Starting phenix.real_space_refine on Sun Oct 25 13:22:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.map" model { file = "/net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wre_66187/10_2026/9wre_66187.cif" } resolution = 3.43 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= 0.004 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 12 5.16 5 C 10686 2.51 5 N 2796 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16644 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "D" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "F" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "G" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2729 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1YC': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1' 1YC A 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC A 401 " occ=0.00 residue: pdb=" C1' 1YC B 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC B 401 " occ=0.00 residue: pdb=" C1' 1YC D 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC D 401 " occ=0.00 residue: pdb=" C1' 1YC E 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC E 401 " occ=0.00 residue: pdb=" C1' 1YC F 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC F 401 " occ=0.00 residue: pdb=" C1' 1YC G 401 " occ=0.00 ... (43 atoms not shown) pdb=" PBS 1YC G 401 " occ=0.00 Time building chain proxies: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16644 At special positions: 0 Unit cell: (101.66, 136.136, 135.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 12 15.00 O 3138 8.00 N 2796 7.00 C 10686 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 643.3 milliseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 13 sheets defined 46.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 removed outlier: 4.173A pdb=" N PHE A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 69 Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.891A pdb=" N LEU A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 106 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.699A pdb=" N GLN A 125 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 154 through 157 removed outlier: 3.553A pdb=" N ASN A 157 " --> pdb=" O THR A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.776A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 243' Processing helix chain 'A' and resid 261 through 265 removed outlier: 4.333A pdb=" N GLN A 265 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 309 removed outlier: 3.656A pdb=" N ASN A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.827A pdb=" N PHE B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 83 through 104 Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.939A pdb=" N GLN B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 158 through 177 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.795A pdb=" N THR B 243 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 3.900A pdb=" N ASN B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.595A pdb=" N PHE B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.608A pdb=" N PHE D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 69 Processing helix chain 'D' and resid 70 through 76 removed outlier: 4.059A pdb=" N LYS D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 76 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 removed outlier: 3.885A pdb=" N LEU D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 154 through 177 removed outlier: 3.642A pdb=" N VAL D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.813A pdb=" N SER D 241 " --> pdb=" O GLN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 309 removed outlier: 4.023A pdb=" N ASN D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'E' and resid 33 through 49 removed outlier: 3.656A pdb=" N PHE E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 69 Processing helix chain 'E' and resid 70 through 76 removed outlier: 3.919A pdb=" N LYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 104 Processing helix chain 'E' and resid 142 through 153 Processing helix chain 'E' and resid 154 through 157 removed outlier: 3.618A pdb=" N ASN E 157 " --> pdb=" O THR E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 157' Processing helix chain 'E' and resid 158 through 177 Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.869A pdb=" N THR E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 287 through 309 removed outlier: 3.599A pdb=" N ASN E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'F' and resid 33 through 49 removed outlier: 4.039A pdb=" N PHE F 37 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 69 Processing helix chain 'F' and resid 70 through 76 removed outlier: 3.783A pdb=" N LEU F 76 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 106 Processing helix chain 'F' and resid 124 through 129 removed outlier: 4.155A pdb=" N LEU