038 2858 Dihedral : 11.396 83.419 2469 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.73 % Allowed : 27.57 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 2037 helix: 1.24 (0.16), residues: 1125 sheet: -0.36 (0.45), residues: 146 loop : 0.42 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 252 TYR 0.014 0.001 TYR B 167 PHE 0.019 0.001 PHE G 190 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00407 (16867) covalent geometry : angle 0.57365 (22778) hydrogen bonds : bond 0.03586 ( 799) hydrogen bonds : angle 4.60763 ( 2292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: G 103 LEU cc_start: 0.9115 (tp) cc_final: 0.8905 (tt) REVERT: G 275 LYS cc_start: 0.8462 (tptt) cc_final: 0.7635 (mtmt) REVERT: G 311 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8489 (pttp) REVERT: G 313 TYR cc_start: 0.7981 (t80) cc_final: 0.7272 (t80) REVERT: A 88 ILE cc_start: 0.7964 (mm) cc_final: 0.7635 (mt) REVERT: A 124 GLN cc_start: 0.8360 (mt0) cc_final: 0.7680 (mm-40) REVERT: A 139 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6668 (mttp) REVERT: A 141 MET cc_start: 0.8789 (mmm) cc_final: 0.8237 (mtp) REVERT: A 219 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 113 MET cc_start: 0.8810 (ptp) cc_final: 0.8589 (ptp) REVERT: B 342 LYS cc_start: 0.8872 (tttt) cc_final: 0.8421 (tptt) REVERT: D 91 GLN cc_start: 0.8875 (mp10) cc_final: 0.8642 (mp10) REVERT: D 108 ILE cc_start: 0.9084 (mm) cc_final: 0.8830 (mm) REVERT: D 265 LYS cc_start: 0.8952 (mttp) cc_final: 0.8186 (tttp) REVERT: D 273 ASP cc_start: 0.8074 (t70) cc_final: 0.7872 (t70) REVERT: D 289 ASN cc_start: 0.8674 (m-40) cc_final: 0.8402 (m-40) REVERT: E 344 PHE cc_start: 0.8342 (m-80) cc_final: 0.8132 (m-80) REVERT: F 273 ASP cc_start: 0.7579 (t0) cc_final: 0.7294 (t0) REVERT: F 347 LYS cc_start: 0.8624 (tppt) cc_final: 0.8397 (mttp) outliers start: 68 outliers final: 32 residues processed: 381 average time/residue: 0.1206 time to fit residues: 71.4719 Evaluate side-chains 357 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 142 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN B 50 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN E 262 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114460 restraints weight = 27080.760| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.66 r_work: 0.3296 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16867 Z= 0.122 Angle : 0.543 9.471 22778 Z= 0.265 Chirality : 0.040 0.174 2603 Planarity : 0.003 0.039 2858 Dihedral : 10.982 82.465 2467 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.29 % Allowed : 28.06 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 2037 helix: 1.39 (0.16), residues: 1118 sheet: -0.51 (0.44), residues: 154 loop : 0.51 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 263 TYR 0.020 0.001 TYR B 167 PHE 0.017 0.001 PHE G 190 TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00288 (16867) covalent geometry : angle 0.54311 (22778) hydrogen bonds : bond 0.03245 ( 799) hydrogen bonds : angle 4.51599 ( 2292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 343 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7795 (tp-100) REVERT: G 275 LYS cc_start: 0.8473 (tptt) cc_final: 0.7528 (mmtt) REVERT: G 311 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8492 (pttp) REVERT: G 313 TYR cc_start: 0.7983 (t80) cc_final: 0.7289 (t80) REVERT: A 88 ILE cc_start: 0.7967 (mm) cc_final: 0.7671 (mt) REVERT: A 124 GLN cc_start: 0.8339 (mt0) cc_final: 0.7668 (mm-40) REVERT: A 139 LYS cc_start: 0.7087 (mtpt) cc_final: 0.6816 (mttp) REVERT: A 141 MET cc_start: 0.8794 (mmm) cc_final: 0.8274 (mtp) REVERT: A 219 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8771 (mm) REVERT: B 113 MET cc_start: 0.8856 (ptp) cc_final: 0.8508 (ptp) REVERT: B 342 LYS cc_start: 0.8808 (tttt) cc_final: 0.8381 (tptt) REVERT: D 91 GLN cc_start: 0.8900 (mp10) cc_final: 0.8670 (mp10) REVERT: D 108 ILE cc_start: 0.9074 (mm) cc_final: 0.8807 (mm) REVERT: D 265 LYS cc_start: 0.8946 (mttp) cc_final: 0.8244 (tttp) REVERT: D 289 ASN cc_start: 0.8686 (m-40) cc_final: 0.8418 (m-40) REVERT: E 344 PHE cc_start: 0.8271 (m-80) cc_final: 0.8015 (m-80) REVERT: F 273 ASP cc_start: 0.7597 (t0) cc_final: 0.7299 (t0) REVERT: F 347 LYS cc_start: 0.8592 (tppt) cc_final: 0.8273 (mttp) outliers start: 60 outliers final: 36 residues processed: 376 average time/residue: 0.1228 time to fit residues: 71.6903 Evaluate side-chains 355 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 318 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN G 284 GLN A 50 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 284 GLN E 262 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114697 restraints weight = 26871.579| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.63 r_work: 0.3282 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16867 Z= 0.133 Angle : 0.547 10.062 22778 Z= 0.266 Chirality : 0.040 0.145 2603 Planarity : 0.003 0.040 2858 Dihedral : 10.765 84.586 2467 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.62 % Allowed : 28.39 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2037 helix: 1.51 (0.16), residues: 1118 sheet: -0.44 (0.44), residues: 159 loop : 0.56 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 263 TYR 0.022 0.001 TYR B 167 PHE 0.020 0.001 PHE G 253 TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00319 (16867) covalent geometry : angle 0.54666 (22778) hydrogen bonds : bond 0.03138 ( 799) hydrogen bonds : angle 4.40995 ( 2292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 336 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7811 (tp40) REVERT: G 275 LYS cc_start: 0.8480 (tptt) cc_final: 0.7594 (mmtt) REVERT: G 298 LEU cc_start: 0.8715 (mt) cc_final: 0.8467 (mt) REVERT: G 313 TYR cc_start: 0.7967 (t80) cc_final: 0.7387 (t80) REVERT: A 47 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7350 (mptt) REVERT: A 88 ILE cc_start: 0.8059 (mm) cc_final: 0.7767 (mt) REVERT: A 124 GLN cc_start: 0.8380 (mt0) cc_final: 0.7697 (mm-40) REVERT: A 141 MET cc_start: 0.8818 (mmm) cc_final: 0.8218 (mtp) REVERT: A 219 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8760 (mm) REVERT: B 342 LYS cc_start: 0.8815 (tttt) cc_final: 0.8436 (tptt) REVERT: D 91 GLN cc_start: 0.8919 (mp10) cc_final: 0.8683 (mp10) REVERT: D 108 ILE cc_start: 0.9080 (mm) cc_final: 0.8822 (mm) REVERT: D 265 LYS cc_start: 0.8950 (mttp) cc_final: 0.8252 (tttp) REVERT: D 289 ASN cc_start: 0.8714 (m-40) cc_final: 0.8396 (m-40) REVERT: E 267 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9080 (mm) REVERT: F 159 MET cc_start: 0.8213 (tpp) cc_final: 0.7918 (mmm) REVERT: F 273 ASP cc_start: 0.7639 (t0) cc_final: 0.7326 (t0) REVERT: F 347 LYS cc_start: 0.8583 (tppt) cc_final: 0.8245 (mttp) outliers start: 66 outliers final: 44 residues processed: 376 average time/residue: 0.1184 time to fit residues: 70.0818 Evaluate side-chains 366 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 119 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN D 284 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114914 restraints weight = 27197.936| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.66 