Starting phenix.real_space_refine on Sun May 3 18:37:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qpp_53277/05_2026/9qpp_53277.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 9167 2.51 5 N 2543 2.21 5 O 2891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14658 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2980 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 367} Chain: "E" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2881 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2864 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain breaks: 1 Chain: "D" Number of atoms: 2887 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 371, 2887 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 1 Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain breaks: 1 Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain breaks: 1 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Residues with excluded nonbonded symmetry interactions: 31 residue: pdb=" N AGLU F 7 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU F 7 " occ=0.50 residue: pdb=" N ALEU F 8 " occ=0.50 ... (6 atoms not shown) pdb=" CD2ALEU F 8 " occ=0.50 residue: pdb=" N ASER F 9 " occ=0.50 ... (4 atoms not shown) pdb=" OG ASER F 9 " occ=0.50 residue: pdb=" N AILE F 10 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE F 10 " occ=0.50 residue: pdb=" N AHIS F 11 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS F 11 " occ=0.50 residue: pdb=" N APHE F 12 " occ=0.50 ... (9 atoms not shown) pdb=" CZ APHE F 12 " occ=0.50 residue: pdb=" N AVAL F 13 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL F 13 " occ=0.50 residue: pdb=" N APRO F 14 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO F 14 " occ=0.50 residue: pdb=" N AGLY F 15 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY F 15 " occ=0.50 residue: pdb=" N ASER F 16 " occ=0.50 ... (4 atoms not shown) pdb=" OG ASER F 16 " occ=0.50 residue: pdb=" N ACYS F 17 " occ=0.50 ... (4 atoms not shown) pdb=" SG ACYS F 17 " occ=0.50 residue: pdb=" N AARG F 18 " occ=0.50 ... (9 atoms not shown) pdb=" NH2AARG F 18 " occ=0.50 ... (remaining 19 not shown) Time building chain proxies: 3.65, per 1000 atoms: 0.25 Number of scatterers: 14658 At special positions: 0 Unit cell: (82.88, 97.68, 167.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2891 8.00 N 2543 7.00 C 9167 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 670.0 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 21 sheets defined 38.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.847A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 151 through 170 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.928A pdb=" N GLN B 256 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 289 through 308 removed outlier: 3.758A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.532A pdb=" N VAL B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 105 through 114 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.551A pdb=" N GLU E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.816A pdb=" N SER E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 224 through 241 removed outlier: 3.774A pdb=" N LEU E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 269 Processing helix chain 'E' and resid 297 through 303 Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.807A pdb=" N LYS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 3.596A pdb=" N TRP E 328 " --> pdb=" O ILE E 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 49 removed outlier: 3.942A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.065A pdb=" N GLN A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.549A pdb=" N TYR A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 308 removed outlier: 4.260A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.799A pdb=" N VAL A 361 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'C' and resid 29 through 49 removed outlier: 3.929A pdb=" N GLN C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 151 through 170 Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.939A pdb=" N GLN C 256 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.613A pdb=" N TYR C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 308 removed outlier: 3.579A pdb=" N SER C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 356 through 365 removed outlier: 3.880A pdb=" N VAL C 361 " --> pdb=" O PRO C 357 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 362 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'D' and resid 29 through 47 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 253 through 257 removed outlier: 3.815A pdb=" N GLN D 256 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.517A