F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 152 Processing helix chain 'F' and resid 158 through 177 Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 237 through 243 removed outlier: 3.738A pdb=" N SER F 241 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 265 removed outlier: 4.469A pdb=" N GLN F 265 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 309 removed outlier: 3.637A pdb=" N ASN F 309 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'G' and resid 33 through 49 removed outlier: 4.258A pdb=" N PHE G 37 " --> pdb=" O GLY G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 69 removed outlier: 3.568A pdb=" N ASP G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 76 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 120 through 129 removed outlier: 4.162A pdb=" N GLN G 125 " --> pdb=" O GLU G 122 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS G 126 " --> pdb=" O ASN G 123 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER G 127 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 153 Processing helix chain 'G' and resid 154 through 157 Processing helix chain 'G' and resid 158 through 177 Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 261 through 265 removed outlier: 3.559A pdb=" N SER G 264 " --> pdb=" O HIS G 261 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN G 265 " --> pdb=" O ASP G 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 261 through 265' Processing helix chain 'G' and resid 287 through 309 removed outlier: 3.874A pdb=" N ASN G 309 " --> pdb=" O ILE G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 141 removed outlier: 5.661A pdb=" N ILE A 108 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A 138 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE A 110 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 140 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN A 112 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 109 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR A 185 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU A 111 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE A 187 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 113 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR A 209 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A 184 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG A 211 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N GLY A 186 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.570A pdb=" N ILE A 319 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE A 346 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 353 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 135 through 141 removed outlier: 6.836A pdb=" N ILE B 108 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 138 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 110 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE B 140 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN B 112 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG B 182 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR B 209 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR B 184 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ARG B 211 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N GLY B 186 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 276 removed outlier: 6.800A pdb=" N ALA B 248 " --> pdb=" O HIS B 316 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 318 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 250 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 344 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE B 319 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE B 346 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP B 353 " --> pdb=" O HIS B 345 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 364 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 135 through 141 removed outlier: 6.278A pdb=" N ILE D 108 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ARG D 138 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE D 110 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE D 140 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN D 112 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG D 182 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR D 209 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR D 184 " --> pdb=" O TYR D 209 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG D 211 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N GLY D 186 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 217 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 272 through 276 removed outlier: 8.637A pdb=" N VAL D 273 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 249 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 275 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS D 251 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA D 248 " --> pdb=" O HIS D 316 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU D 318 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU D 250 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 344 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE D 319 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE D 346 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP D 353 " --> pdb=" O HIS D 345 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 364 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 135 through 141 removed outlier: 6.061A pdb=" N ILE E 108 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG E 138 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 110 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE E 140 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN E 112 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG E 182 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR E 209 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR E 184 " --> pdb=" O TYR E 209 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARG E 211 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLY E 186 " --> pdb=" O ARG E 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 232 through 233 removed outlier: 3.665A pdb=" N THR E 232 " --> pdb=" O LYS E 276 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS E 276 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA E 248 " --> pdb=" O HIS E 316 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 318 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU E 250 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA E 320 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL E 252 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE E 319 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE E 346 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP E 353 " --> pdb=" O HIS E 345 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR E 364 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 135 through 141 removed outlier: 6.452A pdb=" N ILE F 108 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG F 138 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE F 110 " --> pdb=" O ARG F 138 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE F 140 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN F 112 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG F 182 " --> pdb=" O HIS F 207 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N TYR F 209 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR F 184 " --> pdb=" O TYR F 209 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ARG F 211 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLY F 186 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 232 through 233 removed outlier: 3.675A pdb=" N THR F 232 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 248 " --> pdb=" O HIS F 316 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU F 318 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU F 250 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA F 320 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL F 252 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE F 319 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE F 346 " --> pdb=" O ILE F 319 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP F 353 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 141 removed outlier: 5.796A pdb=" N ILE G 108 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG G 138 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE G 110 " --> pdb=" O ARG G 138 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE G 140 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN G 112 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR G 109 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR G 185 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU G 111 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE G 187 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE G 113 " --> pdb=" O ILE G 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 209 through 212 Processing sheet with id=AB4, first strand: chain 'G' and resid 232 through 233 removed outlier: 3.689A pdb=" N THR G 232 " --> pdb=" O LYS G 276 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N VAL G 273 " --> pdb=" O GLU G 247 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE G 249 " --> pdb=" O VAL G 273 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU G 275 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS G 251 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE G 319 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE G 346 " --> pdb=" O ILE G 319 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP G 353 " --> pdb=" O HIS G 345 