r_work: 0.3264 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16867 Z= 0.151 Angle : 0.559 10.144 22778 Z= 0.271 Chirality : 0.040 0.144 2603 Planarity : 0.003 0.046 2858 Dihedral : 10.656 86.403 2467 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.12 % Allowed : 28.06 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2037 helix: 1.53 (0.16), residues: 1125 sheet: -0.53 (0.43), residues: 159 loop : 0.61 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 263 TYR 0.024 0.001 TYR B 167 PHE 0.014 0.001 PHE A 154 TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00364 (16867) covalent geometry : angle 0.55854 (22778) hydrogen bonds : bond 0.03112 ( 799) hydrogen bonds : angle 4.38637 ( 2292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 331 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7798 (tp40) REVERT: G 275 LYS cc_start: 0.8492 (tptt) cc_final: 0.7635 (mmtt) REVERT: G 298 LEU cc_start: 0.8725 (mt) cc_final: 0.8441 (mt) REVERT: G 313 TYR cc_start: 0.7948 (t80) cc_final: 0.7406 (t80) REVERT: A 124 GLN cc_start: 0.8400 (mt0) cc_final: 0.7708 (mm-40) REVERT: A 141 MET cc_start: 0.8844 (mmm) cc_final: 0.8299 (mtp) REVERT: A 219 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8778 (mm) REVERT: B 60 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8616 (ttp80) REVERT: B 342 LYS cc_start: 0.8803 (tttt) cc_final: 0.8418 (tptt) REVERT: D 91 GLN cc_start: 0.8932 (mp10) cc_final: 0.8703 (mp10) REVERT: D 108 ILE cc_start: 0.9113 (mm) cc_final: 0.8889 (mm) REVERT: D 265 LYS cc_start: 0.8960 (mttp) cc_final: 0.8268 (tttp) REVERT: D 289 ASN cc_start: 0.8741 (m-40) cc_final: 0.8429 (m-40) REVERT: E 262 GLN cc_start: 0.7814 (mt0) cc_final: 0.7183 (mm-40) REVERT: F 262 GLN cc_start: 0.8154 (mp10) cc_final: 0.7675 (mp10) REVERT: F 273 ASP cc_start: 0.7692 (t0) cc_final: 0.7395 (t0) outliers start: 75 outliers final: 46 residues processed: 376 average time/residue: 0.1228 time to fit residues: 72.0826 Evaluate side-chains 364 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 12 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 284 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116452 restraints weight = 27150.585| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.67 r_work: 0.3288 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16867 Z= 0.124 Angle : 0.557 9.918 22778 Z= 0.268 Chirality : 0.040 0.207 2603 Planarity : 0.003 0.044 2858 Dihedral : 10.555 87.058 2467 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.51 % Allowed : 28.45 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 2037 helix: 1.59 (0.16), residues: 1115 sheet: -0.54 (0.43), residues: 159 loop : 0.58 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 263 TYR 0.017 0.001 TYR B 167 PHE 0.013 0.001 PHE A 154 TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00298 (16867) covalent geometry : angle 0.55695 (22778) hydrogen bonds : bond 0.03014 ( 799) hydrogen bonds : angle 4.36798 ( 2292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7806 (tp40) REVERT: G 265 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8618 (mttm) REVERT: G 275 LYS cc_start: 0.8496 (tptt) cc_final: 0.7636 (mmtt) REVERT: G 284 GLN cc_start: 0.8856 (tp40) cc_final: 0.8407 (tp-100) REVERT: G 313 TYR cc_start: 0.7946 (t80) cc_final: 0.7425 (t80) REVERT: A 124 GLN cc_start: 0.8398 (mt0) cc_final: 0.7699 (mm-40) REVERT: A 141 MET cc_start: 0.8850 (mmm) cc_final: 0.8313 (mtp) REVERT: A 219 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 47 LYS cc_start: 0.8846 (mttt) cc_final: 0.8566 (mptt) REVERT: B 60 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8610 (ttp80) REVERT: B 113 MET cc_start: 0.8822 (ptp) cc_final: 0.8494 (ptp) REVERT: B 342 LYS cc_start: 0.8777 (tttt) cc_final: 0.8393 (tptt) REVERT: D 60 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8158 (tpp-160) REVERT: D 91 GLN cc_start: 0.8939 (mp10) cc_final: 0.8698 (mp10) REVERT: D 108 ILE cc_start: 0.9043 (mm) cc_final: 0.8807 (mm) REVERT: D 109 TYR cc_start: 0.8924 (m-80) cc_final: 0.8663 (m-80) REVERT: D 265 LYS cc_start: 0.8949 (mttp) cc_final: 0.8240 (tttp) REVERT: E 267 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9052 (mm) REVERT: F 262 GLN cc_start: 0.8148 (mp10) cc_final: 0.7690 (mp10) REVERT: F 273 ASP cc_start: 0.7720 (t0) cc_final: 0.7396 (t0) outliers start: 64 outliers final: 45 residues processed: 386 average time/residue: 0.1228 time to fit residues: 73.1974 Evaluate side-chains 367 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 307 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 124 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN G 206 HIS A 50 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN D 284 GLN D 289 ASN F 50 GLN F 236 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113371 restraints weight = 27331.854| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.68 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16867 Z= 0.182 Angle : 0.608 9.772 22778 Z= 0.291 Chirality : 0.041 0.204 2603 Planarity : 0.004 0.044 2858 Dihedral : 10.620 89.992 2467 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.73 % Allowed : 29.21 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 2037 helix: 1.57 (0.16), residues: 1121 sheet: -0.43 (0.43), residues: 159 loop : 0.58 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 237 TYR 0.030 0.001 TYR B 167 PHE 0.014 0.001 PHE A 154 TRP 0.008 0.001 TRP E 220 HIS 0.003 0.001 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00440 (16867) covalent geometry : angle 0.60847 (22778) hydrogen bonds : bond 0.03179 ( 799) hydrogen bonds : angle 4.41115 ( 2292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 322 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7788 (tp40) REVERT: G 262 GLN cc_start: 0.8209 (mp10) cc_final: 0.7969 (pm20) REVERT: G 265 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8675 (mttm) REVERT: G 275 LYS cc_start: 0.8524 (tptt) cc_final: 0.7667 (mmtt) REVERT: G 284 GLN cc_start: 0.8842 (tp40) cc_final: 0.8397 (tp-100) REVERT: G 313 TYR cc_start: 0.7927 (t80) cc_final: 0.7289 (t80) REVERT: A 124 GLN cc_start: 0.8429 (mt0) cc_final: 0.7725 (mm-40) REVERT: A 141 MET cc_start: 0.8879 (mmm) cc_final: 0.8330 (mtp) REVERT: A 219 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8817 (mm) REVERT: B 60 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8623 (ttp80) REVERT: B 342 LYS cc_start: 0.8786 (tttt) cc_final: 0.8403 (tptt) REVERT: C 311 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8350 (ptpp) REVERT: D 91 GLN cc_start: 0.8957 (mp10) cc_final: 0.8725 (mp10) REVERT: D 108 ILE cc_start: 0.9056 (mm) cc_final: 0.8837 (mm) REVERT: D 109 TYR cc_start: 0.8960 (m-80) cc_final: 0.8641 (m-80) REVERT: D 265 LYS cc_start: 0.8971 (mttp) cc_final: 0.8285 (tttp) REVERT: D 289 ASN cc_start: 0.8761 (m-40) cc_final: 0.8554 (m-40) REVERT: E 262 GLN cc_start: 0.7913 (mt0) cc_final: 0.7116 (mm-40) REVERT: E 267 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9071 (mm) REVERT: F 262 GLN cc_start: 0.8196 (mp10) cc_final: 0.7735 (mp10) REVERT: F 273 ASP cc_start: 0.7764 (t0) cc_final: 0.7447 (t0) outliers start: 68 outliers final: 45 residues processed: 366 average time/residue: 0.1183 time to fit residues: 68.0267 Evaluate side-chains 366 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 138 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111698 restraints weight = 27061.047| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.67 r_work: 0.3257 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16867 Z= 0.160 Angle : 0.597 9.973 22778 Z= 0.285 Chirality : 0.042 0.200 2603 Planarity : 0.004 0.045 2858 Dihedral : 10.585 89.360 2467 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.29 % Allowed : 29.05 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2037 helix: 1.58 (0.16), residues: 1122 sheet: -0.50 (0.43), residues: 159 loop : 0.60 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 237 TYR 0.019 0.001 TYR B 167 PHE 0.013 0.001 PHE A 154 TRP 0.007 0.001 TRP A 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00390 (16867) covalent geometry : angle 0.59743 (22778) hydrogen bonds : bond 0.03147 ( 799) hydrogen bonds : angle 4.41020 ( 2292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7782 (tp40) REVERT: G 248 ARG cc_start: 0.8299 (mmt90) cc_final: 0.8081 (mmt180) REVERT: G 265 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8683 (mttm) REVERT: G 275 LYS cc_start: 0.8527 (tptt) cc_final: 0.7676 (mmtt) REVERT: G 284 GLN cc_start: 0.8827 (tp40) cc_final: 0.8397 (tp-100) REVERT: G 313 TYR cc_start: 0.7918 (t80) cc_final: 0.7316 (t80) REVERT: A 124 GLN cc_start: 0.8413 (mt0) cc_final: 0.7708 (mm-40) REVERT: A 141 MET cc_start: 0.8891 (mmm) cc_final: 0.8350 (mtp) REVERT: A 219 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8829 (mm) REVERT: B 60 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8609 (ttp80) REVERT: B 113 MET cc_start: 0.8825 (ptp) cc_final: 0.8572 (ptp) REVERT: B 342 LYS cc_start: 0.8784 (tttt) cc_final: 0.8393 (tptt) REVERT: C 311 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8327 (ptpp) REVERT: D 91 GLN cc_start: 0.8936 (mp10) cc_final: 0.8697 (mp10) REVERT: D 108 ILE cc_start: 0.9039 (mm) cc_final: 0.8831 (mm) REVERT: D 109 TYR cc_start: 0.8940 (m-80) cc_final: 0.8646 (m-80) REVERT: D 265 LYS cc_start: 0.8960 (mttp) cc_final: 0.8275 (tttp) REVERT: D 285 LEU cc_start: 0.8057 (mm) cc_final: 0.7686 (mm) REVERT: D 289 ASN cc_start: 0.8802 (m-40) cc_final: 0.8472 (m-40) REVERT: E 73 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: E 74 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8143 (mtp180) REVERT: E 215 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: E 262 GLN cc_start: 0.7885 (mt0) cc_final: 0.7076 (mm-40) REVERT: F 262 GLN cc_start: 0.8184 (mp10) cc_final: 0.7751 (mp10) REVERT: F 273 ASP cc_start: 0.7777 (t0) cc_final: 0.7455 (t0) outliers start: 60 outliers final: 48 residues processed: 364 average time/residue: 0.1203 time to fit residues: 68.4385 Evaluate side-chains 372 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 160 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 125 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN F 50 GLN F 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116467 restraints weight = 27001.893| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.66 r_work: 0.3293 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16867 Z= 0.123 Angle : 0.591 9.870 22778 Z= 0.280 Chirality : 0.041 0.204 2603 Planarity : 0.003 0.045 2858 Dihedral : 10.396 89.200 2467 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.19 % Allowed : 29.43 