pdb=" N TYR D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 308 removed outlier: 3.754A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 356 through 365 removed outlier: 3.758A pdb=" N VAL D 361 " --> pdb=" O PRO D 357 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 25 removed outlier: 5.842A pdb=" N ARG B 177 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B 209 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP B 179 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 207 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 181 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 205 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 203 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR B 185 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 199 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET B 189 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 191 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N ILE B 241 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS B 201 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N HIS B 243 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 203 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 113 removed outlier: 6.292A pdb=" N ILE B 65 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA B 109 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 67 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU B 111 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 69 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLN B 113 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 71 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.641A pdb=" N PHE B 99 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 143 removed outlier: 3.739A pdb=" N SER B 329 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 13 removed outlier: 4.749A pdb=" N GLU E 7 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.522A pdb=" N ILE E 134 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 179 " --> pdb=" O PHE E 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AA8, first strand: chain 'E' and resid 211 through 214 Processing sheet with id=AA9, first strand: chain 'A' and resid 17 through 25 removed outlier: 5.743A pdb=" N ASP A 179 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 187 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL A 200 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 198 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP A 191 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 196 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N ILE A 241 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N HIS A 201 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS A 243 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 203 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.284A pdb=" N ILE A 65 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A 109 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU A 67 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU A 111 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 69 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.609A pdb=" N PHE A 99 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 143 removed outlier: 3.632A pdb=" N GLY A 136 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 329 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 25 removed outlier: 5.808A pdb=" N ASP C 179 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN C 187 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C 200 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N ILE C 241 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS C 201 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS C 243 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 203 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 105 through 112 removed outlier: 6.298A pdb=" N ILE C 65 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ALA C 109 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 67 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU C 111 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY C 69 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.551A pdb=" N PHE C 99 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 143 removed outlier: 3.846A pdb=" N GLY C 136 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 329 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AB9, first strand: chain 'D' and resid 17 through 25 removed outlier: 5.702A pdb=" N ASP D 179 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLN D 187 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL D 200 