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2211 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: 2.45 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2718 1.31 - 1.43: 4353 1.43 - 1.56: 9896 1.56 - 1.68: 7 1.68 - 1.81: 36 Bond restraints: 17010 Sorted by residual: bond pdb=" CBA 1YC F 401 " pdb=" NAS 1YC F 401 " ideal model delta sigma weight residual 1.317 1.460 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" CBA 1YC B 401 " pdb=" NAS 1YC B 401 " ideal model delta sigma weight residual 1.317 1.460 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" CBA 1YC E 401 " pdb=" NAS 1YC E 401 " ideal model delta sigma weight residual 1.317 1.460 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" CBA 1YC D 401 " pdb=" NAS 1YC D 401 " ideal model delta sigma weight residual 1.317 1.460 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" CBA 1YC G 401 " pdb=" NAS 1YC G 401 " ideal model delta sigma weight residual 1.317 1.458 -0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 17005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 22779 3.20 - 6.39: 165 6.39 - 9.59: 59 9.59 - 12.78: 29 12.78 - 15.98: 44 Bond angle restraints: 23076 Sorted by residual: angle pdb=" OAH 1YC A 401 " pdb=" PBS 1YC A 401 " pdb=" OAI 1YC A 401 " ideal model delta sigma weight residual 122.06 106.08 15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C1' 1YC F 401 " pdb=" N9 1YC F 401 " pdb=" C8 1YC F 401 " ideal model delta sigma weight residual 127.48 111.51 15.97 3.00e+00 1.11e-01 2.83e+01 angle pdb=" C1' 1YC B 401 " pdb=" N9 1YC B 401 " pdb=" C8 1YC B 401 " ideal model delta sigma weight residual 127.48 111.68 15.80 3.00e+00 1.11e-01 2.77e+01 angle pdb=" C1' 1YC G 401 " pdb=" N9 1YC G 401 " pdb=" C8 1YC G 401 " ideal model delta sigma weight residual 127.48 111.69 15.79 3.00e+00 1.11e-01 2.77e+01 angle pdb=" C1' 1YC A 401 " pdb=" N9 1YC A 401 " pdb=" C8 1YC A 401 " ideal model delta sigma weight residual 127.48 111.85 15.63 3.00e+00 1.11e-01 2.72e+01 ... (remaining 23071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9860 35.92 - 71.84: 397 71.84 - 107.76: 81 107.76 - 143.68: 0 143.68 - 179.61: 24 Dihedral angle restraints: 10362 sinusoidal: 4416 harmonic: 5946 Sorted by residual: dihedral pdb=" C8 1YC F 401 " pdb=" C1' 1YC F 401 " pdb=" N9 1YC F 401 " pdb=" O4' 1YC F 401 " ideal model delta sinusoidal sigma weight residual 298.76 119.15 179.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 1YC G 401 " pdb=" C1' 1YC G 401 " pdb=" N9 1YC G 401 " pdb=" O4' 1YC G 401 " ideal model delta sinusoidal sigma weight residual 125.19 -55.38 -179.43 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C8 1YC A 401 " pdb=" C1' 1YC A 401 " pdb=" N9 1YC A 401 " pdb=" O4' 1YC A 401 " ideal model delta sinusoidal sigma weight residual -61.24 118.13 -179.37 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2136 0.051 - 0.101: 387 0.101 - 0.152: 110 0.152 - 0.202: 6 0.202 - 0.253: 7 Chirality restraints: 2646 Sorted by residual: chirality pdb=" CBI 1YC B 401 " pdb=" CBK 1YC B 401 " pdb=" CBM 1YC B 401 " pdb=" OAE 1YC B 401 " both_signs ideal model delta sigma weight residual False 2.73 2.48 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CBI 1YC A 401 " pdb=" CBK 1YC A 401 " pdb=" CBM 1YC A 401 " pdb=" OAE 1YC A 401 " both_signs ideal model delta sigma weight residual False 2.73 2.51 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3' 1YC E 401 " pdb=" C2' 1YC E 401 " pdb=" C4' 1YC E 401 " pdb=" O3' 1YC E 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2643 not shown) Planarity restraints: 2874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 348 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 349 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 348 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO F 349 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 349 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 349 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 325 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO G 326 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 326 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 326 " 0.019 5.00e-02 4.00e+02 ... (remaining 2871 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2235 2.75 - 3.29: 15929 3.29 - 3.83: 28069 3.83 - 4.36: 31867 4.36 - 4.90: 57518 Nonbonded interactions: 135618 Sorted by model distance: nonbonded pdb=" O ARG B 211 " pdb=" NAA 1YC B 401 " model vdw 2.217 3.120 nonbonded pdb=" O GLU F 229 " pdb=" OH TYR F 294 " model vdw 2.228 3.040 nonbonded pdb=" O PRO D 339 " pdb=" ND2 ASN D 358 " model vdw 2.269 3.120 nonbonded pdb=" OD1 ASN E 106 " pdb=" NZ LYS G 105 " model vdw 2.290 3.120 nonbonded pdb=" O ILE G 356 " pdb=" N GLY G 363 " model vdw 2.290 3.120 ... (remaining 135613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=0.98 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.008 