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.19), residues: 2037 helix: 1.61 (0.16), residues: 1122 sheet: -0.38 (0.45), residues: 143 loop : 0.56 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 263 TYR 0.024 0.001 TYR B 167 PHE 0.013 0.001 PHE A 245 TRP 0.006 0.001 TRP F 166 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00296 (16867) covalent geometry : angle 0.59143 (22778) hydrogen bonds : bond 0.03029 ( 799) hydrogen bonds : angle 4.38503 ( 2292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 332 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7779 (tp40) REVERT: G 248 ARG cc_start: 0.8268 (mmt90) cc_final: 0.8052 (mtt180) REVERT: G 265 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8623 (mttm) REVERT: G 275 LYS cc_start: 0.8538 (tptt) cc_final: 0.7675 (mmtt) REVERT: G 284 GLN cc_start: 0.8795 (tp40) cc_final: 0.8382 (tp-100) REVERT: G 313 TYR cc_start: 0.7924 (t80) cc_final: 0.7339 (t80) REVERT: A 124 GLN cc_start: 0.8384 (mt0) cc_final: 0.7659 (mm-40) REVERT: A 141 MET cc_start: 0.8852 (mmm) cc_final: 0.8345 (mtp) REVERT: A 219 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8773 (mm) REVERT: B 60 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8629 (ttp80) REVERT: B 113 MET cc_start: 0.8837 (ptp) cc_final: 0.8559 (ptp) REVERT: B 342 LYS cc_start: 0.8781 (tttt) cc_final: 0.8366 (tptt) REVERT: C 311 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8319 (ptpp) REVERT: D 91 GLN cc_start: 0.9023 (mp10) cc_final: 0.8778 (mp10) REVERT: D 108 ILE cc_start: 0.8974 (mm) cc_final: 0.8750 (mm) REVERT: D 109 TYR cc_start: 0.8870 (m-80) cc_final: 0.8628 (m-80) REVERT: D 265 LYS cc_start: 0.8951 (mttp) cc_final: 0.8244 (tttp) REVERT: D 285 LEU cc_start: 0.8055 (mm) cc_final: 0.7722 (mm) REVERT: D 289 ASN cc_start: 0.8812 (m-40) cc_final: 0.8502 (m-40) REVERT: E 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: E 74 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8115 (mtp180) REVERT: E 215 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: E 262 GLN cc_start: 0.7972 (mt0) cc_final: 0.7110 (mm-40) REVERT: E 267 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9066 (mm) REVERT: F 262 GLN cc_start: 0.8182 (mp10) cc_final: 0.7765 (mp10) REVERT: F 273 ASP cc_start: 0.7771 (t0) cc_final: 0.7459 (t0) outliers start: 58 outliers final: 46 residues processed: 369 average time/residue: 0.1302 time to fit residues: 73.9011 Evaluate side-chains 372 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 ASN A 50 GLN D 236 ASN F 50 GLN F 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110429 restraints weight = 27092.446| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.67 r_work: 0.3212 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16867 Z= 0.217 Angle : 0.646 10.358 22778 Z= 0.309 Chirality : 0.043 0.191 2603 Planarity : 0.004 0.045 2858 Dihedral : 10.602 88.914 2467 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 29.87 % Favored : 67.22 % 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: 1.47 (0.19), residues: 2037 helix: 1.53 (0.16), residues: 1134 sheet: -0.53 (0.43), residues: 159 loop : 0.66 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.025 0.001 TYR B 167 PHE 0.016 0.001 PHE D 178 TRP 0.011 0.001 TRP E 220 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00526 (16867) covalent geometry : angle 0.64621 (22778) hydrogen bonds : bond 0.03290 ( 799) hydrogen bonds : angle 4.48954 ( 2292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4430.59 seconds wall clock time: 76 minutes 49.88 seconds (4609.88 seconds total)