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET D 189 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE D 198 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP D 191 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 196 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ILE D 241 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS D 201 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N HIS D 243 " --> pdb=" O HIS D 201 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 203 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 105 through 112 removed outlier: 6.135A pdb=" N ILE D 65 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA D 109 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU D 67 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU D 111 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY D 69 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.534A pdb=" N ASP D 94 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 99 " --> pdb=" O ASP D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 136 through 142 removed outlier: 3.690A pdb=" N GLY D 136 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER D 329 " --> pdb=" O SER D 319 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1725 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: 2.47 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4841 1.34 - 1.46: 2613 1.46 - 1.58: 7245 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 14781 Sorted by residual: bond pdb=" N ALEU F 8 " pdb=" CA ALEU F 8 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.34e+00 bond pdb=" N BLEU G 8 " pdb=" CA BLEU G 8 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.81e+00 bond pdb=" N AVAL F 335 " pdb=" CA AVAL F 335 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" N BGLU G 7 " pdb=" CA BGLU G 7 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" CA BSER G 9 " pdb=" CB BSER G 9 " ideal model delta sigma weight residual 1.530 1.503 0.027 1.69e-02 3.50e+03 2.51e+00 ... (remaining 14776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 19526 1.72 - 3.44: 405 3.44 - 5.16: 54 5.16 - 6.88: 12 6.88 - 8.60: 3 Bond angle restraints: 20000 Sorted by residual: angle pdb=" C ASP B 269 " pdb=" N THR B 270 " pdb=" CA THR B 270 " ideal model delta sigma weight residual 122.44 117.03 5.41 1.19e+00 7.06e-01 2.06e+01 angle pdb=" O GLY B 133 " pdb=" C GLY B 133 " pdb=" N ASP B 134 " ideal model delta sigma weight residual 122.84 117.65 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" C ASP A 383 " pdb=" N SER A 384 " pdb=" CA SER A 384 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C GLY B 133 " pdb=" N ASP B 134 " pdb=" CA ASP B 134 " ideal model delta sigma weight residual 121.80 128.54 -6.74 1.71e+00 3.42e-01 1.55e+01 angle pdb=" CA GLY B 133 " pdb=" C GLY B 133 " pdb=" N ASP B 134 " ideal model delta sigma weight residual 118.13 123.20 -5.07 1.30e+00 5.92e-01 1.52e+01 ... (remaining 19995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 7839 18.05 - 36.10: 771 36.10 - 54.15: 190 54.15 - 72.20: 48 72.20 - 90.24: 27 Dihedral angle restraints: 8875 sinusoidal: 3567 harmonic: 5308 Sorted by residual: dihedral pdb=" CA ILE A 370 " pdb=" C ILE A 370 " pdb=" N TYR A 371 " pdb=" CA TYR A 371 " ideal model delta harmonic sigma weight residual 180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE D 370 " pdb=" C ILE D 370 " pdb=" N TYR D 371 " pdb=" CA TYR D 371 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ILE B 370 " pdb=" C ILE B 370 " pdb=" N TYR B 371 " pdb=" CA TYR B 371 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1366 0.037 - 0.074: 590 0.074 - 0.111: 207 0.111 - 0.148: 55 0.148 - 0.185: 2 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CA BLEU G 8 " pdb=" N BLEU G 8 " pdb=" C BLEU G 8 " pdb=" CB BLEU G 8 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA VAL C 316 " pdb=" N VAL C 316 " pdb=" C VAL C 316 " pdb=" CB VAL C 316 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VAL B 316 " pdb=" N VAL B 316 " pdb=" C VAL B 316 " pdb=" CB VAL B 316 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 2217 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 122 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C HIS B 122 " -0.036 2.00e-02 2.50e+03 pdb=" O HIS B 122 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 123 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 356 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 357 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 357 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 357 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 117 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ILE B 117 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE B 117 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.63: 3 1.63 - 2.45: 75 2.45 - 3.27: 14527 3.27 - 4.08: 39068 4.08 - 4.90: 72071 Warning: very small nonbonded interaction distances. Nonbonded interactions: 125744 Sorted by model distance: nonbonded pdb=" NE2BHIS D 89 " pdb=" CA BGLY G 15 " model vdw 0.814 2.816 nonbonded pdb=" ND1BHIS D 89 " pdb=" CA BGLY G 15 " model vdw 1.551 2.816 nonbonded pdb=" CD2BHIS D 89 " pdb=" CA BGLY G 15 " model vdw 1.595 3.660 nonbonded pdb=" CD2AHIS C 89 " pdb=" N AGLY F 15 " model vdw 1.680 2.672 nonbonded pdb=" NE2BHIS D 89 " pdb=" C BGLY G 15 " model vdw 1.688 3.350 ... (remaining 125739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 127 or resid 129 through 395)) selection = (chain 'B' and (resid 16 through 113 or resid 127 or resid 129 through 395)) selection = (chain 'C' and resid 16 through 395) selection = (chain 'D' and (resid 16 through 113 or resid 127 or resid 129 through 395)) } ncs_group { reference = 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=0.50 max=1.00 mean=0.99 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.270 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:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.009 0.781 14783 Z= 0.863 Angle : 0.627 8.597 20000 Z= 0.359 Chirality : 0.047 0.185 2220 Planarity : 0.004 0.040 2595 Dihedral : 16.331 90.244 5475 Min Nonbonded Distance : 0.814 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.98 % Favored : 97.74 % Rotamer: Outliers : 1.61 % Allowed : 14.97 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.49 (0.19), residues: 1830 helix: 1.00 (0.21), residues: 567 sheet: 0.95 (0.29), residues: 361 loop : -0.31 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 30 TYR 0.015 0.002 TYR E 186 PHE 0.019 0.002 APHE F 336 TRP 0.013 0.001 TRP E 250 HIS 0.005 0.001 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00381 (14781) covalent geometry : angle 0.62736 (20000) hydrogen bonds : bond 0.17942 ( 621) hydrogen bonds : angle 6.14870 ( 1725) Misc. bond : bond 0.72559 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8469 (m90) REVERT: E 256 MET cc_start: 0.8213 (mtt) cc_final: 0.7762 (mtp) outliers start: 25 outliers final: 10 residues processed: 166 average time/residue: 0.7716 time to fit residues: 137.9015 Evaluate side-chains 100 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain G residue 8 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 25 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN ** D 334 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.102624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069324 restraints weight = 29644.807| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.09 r_work: 0.2839 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14783 Z= 0.126 Angle : 0.560 10.601 20000 Z= 0.295 Chirality : 0.044 0.188 2220 Planarity : 0.004 0.036 2595 Dihedral : 5.655 77.482 2034 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.82 % Favored : 98.07 % Rotamer: Outliers : 2.06 % Allowed : 17.03 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.78 (0.19), residues: 1830 helix: 1.39 (0.21), residues: 577 sheet: 1.12 (0.28), residues: 353 loop : -0.26 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 30 TYR 0.011 0.001 TYR E 259 PHE 0.010 0.001 PHE B 18 TRP 0.008 0.001 TRP A 387 HIS 0.008 0.001 AHIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00268 (14781) covalent geometry : angle 0.55984 (20000) hydrogen bonds : bond 0.04174 ( 621) hydrogen bonds : angle 4.57414 ( 1725) Misc. bond : bond 0.00591 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: B 70 GLU cc_start: 0.8176 (mp0) cc_final: 0.7954 (mp0) REVERT: E 203 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8882 (mtmt) REVERT: E 244 ILE cc_start: 0.8441 (mt) cc_final: 0.7795 (pp) REVERT: E 256 MET cc_start: 0.8981 (mtt) cc_final: 0.8292 (mtp) REVERT: E 261 MET cc_start: 0.8556 (mmm) cc_final: 0.8245 (mmt) REVERT: A 85 GLU cc_start: 0.8681 (tp30) cc_final: 0.8472 (tp30) REVERT: A 189 MET cc_start: 0.9116 (ttp) cc_final: 0.8913 (ttm) REVERT: C 191 ASP cc_start: 0.8407 (t0) cc_final: 0.8135 (OUTLIER) REVERT: D 81 LYS cc_start: 0.9254 (tttm) cc_final: 0.9047 (ttpp) REVERT: D 317 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8525 (tp40) outliers start: 32 outliers final: 12 residues processed: 130 average time/residue: 0.6659 time to fit residues: 94.5939 Evaluate side-chains 102 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain F residue 7 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 37 optimal weight: 0.0040 chunk 104 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS E 270 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 