0.143 17011 Z= 0.385 Angle : 1.032 15.975 23076 Z= 0.392 Chirality : 0.044 0.253 2646 Planarity : 0.003 0.038 2874 Dihedral : 22.172 179.606 6522 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.11 % Allowed : 25.11 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 2022 helix: 2.73 (0.18), residues: 843 sheet: -0.70 (0.30), residues: 338 loop : -0.45 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 120 TYR 0.011 0.001 TYR B 294 PHE 0.012 0.001 PHE G 228 TRP 0.005 0.001 TRP D 99 HIS 0.003 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.38 (17010) covalent geometry : angle 1.03220 / 0.39 (23076) hydrogen bonds : bond 0.11573 / 7.77 ( 770) hydrogen bonds : angle 4.72539 / 3.35 ( 2211) Misc. bond : bond 0.00114 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.672 Fit side-chains REVERT: A 227 ASN cc_start: 0.7518 (t0) cc_final: 0.7239 (p0) REVERT: D 204 LYS cc_start: 0.6709 (tptt) cc_final: 0.6296 (tppt) outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 0.1627 time to fit residues: 30.3475 Evaluate side-chains 123 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91] chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097762 restraints weight = 25440.274| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.25 r_work: 0.3092 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17011 Z= 0.117 Angle : 0.489 8.533 23076 Z= 0.251 Chirality : 0.042 0.155 2646 Planarity : 0.004 0.041 2874 Dihedral : 21.385 179.978 2537 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.64 % Allowed : 22.53 % Favored : 75.82 % 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: 1.28 (0.20), residues: 2022 helix: 2.73 (0.18), residues: 862 sheet: -1.04 (0.28), residues: 365 loop : -0.28 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 120 TYR 0.018 0.001 TYR D 299 PHE 0.012 0.001 PHE E 146 TRP 0.006 0.001 TRP D 99 HIS 0.005 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17010) covalent geometry : angle 0.48914 / 0.25 (23076) hydrogen bonds : bond 0.03637 / 2.47 ( 770) hydrogen bonds : angle 3.87907 / 2.73 ( 2211) Misc. bond : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.658 Fit side-chains REVERT: A 182 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8802 (mtm-85) REVERT: A 227 ASN cc_start: 0.7787 (t0) cc_final: 0.7357 (p0) REVERT: D 145 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8287 (mtm180) REVERT: D 204 LYS cc_start: 0.6800 (tptt) cc_final: 0.6290 (tppt) REVERT: E 137 GLU cc_start: 0.8896 (tt0) cc_final: 0.8669 (tt0) REVERT: G 44 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (mp) outliers start: 30 outliers final: 13 residues processed: 163 average time/residue: 0.1545 time to fit residues: 36.4926 Evaluate side-chains 142 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [121, 86, 78, 88, 160, 38, 110, 69, 105, 140, 42] chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 105 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097801 restraints weight = 25679.954| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.27 r_work: 0.3097 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17011 Z= 0.114 Angle : 0.475 9.200 23076 Z= 0.244 Chirality : 0.042 0.158 2646 Planarity : 0.003 0.041 2874 Dihedral : 21.141 179.679 2532 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.30 % Allowed : 22.20 % Favored : 75.49 % 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: 1.32 (0.20), residues: 2022 helix: 2.77 (0.18), residues: 858 sheet: -0.90 (0.28), residues: 354 loop : -0.34 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 120 TYR 0.016 0.001 TYR D 299 PHE 0.011 0.001 PHE E 146 TRP 0.005 0.001 TRP D 99 HIS 0.006 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (17010) covalent geometry : angle 0.47506 / 0.24 (23076) hydrogen bonds : bond 0.03438 / 2.34 ( 770) hydrogen bonds : angle 3.75641 / 2.63 ( 2211) Misc. bond : bond 0.00156 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.664 Fit side-chains REVERT: A 182 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8743 (ttm110) REVERT: A 227 ASN cc_start: 0.7810 (t0) cc_final: 0.7390 (p0) REVERT: B 138 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8534 (mmp80) REVERT: D 145 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8290 (mtm180) REVERT: D 204 LYS cc_start: 0.6830 (tptt) cc_final: 0.6310 (tppt) REVERT: E 137 GLU cc_start: 0.8908 (tt0) cc_final: 0.8669 (tt0) REVERT: G 44 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7954 (mp) REVERT: G 106 ASN cc_start: 0.8441 (m110) cc_final: 0.8194 (m110) REVERT: G 116 TYR cc_start: 0.8909 (m-80) cc_final: 0.8421 (m-80) REVERT: G 251 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8657 (ptpt) outliers start: 42 outliers final: 18 residues processed: 167 average time/residue: 0.1577 time to fit residues: 38.5885 Evaluate side-chains 147 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 