Starting phenix.real_space_refine on Fri Jul 3 15:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j10_61064/07_2026/9j10_61064.map" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 72 5.16 5 C 9748 2.51 5 N 2444 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14816 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3702 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3702 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3702 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3702 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 13, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.48, per 1000 atoms: 0.17 Number of scatterers: 14816 At special positions: 0 Unit cell: (109.044, 109.044, 123.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 72 16.00 O 2548 8.00 N 2444 7.00 C 9748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 530.3 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 66.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 64 through 90 removed outlier: 3.797A pdb=" N MET A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 4.025A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 115 removed outlier: 4.131A pdb=" N GLN A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.554A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.671A pdb=" N ASP A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.710A pdb=" N ILE A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 176 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.628A pdb=" N GLU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 removed outlier: 3.693A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 removed outlier: 4.027A pdb=" N LEU A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.751A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.512A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 3.601A pdb=" N ARG A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 312 removed outlier: 3.619A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 333 removed outlier: 3.638A pdb=" N ASP A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 351 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.662A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 360' Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.642A pdb=" N TYR A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.673A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.048A pdb=" N ILE A 400 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 401 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 402' Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.932A pdb=" N PHE A 485 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'B' and resid 64 through 90 removed outlier: 3.797A pdb=" N MET B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 4.025A pdb=" N PHE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 115 removed outlier: 4.132A pdb=" N GLN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.555A pdb=" N ARG B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.671A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.710A pdb=" N ILE B 173 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 176 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.628A pdb=" N GLU B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 removed outlier: 3.693A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 210 " --> pdb=" O PHE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 4.028A pdb=" N LEU B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.751A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.513A pdb=" N ILE B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.601A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 312 removed outlier: 3.619A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 333 removed outlier: 3.638A pdb=" N ASP B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 354 through 360 removed outlier: 4.662A pdb=" N THR B 358 " --> pdb=" O HIS B 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 360' Processing helix chain 'B' and resid 367 through 377 removed outlier: 3.642A pdb=" N TYR B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.673A pdb=" N PHE B 387 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 402 removed outlier: 4.049A pdb=" N ILE B 400 " --> pdb=" O GLN B 397 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 401 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 481 through 490 removed outlier: 3.933A pdb=" N PHE B 485 " --> pdb=" O ASP B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'C' and resid 64 through 90 removed outlier: 3.797A pdb=" N MET C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 74 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 75 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 4.026A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 115 removed outlier: 4.131A pdb=" N GLN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.555A pdb=" N ARG C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.671A pdb=" N ASP C 147 " --> pdb=" O