161 ASN ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066171 restraints weight = 30166.822| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.04 r_work: 0.2773 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14783 Z= 0.233 Angle : 0.576 8.521 20000 Z= 0.302 Chirality : 0.046 0.202 2220 Planarity : 0.004 0.037 2595 Dihedral : 5.023 66.186 2021 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 2.97 % Allowed : 16.06 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.81 (0.19), residues: 1830 helix: 1.61 (0.21), residues: 578 sheet: 0.92 (0.27), residues: 366 loop : -0.30 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.015 0.001 TYR A 287 PHE 0.010 0.001 PHE A 139 TRP 0.010 0.001 TRP E 250 HIS 0.008 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00546 (14781) covalent geometry : angle 0.57603 (20000) hydrogen bonds : bond 0.04554 ( 621) hydrogen bonds : angle 4.45854 ( 1725) Misc. bond : bond 0.00390 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 GLU cc_start: 0.8219 (mp0) cc_final: 0.7989 (mp0) REVERT: B 239 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8969 (m-30) REVERT: E 203 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8908 (mtmt) REVERT: E 244 ILE cc_start: 0.8576 (mt) cc_final: 0.8025 (pp) REVERT: E 256 MET cc_start: 0.9033 (mtt) cc_final: 0.8340 (mtp) REVERT: E 261 MET cc_start: 0.8604 (mmt) cc_final: 0.8181 (mmm) REVERT: A 85 GLU cc_start: 0.8744 (tp30) cc_final: 0.8421 (tp30) REVERT: C 57 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: C 134 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 147 GLU cc_start: 0.9009 (tp30) cc_final: 0.8583 (tp30) REVERT: C 191 ASP cc_start: 0.8361 (t0) cc_final: 0.8121 (OUTLIER) REVERT: D 81 LYS cc_start: 0.9259 (tttm) cc_final: 0.8996 (ttpp) REVERT: D 317 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8331 (tt0) outliers start: 46 outliers final: 19 residues processed: 130 average time/residue: 0.6493 time to fit residues: 92.0605 Evaluate side-chains 105 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain F residue 7 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 HIS E 80 HIS A 135 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065677 restraints weight = 30046.163| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.05 r_work: 0.2760 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14783 Z= 0.236 Angle : 0.566 8.116 20000 Z= 0.300 Chirality : 0.046 0.248 2220 Planarity : 0.004 0.040 2595 Dihedral : 5.012 63.117 2021 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.98 % Favored : 97.91 % Rotamer: Outliers : 2.84 % Allowed : 16.19 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1830 helix: 1.67 (0.21), residues: 578 sheet: 0.79 (0.27), residues: 365 loop : -0.32 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.013 0.001 TYR A 287 PHE 0.011 0.001 PHE A 139 TRP 0.011 0.001 TRP E 250 HIS 0.012 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00553 (14781) covalent geometry : angle 0.56618 (20000) hydrogen bonds : bond 0.04430 ( 621) hydrogen bonds : angle 4.38032 ( 1725) Misc. bond : bond 0.00322 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: B 238 GLU cc_start: 0.8583 (pm20) cc_final: 0.8299 (pm20) REVERT: B 239 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8824 (m-30) REVERT: E 203 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8994 (mttp) REVERT: E 244 ILE cc_start: 0.8625 (mt) cc_final: 0.7965 (pp) REVERT: E 245 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7958 (mtpp) REVERT: E 256 MET cc_start: 0.9080 (mtt) cc_final: 0.8388 (mtp) REVERT: E 261 MET cc_start: 0.8587 (mmt) cc_final: 0.8203 (mmm) REVERT: A 85 GLU cc_start: 0.8784 (tp30) cc_final: 0.8453 (tp30) REVERT: A 258 ASP cc_start: 0.7321 (t70) cc_final: 0.7063 (t0) REVERT: C 57 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: C 134 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (t0) REVERT: C 191 ASP cc_start: 0.8311 (t0) cc_final: 0.7969 (OUTLIER) REVERT: C 196 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8661 (mm) REVERT: D 57 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: D 81 LYS cc_start: 0.9251 (tttm) cc_final: 0.8984 (ttpp) REVERT: D 192 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.5907 (mtt180) REVERT: D 317 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8285 (tt0) outliers start: 44 outliers final: 18 residues processed: 126 average time/residue: 0.6666 time to fit residues: 91.5595 Evaluate side-chains 105 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain F residue 7 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 124 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.064955 restraints weight = 