251 LYS Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [60, 82, 154, 4, 196, 52, 19, 143, 80, 163, 90] chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094067 restraints weight = 25793.441| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.35 r_work: 0.3035 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17011 Z= 0.191 Angle : 0.524 9.085 23076 Z= 0.270 Chirality : 0.044 0.155 2646 Planarity : 0.004 0.041 2874 Dihedral : 21.083 179.390 2532 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 22.86 % Favored : 74.56 % 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: 1.17 (0.20), residues: 2022 helix: 2.60 (0.18), residues: 870 sheet: -1.07 (0.27), residues: 385 loop : -0.32 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 120 TYR 0.014 0.001 TYR D 299 PHE 0.015 0.001 PHE E 146 TRP 0.006 0.001 TRP D 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (17010) covalent geometry : angle 0.52361 / 0.27 (23076) hydrogen bonds : bond 0.03896 / 2.68 ( 770) hydrogen bonds : angle 3.84275 / 2.70 ( 2211) Misc. bond : bond 0.00140 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 182 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8679 (ttm110) REVERT: B 138 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8520 (mmp80) REVERT: B 217 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (t0) REVERT: D 145 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (mtm180) REVERT: D 204 LYS cc_start: 0.6536 (tptt) cc_final: 0.5906 (tppt) REVERT: G 44 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7952 (mp) REVERT: G 116 TYR cc_start: 0.8963 (m-80) cc_final: 0.8400 (m-80) outliers start: 47 outliers final: 30 residues processed: 168 average time/residue: 0.1592 time to fit residues: 38.1908 Evaluate side-chains 151 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [84, 139, 175, 42, 76, 6, 9, 129, 110, 3, 131] chunk 84 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 348 ASN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092854 restraints weight = 25880.129| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.33 r_work: 0.3010 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17011 Z= 0.240 Angle : 0.559 9.570 23076 Z= 0.289 Chirality : 0.045 0.161 2646 Planarity : 0.004 0.041 2874 Dihedral : 21.096 179.225 2532 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.02 % Allowed : 22.86 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 2022 helix: 2.47 (0.18), residues: 871 sheet: -1.26 (0.26), residues: 385 loop : -0.42 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 211 TYR 0.015 0.001 TYR D 299 PHE 0.016 0.001 PHE E 146 TRP 0.007 0.001 TRP D 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.24 (17010) covalent geometry : angle 0.55921 / 0.29 (23076) hydrogen bonds : bond 0.04209 / 2.89 ( 770) hydrogen bonds : angle 3.95762 / 2.79 ( 2211) Misc. bond : bond 0.00151 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8645 (m-30) cc_final: 0.8308 (m-30) REVERT: A 182 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8689 (ttm110) REVERT: B 138 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8512 (mmp80) REVERT: B 217 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8129 (t0) REVERT: B 257 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8018 (t0) REVERT: D 145 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8297 (mtm180) REVERT: D 204 LYS cc_start: 0.6523 (tptt) cc_final: 0.5785 (tppt) REVERT: D 334 ASP cc_start: 0.8098 (t0) cc_final: 0.7665 (m-30) REVERT: F 126 LYS cc_start: 0.8760 (tppt) cc_final: 0.8464 (tppt) REVERT: G 116 TYR cc_start: 0.9016 (m-80) cc_final: 0.8412 (m-80) outliers start: 55 outliers final: 37 residues processed: 175 average time/residue: 0.1660 time to fit residues: 41.4356 Evaluate side-chains 161 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 324 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [55, 33, 28, 2, 61, 89, 185, 134, 47, 137, 12] chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN ** E 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.094729 restraints weight = 25621.150| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.34 r_work: 0.3049 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17011 Z= 0.132 Angle : 0.500 10.853 23076 Z= 0.256 Chirality : 0.043 0.161 2646 Planarity : 0.004 0.042 2874 Dihedral : 20.979 179.686 2532 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.69 % Allowed : 23.25 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 2022 helix: 2.58 (0.18), residues: 869 sheet: -1.26 (0.27), residues: 362 loop : -0.41 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 120 TYR 0.016 0.001 TYR D 299 PHE 0.013 0.001 PHE E 146 TRP 0.004 0.001 TRP G 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (17010) covalent geometry : angle 0.49959 / 0.26 (23076) hydrogen bonds : bond 0.03572 / 2.45 ( 770) hydrogen bonds : angle 3.79853 / 2.66 ( 2211) Misc. bond : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8650 (m-30) cc_final: 0.8312 (m-30) REVERT: A 182 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8629 (ttm110) REVERT: B 118 ASP cc_start: 0.8284 (t0) cc_final: 0.7864 (t0) REVERT: B 138 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8529 (mmp80) REVERT: B 226 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8352 (mmmm) REVERT: D 145 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8290 (mtm180) REVERT: D 204 LYS cc_start: 0.6446 (tptt) cc_final: 0.5696 (tppt) REVERT: F 126 LYS cc_start: 0.8756 (tppt) cc_final: 0.8340 (tppt) REVERT: G 116 TYR cc_start: 0.9023 (m-80) cc_final: 0.8373 (m-80) outliers start: 49 outliers final: 26 residues processed: 177 average time/residue: 0.1527 time to fit residues: 39.1521 Evaluate side-chains 150 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [31, 101, 115, 47, 191, 50, 58, 14, 44, 153, 0] chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN E 150 GLN E 283 ASN G 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097690 restraints weight = 25449.250| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.25 r_work: 0.3096 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17011 Z= 0.102 Angle : 0.484 11.515 23076 Z= 0.248 Chirality : 0.042 0.160 2646 Planarity : 0.003 0.042 2874 Dihedral : 20.876 179.012 2532 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.14 % Allowed : 23.90 % Favored : 73.96 % 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: 1.17 (0.20), residues: 2022 helix: 2.63 (0.18), residues: 870 sheet: -1.05 (0.28), residues: 342 loop : -0.42 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 120 TYR 0.015 0.001 TYR D 299 PHE 0.011 0.001 PHE E 146 TRP 0.004 0.001 TRP G 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (17010) covalent geometry : angle 0.48441 / 0.25 (23076) hydrogen bonds : bond 0.03217 / 2.20 ( 770) hydrogen bonds : angle 3.68063 / 2.57 ( 2211) Misc. bond : bond 0.00141 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8651 (m-30) cc_final: 0.8089 (m-30) REVERT: A 182 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8647 (ttm110) REVERT: B 118 ASP cc_start: 0.8293 (t0) cc_final: 0.7864 (t0) REVERT: B 138 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8518 (mmp80) REVERT: B 226 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8315 (mmmm) REVERT: B 359 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7833 (mmtm) REVERT: D 204 LYS cc_start: 0.6490 (tptt) cc_final: 0.5758 (tppt) REVERT: F 126 LYS cc_start: 0.8766 (tppt) cc_final: 0.8381 (tppt) REVERT: G 116 TYR cc_start: 0.8968 (m-80) cc_final: 0.8330 (m-80) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 0.1513 time to fit residues: 36.0639 Evaluate side-chains 153 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [108, 15, 28, 180, 19, 164, 68, 60, 186, 38, 176] chunk 108 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 180 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094310 restraints weight = 25870.505| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.32 r_work: 0.3043 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17011 Z= 0.179 Angle : 0.524 11.442 23076 Z= 0.267 Chirality : 0.044 0.157 2646 Planarity : 0.004 0.042 2874 Dihedral : 20.925 179.849 2532 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.47 % Allowed : 23.63 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 2022 helix: 2.58 (0.18), residues: 869 sheet: -1.22 (0.27), residues: 362 loop : -0.38 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 120 TYR 0.012 0.001 TYR D 299 PHE 0.014 0.001 PHE E 146 TRP 0.005 0.001 TRP D 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (17010) covalent geometry : angle 0.52400 / 0.27 (23076) hydrogen bonds : bond 0.03693 / 2.53 ( 770) hydrogen bonds : angle 3.76788 / 2.65 ( 2211) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8639 (m-30) cc_final: 0.8319 (m-30) REVERT: B 138 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8516 (mmp80) REVERT: B 226 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8369 (mmmm) REVERT: D 108 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8369 (pt) REVERT: D 145 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8220 (mtm180) REVERT: D 204 LYS cc_start: 0.6566 (tptt) cc_final: 0.5812 (tppt) REVERT: F 126 LYS cc_start: 0.8778 (tppt) cc_final: 0.8367 (tppt) REVERT: G 116 TYR cc_start: 0.9032 (m-80) cc_final: 0.8348 (m-80) outliers start: 45 outliers final: 34 residues processed: 163 average time/residue: 0.1537 time to fit residues: 36.1750 Evaluate side-chains 159 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [93, 15, 181, 179, 8, 94, 191, 69, 67, 3, 34] chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 181 optimal weight: 0.1980 chunk 179 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN B 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097639 