HIS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.710A pdb=" N ILE C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 176 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.628A pdb=" N GLU C 189 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 removed outlier: 3.693A pdb=" N THR C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 210 " --> pdb=" O PHE C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 removed outlier: 4.028A pdb=" N LEU C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.750A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.512A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.601A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 312 removed outlier: 3.619A pdb=" N MET C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.638A pdb=" N ASP C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 351 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.662A pdb=" N THR C 358 " --> pdb=" O HIS C 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 359 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 360' Processing helix chain 'C' and resid 367 through 377 removed outlier: 3.641A pdb=" N TYR C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.673A pdb=" N PHE C 387 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 402 removed outlier: 4.049A pdb=" N ILE C 400 " --> pdb=" O GLN C 397 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 401 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 481 through 490 removed outlier: 3.932A pdb=" N PHE C 485 " --> pdb=" O ASP C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'D' and resid 64 through 90 removed outlier: 3.798A pdb=" N MET D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 74 " --> pdb=" O MET D 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 4.025A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 115 removed outlier: 4.132A pdb=" N GLN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 131 through 143 removed outlier: 3.554A pdb=" N ARG D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 150 removed outlier: 3.671A pdb=" N ASP D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.710A pdb=" N ILE D 173 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 176 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.629A pdb=" N GLU D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 removed outlier: 3.694A pdb=" N THR D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 210 " --> pdb=" O PHE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 removed outlier: 4.027A pdb=" N LEU D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 226' Processing helix chain 'D' and resid 227 through 234 removed outlier: 3.751A pdb=" N GLU D 231 " --> pdb=" O PRO D 228 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.512A pdb=" N ILE D 252 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.601A pdb=" N ARG D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 312 removed outlier: 3.619A pdb=" N MET D 285 " --> pdb=" O ASN D 281 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 333 removed outlier: 3.637A pdb=" N ASP D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS D 333 " --> pdb=" O PHE D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 351 Processing helix chain 'D' and resid 354 through 360 removed outlier: 4.662A pdb=" N THR D 358 " --> pdb=" O HIS D 354 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 360' Processing helix chain 'D' and resid 367 through 377 removed outlier: 3.641A pdb=" N TYR D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 381 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.673A pdb=" N PHE D 387 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 402 removed outlier: 4.049A pdb=" N ILE D 400 " --> pdb=" O GLN D 397 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG D 401 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU D 402 " --> pdb=" O VAL D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 397 through 402' Processing helix chain 'D' and resid 481 through 490 removed outlier: 3.932A pdb=" N PHE D 485 " --> pdb=" O ASP D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.672A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA3, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.580A pdb=" N GLU A 405 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 477 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS A 476 " --> pdb=" O CYS A 427 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 424 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 454 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 removed outlier: 3.537A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.671A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.579A pdb=" N GLU B 405 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 477 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS B 476 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 424 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 454 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 448 removed outlier: 3.537A pdb=" N THR B 446 