29936.435| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.02 r_work: 0.2768 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14783 Z= 0.235 Angle : 0.562 10.694 20000 Z= 0.294 Chirality : 0.046 0.170 2220 Planarity : 0.004 0.044 2595 Dihedral : 4.960 60.937 2021 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 2.65 % Allowed : 16.77 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.75 (0.19), residues: 1830 helix: 1.63 (0.21), residues: 584 sheet: 0.76 (0.27), residues: 364 loop : -0.35 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.013 0.001 TYR A 287 PHE 0.011 0.001 PHE A 139 TRP 0.011 0.001 TRP E 250 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00551 (14781) covalent geometry : angle 0.56209 (20000) hydrogen bonds : bond 0.04370 ( 621) hydrogen bonds : angle 4.35859 ( 1725) Misc. bond : bond 0.00245 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: B 238 GLU cc_start: 0.8649 (pm20) cc_final: 0.8431 (pm20) REVERT: B 239 ASP cc_start: 0.9320 (OUTLIER) cc_final: 0.8933 (m-30) REVERT: E 203 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8702 (mtmt) REVERT: E 244 ILE cc_start: 0.8686 (mt) cc_final: 0.8057 (pp) REVERT: E 245 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (mtpp) REVERT: E 256 MET cc_start: 0.9079 (mtt) cc_final: 0.8397 (mtp) REVERT: E 261 MET cc_start: 0.8609 (mmt) cc_final: 0.8223 (mmm) REVERT: A 85 GLU cc_start: 0.8769 (tp30) cc_final: 0.8424 (tp30) REVERT: A 112 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: C 57 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: C 134 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8354 (t0) REVERT: C 191 ASP cc_start: 0.8272 (t0) cc_final: 0.7943 (OUTLIER) REVERT: C 196 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 57 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: D 81 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9004 (ttpp) REVERT: D 192 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.5906 (mtt180) REVERT: D 317 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8267 (tp40) outliers start: 41 outliers final: 17 residues processed: 119 average time/residue: 0.6166 time to fit residues: 80.9162 Evaluate side-chains 106 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 317 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 178 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065564 restraints weight = 29994.262| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.05 r_work: 0.2775 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14783 Z= 0.156 Angle : 0.527 10.186 20000 Z= 0.277 Chirality : 0.044 0.182 2220 Planarity : 0.004 0.044 2595 Dihedral : 4.495 48.155 2018 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.82 % Favored : 98.07 % Rotamer: Outliers : 2.39 % Allowed : 17.16 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.85 (0.19), residues: 1830 helix: 1.68 (0.21), residues: 584 sheet: 0.82 (0.27), residues: 363 loop : -0.27 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 192 TYR 0.015 0.001 TYR E 259 PHE 0.009 0.001 PHE C 139 TRP 0.011 0.001 TRP E 250 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00362 (14781) covalent geometry : angle 0.52715 (20000) hydrogen bonds : bond 0.03899 ( 621) hydrogen bonds : angle 4.21156 ( 1725) Misc. bond : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: B 239 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.9007 (m-30) REVERT: B 342 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8231 (mp0) REVERT: E 203 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8962 (mttp) REVERT: E 244 ILE cc_start: 0.8725 (mt) cc_final: 0.8128 (pp) REVERT: E 245 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7914 (mtpp) REVERT: E 256 MET cc_start: 0.9093 (mtt) cc_final: 0.8405 (mtp) REVERT: E 261 MET cc_start: 0.8635 (mmt) cc_final: 0.8273 (mmm) REVERT: A 85 GLU cc_start: 0.8780 (tp30) cc_final: 0.8420 (tp30) REVERT: A 112 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: C 57 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: C 134 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8442 (t0) REVERT: D 57 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: D 81 LYS cc_start: 0.9262 (tttm) cc_final: 0.9027 (ttpp) REVERT: D 317 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8222 (tp40) outliers start: 37 outliers final: 21 residues processed: 118 average time/residue: 0.5693 time to fit residues: 74.3617 Evaluate side-chains 110 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 317 GLN Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 54 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 181 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 334 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.066583 