restraints weight = 25500.870| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.25 r_work: 0.3095 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17011 Z= 0.104 Angle : 0.494 11.674 23076 Z= 0.251 Chirality : 0.042 0.173 2646 Planarity : 0.004 0.058 2874 Dihedral : 20.879 178.864 2532 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.97 % Allowed : 23.96 % Favored : 74.07 % 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: 1.23 (0.20), residues: 2022 helix: 2.66 (0.18), residues: 870 sheet: -0.98 (0.28), residues: 342 loop : -0.39 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 314 TYR 0.018 0.001 TYR D 299 PHE 0.011 0.001 PHE D 146 TRP 0.004 0.001 TRP D 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (17010) covalent geometry : angle 0.49424 / 0.25 (23076) hydrogen bonds : bond 0.03215 / 2.20 ( 770) hydrogen bonds : angle 3.66061 / 2.56 ( 2211) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8640 (m-30) cc_final: 0.8079 (m-30) REVERT: B 118 ASP cc_start: 0.8297 (t0) cc_final: 0.7876 (t0) REVERT: B 226 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8342 (mmmm) REVERT: D 145 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8414 (mtm180) REVERT: D 204 LYS cc_start: 0.6590 (tptt) cc_final: 0.5842 (tppt) REVERT: F 126 LYS cc_start: 0.8776 (tppt) cc_final: 0.8405 (tppt) REVERT: G 116 TYR cc_start: 0.8931 (m-80) cc_final: 0.8316 (m-80) outliers start: 36 outliers final: 29 residues processed: 166 average time/residue: 0.1533 time to fit residues: 37.0290 Evaluate side-chains 158 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 324 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [18, 5, 172, 71, 189, 63, 160, 65, 111, 186, 91] chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 189 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 186 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097840 restraints weight = 25472.670| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.24 r_work: 0.3104 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17011 Z= 0.102 Angle : 0.496 12.414 23076 Z= 0.251 Chirality : 0.042 0.162 2646 Planarity : 0.004 0.047 2874 Dihedral : 20.852 178.864 2532 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.97 % Allowed : 23.96 % Favored : 74.07 % 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: 1.19 (0.20), residues: 2022 helix: 2.58 (0.18), residues: 888 sheet: -0.94 (0.28), residues: 342 loop : -0.45 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 211 TYR 0.017 0.001 TYR D 299 PHE 0.011 0.001 PHE E 146 TRP 0.004 0.001 TRP G 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (17010) covalent geometry : angle 0.49627 / 0.25 (23076) hydrogen bonds : bond 0.03175 / 2.17 ( 770) hydrogen bonds : angle 3.63920 / 2.54 ( 2211) Misc. bond : bond 0.00155 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.723 Fit side-chains REVERT: A 134 ASP cc_start: 0.8636 (m-30) cc_final: 0.8086 (m-30) REVERT: B 118 ASP cc_start: 0.8306 (t0) cc_final: 0.7881 (t0) REVERT: B 226 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8327 (mmmm) REVERT: D 204 LYS cc_start: 0.6672 (tptt) cc_final: 0.5916 (tppt) REVERT: F 112 ASN cc_start: 0.9222 (t0) cc_final: 0.8944 (t0) REVERT: F 126 LYS cc_start: 0.8780 (tppt) cc_final: 0.8433 (tppt) REVERT: G 116 TYR cc_start: 0.8909 (m-80) cc_final: 0.8244 (m-80) outliers start: 36 outliers final: 30 residues processed: 165 average time/residue: 0.1465 time to fit residues: 35.6029 Evaluate side-chains 161 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain D residue 324 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: [58, 90, 52, 179, 100, 125, 115, 42, 154, 95, 28] chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 0.0980 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN F 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099050 restraints weight = 25377.199| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.26 r_work: 0.3118 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17011 Z= 0.096 Angle : 0.488 12.411 23076 Z= 0.247 Chirality : 0.042 0.163 2646 Planarity : 0.004 0.046 2874 Dihedral : 20.821 179.002 2532 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.81 % Allowed : 24.07 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 2022 helix: 2.58 (0.18), residues: 888 sheet: -0.83 (0.28), residues: 335 loop : -0.41 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 314 TYR 0.019 0.001 TYR D 299 PHE 0.012 0.001 PHE E 133 TRP 0.004 0.001 TRP D 99 HIS 0.007 0.001 HIS D 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (17010) covalent geometry : angle 0.48824 / 0.25 (23076) hydrogen bonds : bond 0.03067 / 2.09 ( 770) hydrogen bonds : angle 3.60452 / 2.52 ( 2211) Misc. bond : bond 0.00350 / 0.18 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.17 seconds wall clock time: 66 minutes 22.39 seconds (3982.39 seconds total)