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.672A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.579A pdb=" N GLU C 405 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 477 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR C 424 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE C 454 " --> pdb=" O TYR C 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 446 through 448 removed outlier: 3.538A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.672A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 404 through 407 removed outlier: 3.580A pdb=" N GLU D 405 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 477 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N HIS D 476 " --> pdb=" O CYS D 427 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR D 424 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 454 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 446 through 448 removed outlier: 3.537A pdb=" N THR D 446 " --> pdb=" O ALA D 433 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1824 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: 2.15 Time building geometry restraints manager: 1.26 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: 4503 1.34 - 1.46: 3615 1.46 - 1.58: 6962 1.58 - 1.70: 16 1.70 - 1.82: 112 Bond restraints: 15208 Sorted by residual: bond pdb=" CB GLU A 473 " pdb=" CG GLU A 473 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.83e+00 bond pdb=" CB GLU B 473 " pdb=" CG GLU B 473 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.78e+00 bond pdb=" CB GLU D 473 " pdb=" CG GLU D 473 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" CB GLU C 473 " pdb=" CG GLU C 473 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.23e+00 ... (remaining 15203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 20470 4.98 - 9.95: 106 9.95 - 14.93: 16 14.93 - 19.91: 0 19.91 - 24.89: 4 Bond angle restraints: 20596 Sorted by residual: angle pdb=" C PHE A 407 " pdb=" N LEU A 408 " pdb=" CA LEU A 408 " ideal model delta sigma weight residual 120.97 145.86 -24.89 2.84e+00 1.24e-01 7.68e+01 angle pdb=" C PHE C 407 " pdb=" N LEU C 408 " pdb=" CA LEU C 408 " ideal model delta sigma weight residual 120.97 145.84 -24.87 2.84e+00 1.24e-01 7.67e+01 angle pdb=" C PHE D 407 " pdb=" N LEU D 408 " pdb=" CA LEU D 408 " ideal model delta sigma weight residual 120.97 145.83 -24.86 2.84e+00 1.24e-01 7.66e+01 angle pdb=" C PHE B 407 " pdb=" N LEU B 408 " pdb=" CA LEU B 408 " ideal model delta sigma weight residual 120.97 145.78 -24.81 2.84e+00 1.24e-01 7.63e+01 angle pdb=" CA GLU A 415 " pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " ideal model delta sigma weight residual 114.10 128.46 -14.36 2.00e+00 2.50e-01 5.15e+01 ... (remaining 20591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 7775 16.30 - 32.61: 875 32.61 - 48.91: 189 48.91 - 65.22: 33 65.22 - 81.52: 8 Dihedral angle restraints: 8880 sinusoidal: 3616 harmonic: 5264 Sorted by residual: dihedral pdb=" CA ASN D 418 " pdb=" C ASN D 418 " pdb=" N VAL D 419 " pdb=" CA VAL D 419 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ASN A 418 " pdb=" C ASN A 418 " pdb=" N VAL A 419 " pdb=" CA VAL A 419 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ASN C 418 " pdb=" C ASN C 418 " pdb=" N VAL C 419 " pdb=" CA VAL C 419 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1567 0.056 - 0.112: 544 0.112 - 0.168: 124 0.168 - 0.224: 16 0.224 - 0.280: 13 Chirality restraints: 2264 Sorted by residual: chirality pdb=" CA LEU A 378 " pdb=" N LEU A 378 " pdb=" C LEU A 378 " pdb=" CB LEU A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA LEU C 378 " pdb=" N LEU C 378 " pdb=" C LEU C 378 " pdb=" CB LEU C 378 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LEU B 378 " pdb=" N LEU B 378 " pdb=" C LEU B 378 " pdb=" CB LEU B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2261 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 408 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO D 409 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 409 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 409 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 409 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 409 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.035 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.87: 9 1.87 - 2.69: 364 2.69 - 3.51: 22258 3.51 - 4.32: 41525 4.32 - 5.14: 69982 Nonbonded interactions: 134138 Sorted by model distance: nonbonded pdb=" N LEU A 430 " pdb=" OE2 GLU A 473 " model vdw 1.057 3.120 nonbonded pdb=" CD1 LEU C 430 " pdb=" OE2 GLU C 473 " model vdw 1.277 3.460 nonbonded pdb=" CD1 LEU D 430 " pdb=" OE2 GLU D 473 " model vdw 1.279 3.460 nonbonded pdb=" CD2 LEU D 431 " pdb=" CG2 VAL D 471 " model vdw 1.770 3.880 nonbonded pdb=" CD2 LEU B 431 " pdb=" CG2 VAL B 471 " model vdw 1.770 3.880 ... (remaining 134133 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 48 through 502) selection = chain 'B' selection = (chain 'C' and resid 48 through 502) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.007 0.078 15208 Z= 0.297 Angle : 1.160 24.886 20596 Z= 0.630 Chirality : 0.061 0.280 2264 Planarity : 0.008 0.064 2552 Dihedral : 14.362 81.523 5504 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.15), residues: 1764 helix: -2.92 (0.11), residues: 960 sheet: -2.38 (0.47), residues: 100 loop : -2.24 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 340 TYR 0.020 0.002 TYR D 380 PHE 0.033 0.003 PHE C 319 TRP 0.011 0.001 TRP A 255 HIS 0.006 0.002 HIS C 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.30 (15208) covalent geometry : angle 1.15977 / 0.63 (20596) hydrogen bonds : bond 0.22482 / 13.93 ( 680) hydrogen bonds : angle 6.97228 / 4.89 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7610 (ttt180) REVERT: A 301 TYR cc_start: 0.8388 (t80) cc_final: 0.8131 (t80) REVERT: A 323 MET cc_start: 0.8240 (mmp) cc_final: 0.8024 (mpt) REVERT: B 196 TYR cc_start: 0.8074 (p90) cc_final: 0.7854 (p90) REVERT: B 200 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7493 (ttt180) REVERT: B 301 TYR cc_start: 0.8424 (t80) cc_final: 0.8059 (t80) REVERT: C 200 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7579 (tpt170) REVERT: C 301 TYR cc_start: 0.8468 (t80) cc_final: 0.8205 (t80) REVERT: D 200 ARG cc_start: 0.7840 (ttm170) cc_final: 0.7571 (ttt180) REVERT: D 301 TYR cc_start: 0.8398 (t80) cc_final: 0.8153 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.8483 time to fit residues: 117.7211 Evaluate side-chains 97 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 62 ASN A 186 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 476 HIS B 52 ASN B 62 ASN B 186 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 HIS C 52 ASN C 62 ASN C 186 GLN ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 HIS C 476 HIS D 52 ASN D 62 ASN D 186 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 HIS D 476 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.177955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089171 restraints weight = 23948.062| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.63 r_work: 0.2778 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 : 0.004 0.033 15208 Z= 0.160 Angle : 0.636 8.028 20596 Z= 0.338 Chirality : 0.044 0.184 2264 Planarity : 0.005 0.054 2552 Dihedral : 5.596 19.759 2000 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.56 % Allowed : 12.66 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1764 helix: -0.65 (0.16), residues: 952 sheet: -1.92 (0.50), residues: 100 loop : -1.18 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 168 TYR 0.013 0.001 TYR A 220 PHE 0.023 0.001 PHE C 319 TRP 0.011 0.001 TRP B 255 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (15208) covalent geometry : angle 0.63613 / 0.34 (20596) hydrogen bonds : bond 0.06770 / 4.40 ( 680) hydrogen bonds : angle 4.69620 / 3.29 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8793 (pp20) cc_final: 0.8546 (pp20) REVERT: A 200 ARG cc_start: 0.7717 (ttm170) cc_final: 0.7293 (ttt180) REVERT: A 323 MET cc_start: 0.8175 (mmp) cc_final: 0.7939 (mmp) REVERT: B 200 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7233 (ttt180) REVERT: C 127 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.8004 (pmm-80) REVERT: C 200 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7369 (ttt180) REVERT: C 312 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8920 (ttpp) REVERT: C 362 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8101 (pm20) REVERT: D 200 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7288 (ttt180) REVERT: D 301 TYR cc_start: 0.8986 (t80) cc_final: 0.8767 (t80) outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.9047 time to fit residues: 109.9053 Evaluate side-chains 99 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 354 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN A 59 HIS ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN B 418 ASN C 350 GLN C 418 ASN D 350 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.179321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089680 restraints weight = 24016.348| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.02 r_work: 0.2786 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15208 Z= 0.123 Angle : 0.549 7.469 20596 Z= 0.292 Chirality : 0.042 0.167 2264 Planarity : 0.005 0.054 2552 Dihedral : 4.951 17.297 2000 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.24 % Allowed : 12.66 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1764 helix: 0.33 (0.17), residues: 968 sheet: -1.16 (0.50), residues: 116 loop : -0.81 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 TYR 0.016 0.001 TYR A 351 PHE 0.024 0.001 PHE A 319 TRP 0.010 0.001 TRP D 255 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15208) covalent geometry : angle 0.54909 / 0.29 (20596) hydrogen bonds : bond 0.05573 / 3.62 ( 680) hydrogen bonds : angle 4.27985 / 2.99 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9130 (tpt) cc_final: 0.8911 (tpp) REVERT: A 200 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7239 (ttt180) REVERT: A 323 MET cc_start: 0.8438 (mmp) cc_final: 0.8168 (mmp) REVERT: B 51 HIS