restraints weight = 29756.560| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.04 r_work: 0.2793 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14783 Z= 0.112 Angle : 0.510 9.368 20000 Z= 0.265 Chirality : 0.043 0.174 2220 Planarity : 0.004 0.048 2595 Dihedral : 4.346 46.849 2018 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.60 % Favored : 98.29 % Rotamer: Outliers : 2.13 % Allowed : 17.94 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 0.98 (0.20), residues: 1830 helix: 1.83 (0.21), residues: 585 sheet: 0.89 (0.27), residues: 356 loop : -0.20 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 192 TYR 0.019 0.001 TYR A 287 PHE 0.009 0.001 PHE E 60 TRP 0.011 0.001 TRP E 250 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00256 (14781) covalent geometry : angle 0.51012 (20000) hydrogen bonds : bond 0.03512 ( 621) hydrogen bonds : angle 4.07050 ( 1725) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: B 238 GLU cc_start: 0.8586 (pm20) cc_final: 0.8333 (pm20) REVERT: B 239 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8861 (m-30) REVERT: B 342 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8197 (mp0) REVERT: E 203 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8943 (mttp) REVERT: E 244 ILE cc_start: 0.8769 (mt) cc_final: 0.8263 (pp) REVERT: E 256 MET cc_start: 0.9069 (mtt) cc_final: 0.8371 (mtp) REVERT: E 261 MET cc_start: 0.8590 (mmt) cc_final: 0.8222 (mmm) REVERT: A 85 GLU cc_start: 0.8776 (tp30) cc_final: 0.8394 (tp30) REVERT: A 112 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: C 57 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: C 134 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8426 (t0) REVERT: C 191 ASP cc_start: 0.7992 (t0) cc_final: 0.7711 (OUTLIER) REVERT: D 81 LYS cc_start: 0.9252 (tttm) cc_final: 0.9020 (ttpp) outliers start: 33 outliers final: 19 residues processed: 114 average time/residue: 0.5632 time to fit residues: 71.2462 Evaluate side-chains 105 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 361 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 159 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.068173 restraints weight = 30231.882| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.09 r_work: 0.2811 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14783 Z= 0.096 Angle : 0.492 8.684 20000 Z= 0.257 Chirality : 0.043 0.146 2220 Planarity : 0.003 0.055 2595 Dihedral : 4.209 44.825 2018 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.87 % Allowed : 18.45 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 1.11 (0.20), residues: 1830 helix: 1.94 (0.21), residues: 585 sheet: 0.98 (0.27), residues: 355 loop : -0.13 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 192 TYR 0.014 0.001 TYR D 287 PHE 0.010 0.001 PHE C 139 TRP 0.012 0.001 TRP E 250 HIS 0.010 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00216 (14781) covalent geometry : angle 0.49188 (20000) hydrogen bonds : bond 0.03202 ( 621) hydrogen bonds : angle 3.92872 ( 1725) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: B 238 GLU cc_start: 0.8630 (pm20) cc_final: 0.8271 (pp20) REVERT: B 239 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8835 (m-30) REVERT: B 342 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8179 (mp0) REVERT: E 203 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8976 (mttp) REVERT: E 244 ILE cc_start: 0.8765 (mt) cc_final: 0.8258 (pp) REVERT: E 256 MET cc_start: 0.9112 (mtt) cc_final: 0.8419 (mtp) REVERT: E 259 TYR cc_start: 0.8120 (t80) cc_final: 0.7665 (t80) REVERT: E 261 MET cc_start: 0.8594 (mmt) cc_final: 0.8219 (mmm) REVERT: A 85 GLU cc_start: 0.8798 (tp30) cc_final: 0.8410 (tp30) REVERT: A 112 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: C 57 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: D 57 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8047 (mm-30) outliers start: 29 outliers final: 15 residues processed: 111 average time/residue: 0.5994 time to fit residues: 73.4370 Evaluate side-chains 101 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.067615 restraints weight = 30125.166| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.09 r_work: 0.2816 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14783 Z= 0.102 Angle : 0.496 10.513 20000 Z= 0.256 Chirality : 0.043 0.169 2220 Planarity : 0.004 0.058 2595 Dihedral : 4.123 43.318 2018 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Rotamer: Outliers : 1.55 % Allowed : 18.71 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 1830 helix: 1.99 (0.21), residues: 585 sheet: 1.06 (0.27), residues: 361 loop : -0.09 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 192 TYR 0.014 0.001 TYR D 287 PHE 0.010 0.001 PHE E 60 TRP 