cc_start: 0.6606 (m-70) cc_final: 0.6401 (m-70) REVERT: B 200 ARG cc_start: 0.7588 (ttm170) cc_final: 0.7128 (ttt180) REVERT: B 204 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8757 (tt) REVERT: C 70 MET cc_start: 0.9129 (tpt) cc_final: 0.8868 (tpp) REVERT: C 127 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.8089 (pmm-80) REVERT: C 200 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7191 (ttt180) REVERT: C 418 ASN cc_start: 0.5494 (OUTLIER) cc_final: 0.4892 (p0) REVERT: D 121 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8477 (ttm-80) outliers start: 20 outliers final: 3 residues processed: 120 average time/residue: 0.7878 time to fit residues: 102.1277 Evaluate side-chains 102 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 354 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 40.0000 chunk 89 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.178440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.086620 restraints weight = 23725.571| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.66 r_work: 0.2739 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15208 Z= 0.146 Angle : 0.556 6.300 20596 Z= 0.297 Chirality : 0.042 0.163 2264 Planarity : 0.005 0.057 2552 Dihedral : 4.838 18.420 2000 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 14.08 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1764 helix: 0.65 (0.17), residues: 968 sheet: -0.65 (0.55), residues: 108 loop : -0.60 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 127 TYR 0.021 0.001 TYR C 351 PHE 0.024 0.001 PHE C 319 TRP 0.011 0.001 TRP D 255 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (15208) covalent geometry : angle 0.55650 / 0.30 (20596) hydrogen bonds : bond 0.06256 / 4.09 ( 680) hydrogen bonds : angle 4.19403 / 2.93 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9156 (tpt) cc_final: 0.8942 (tpp) REVERT: A 200 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7212 (ttt180) REVERT: A 320 ARG cc_start: 0.8127 (tpt170) cc_final: 0.7727 (tmm160) REVERT: A 323 MET cc_start: 0.8453 (mmp) cc_final: 0.8103 (mmp) REVERT: A 324 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8158 (t0) REVERT: A 362 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8753 (pm20) REVERT: B 51 HIS cc_start: 0.6461 (m-70) cc_final: 0.6178 (m-70) REVERT: B 127 ARG cc_start: 0.8524 (pmm-80) cc_final: 0.8308 (mpp80) REVERT: B 200 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7133 (ttt180) REVERT: C 70 MET cc_start: 0.9131 (tpt) cc_final: 0.8898 (tpp) REVERT: C 127 ARG cc_start: 0.8489 (ptp-110) cc_final: 0.8037 (pmm-80) REVERT: C 200 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7174 (ttt180) REVERT: C 335 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4757 (mm) outliers start: 19 outliers final: 9 residues processed: 123 average time/residue: 0.7957 time to fit residues: 105.8959 Evaluate side-chains 110 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 9.9990 chunk 78 optimal weight: 40.0000 chunk 106 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 99 optimal weight: 0.6980 chunk 168 optimal weight: 0.0470 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN C 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.179140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088264 restraints weight = 23994.073| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.93 r_work: 0.2772 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15208 Z= 0.122 Angle : 0.545 9.213 20596 Z= 0.285 Chirality : 0.041 0.151 2264 Planarity : 0.004 0.057 2552 Dihedral : 4.637 18.555 2000 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.43 % Allowed : 14.70 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1764 helix: 0.83 (0.17), residues: 980 sheet: -0.65 (0.53), residues: 108 loop : -0.53 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 127 TYR 0.013 0.001 TYR C 351 PHE 0.023 0.001 PHE C 319 TRP 0.009 0.001 TRP A 255 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15208) covalent geometry : angle 0.54509 / 0.28 (20596) hydrogen bonds : bond 0.05410 / 3.54 ( 680) hydrogen bonds : angle 4.03017 / 2.81 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9146 (tpt) cc_final: 0.8909 (tpp) REVERT: A 200 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7034 (ttt180) REVERT: A 320 ARG cc_start: 0.8171 (tpt170) cc_final: 0.7871 (tpt-90) REVERT: A 323 MET cc_start: 0.8474 (mmp) cc_final: 0.8222 (mmp) REVERT: A 324 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8156 (p0) REVERT: A 362 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8684 (pm20) REVERT: B 127 ARG cc_start: 0.8537 (pmm-80) cc_final: 0.8217 (mpp80) REVERT: B 200 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7108 (ttt180) REVERT: C 70 MET cc_start: 0.9123 (tpt) cc_final: 0.8905 (tpp) REVERT: C 127 ARG cc_start: 0.8465 (ptp-110) cc_final: 0.8026 (pmm-80) REVERT: C 200 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7105 (ttt180) outliers start: 23 outliers final: 11 residues processed: 126 average time/residue: 0.7482 time to fit residues: 102.6711 Evaluate side-chains 111 