0.012 0.001 TRP E 250 HIS 0.004 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00232 (14781) covalent geometry : angle 0.49552 (20000) hydrogen bonds : bond 0.03192 ( 621) hydrogen bonds : angle 3.89608 ( 1725) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: B 239 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8912 (m-30) REVERT: B 342 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8188 (mp0) REVERT: E 203 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8971 (mttp) REVERT: E 244 ILE cc_start: 0.8771 (mt) cc_final: 0.8261 (pp) REVERT: E 256 MET cc_start: 0.9131 (mtt) cc_final: 0.8463 (mtp) REVERT: E 259 TYR cc_start: 0.8177 (t80) cc_final: 0.7692 (t80) REVERT: E 261 MET cc_start: 0.8584 (mmt) cc_final: 0.8215 (mmm) REVERT: A 85 GLU cc_start: 0.8804 (tp30) cc_final: 0.8412 (tp30) REVERT: A 112 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: C 57 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: C 191 ASP cc_start: 0.8031 (t0) cc_final: 0.7799 (OUTLIER) REVERT: D 57 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7995 (mm-30) outliers start: 24 outliers final: 15 residues processed: 103 average time/residue: 0.5747 time to fit residues: 65.5341 Evaluate side-chains 100 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 15 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 chunk 166 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 80 HIS ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.067462 restraints weight = 30050.707| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.05 r_work: 0.2808 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14783 Z= 0.115 Angle : 0.494 8.267 20000 Z= 0.257 Chirality : 0.043 0.144 2220 Planarity : 0.004 0.061 2595 Dihedral : 4.078 41.238 2018 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.42 % Allowed : 18.97 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 1.22 (0.20), residues: 1830 helix: 2.03 (0.21), residues: 585 sheet: 1.07 (0.27), residues: 361 loop : -0.09 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 192 TYR 0.014 0.001 TYR D 287 PHE 0.011 0.001 PHE D 139 TRP 0.013 0.001 TRP E 250 HIS 0.013 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00265 (14781) covalent geometry : angle 0.49381 (20000) hydrogen bonds : bond 0.03278 ( 621) hydrogen bonds : angle 3.88558 ( 1725) Misc. bond : bond 0.00099 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: B 342 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8206 (mt-10) REVERT: E 203 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8992 (mttp) REVERT: E 244 ILE cc_start: 0.8789 (mt) cc_final: 0.8281 (pp) REVERT: E 256 MET cc_start: 0.9127 (mtt) cc_final: 0.8457 (mtp) REVERT: E 259 TYR cc_start: 0.8267 (t80) cc_final: 0.7761 (t80) REVERT: E 261 MET cc_start: 0.8583 (mmt) cc_final: 0.8203 (mmm) REVERT: A 85 GLU cc_start: 0.8826 (tp30) cc_final: 0.8433 (tp30) REVERT: A 112 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 57 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: C 134 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 191 ASP cc_start: 0.8101 (t0) cc_final: 0.7841 (OUTLIER) REVERT: D 57 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8020 (mm-30) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.5631 time to fit residues: 65.7642 Evaluate side-chains 103 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 161 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 chunk 79 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 71 optimal weight: 0.0050 chunk 23 optimal weight: 0.1980 chunk 114 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.068430 restraints weight = 30001.726| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.06 r_work: 0.2860 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14783 Z= 0.088 Angle : 0.484 8.304 20000 Z= 0.250 Chirality : 0.042 0.143 2220 Planarity : 0.003 0.062 2595 Dihedral : 3.987 40.144 2018 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.38 % Favored : 98.57 % Rotamer: Outliers : 1.35 % Allowed : 18.97 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % 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: 1830 helix: 2.07 (0.21), residues: 585 sheet: 1.13 (0.27), residues: 361 loop : -0.06 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 192 TYR 0.014 0.001 TYR D 287 PHE 0.009 0.001 PHE C 139 TRP 0.012 0.001 TRP E 250 HIS 0.014 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00193 (14781) covalent geometry : angle 0.48449 (20000) hydrogen bonds : bond 0.03015 ( 621) hydrogen bonds : angle 3.82624 ( 1725) Misc. bond : bond 0.00072 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5183.97 seconds wall clock time: 89 minutes 15.41 seconds (5355.41 seconds total)