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.178471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087217 restraints weight = 23653.825| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.31 r_work: 0.2736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15208 Z= 0.142 Angle : 0.562 8.190 20596 Z= 0.293 Chirality : 0.042 0.162 2264 Planarity : 0.004 0.056 2552 Dihedral : 4.585 19.908 2000 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.61 % Allowed : 15.14 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1764 helix: 0.90 (0.17), residues: 980 sheet: -0.65 (0.52), residues: 108 loop : -0.52 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 127 TYR 0.011 0.001 TYR D 263 PHE 0.022 0.001 PHE C 319 TRP 0.010 0.001 TRP D 255 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (15208) covalent geometry : angle 0.56175 / 0.29 (20596) hydrogen bonds : bond 0.06047 / 3.95 ( 680) hydrogen bonds : angle 4.02841 / 2.80 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9126 (tpt) cc_final: 0.8894 (tpp) REVERT: A 200 ARG cc_start: 0.7594 (ttm170) cc_final: 0.7129 (ttt180) REVERT: A 320 ARG cc_start: 0.8160 (tpt170) cc_final: 0.7912 (tpt-90) REVERT: A 323 MET cc_start: 0.8464 (mmp) cc_final: 0.8186 (mmp) REVERT: A 324 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8193 (p0) REVERT: A 362 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8728 (pm20) REVERT: B 127 ARG cc_start: 0.8565 (pmm-80) cc_final: 0.8241 (pmm-80) REVERT: B 200 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7107 (ttt180) REVERT: C 70 MET cc_start: 0.9143 (tpt) cc_final: 0.8933 (tpp) REVERT: C 127 ARG cc_start: 0.8451 (ptp-110) cc_final: 0.8008 (pmm-80) REVERT: C 200 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7066 (ttt180) REVERT: C 402 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.2063 (tp) REVERT: D 200 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7024 (ttt180) outliers start: 26 outliers final: 11 residues processed: 124 average time/residue: 0.7686 time to fit residues: 103.2348 Evaluate side-chains 112 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 402 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 86 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN C 350 GLN D 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.177330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085896 restraints weight = 23470.592| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.29 r_work: 0.2714 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15208 Z= 0.187 Angle : 0.590 8.139 20596 Z= 0.309 Chirality : 0.044 0.172 2264 Planarity : 0.005 0.057 2552 Dihedral : 4.624 18.527 2000 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.80 % Allowed : 14.95 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1764 helix: 0.85 (0.17), residues: 984 sheet: -0.69 (0.51), residues: 108 loop : -0.49 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 127 TYR 0.013 0.001 TYR A 263 PHE 0.022 0.001 PHE C 319 TRP 0.010 0.001 TRP D 255 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15208) covalent geometry : angle 0.58982 / 0.31 (20596) hydrogen bonds : bond 0.07010 / 4.58 ( 680) hydrogen bonds : angle 4.08409 / 2.84 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9151 (tpt) cc_final: 0.8927 (tpp) REVERT: A 200 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7177 (ttt180) REVERT: A 323 MET cc_start: 0.8536 (mmp) cc_final: 0.8311 (mmp) REVERT: A 324 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8237 (p0) REVERT: A 362 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8715 (pm20) REVERT: B 127 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8197 (pmm-80) REVERT: B 200 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7191 (ttt180) REVERT: C 70 MET cc_start: 0.9137 (tpt) cc_final: 0.8935 (tpp) REVERT: C 200 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7201 (ttt180) REVERT: C 402 LEU cc_start: 0.2252 (OUTLIER) cc_final: 0.2000 (tp) REVERT: D 200 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7166 (ttt180) outliers start: 29 outliers final: 15 residues processed: 125 average time/residue: 0.7016 time to fit residues: 95.4018 Evaluate side-chains 119 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 402 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN C 350 GLN C 354 HIS C 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.175517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083241 restraints weight = 23614.125| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.17 r_work: 0.2677 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15208 Z= 0.298 Angle : 0.675 8.449 20596 Z= 0.355 Chirality : 0.049 0.247 2264 Planarity : 0.005 0.057 2552 Dihedral : 4.810 18.707 2000 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.67 % Allowed : 15.82 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1764 helix: 0.31 (0.16), residues: 1036 sheet: -0.67 (0.51), residues: 108 loop : -1.07 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 127 TYR 0.015 0.002 TYR A 258 PHE 0.020 0.002 PHE A 319 TRP 0.010 0.001 TRP D 255 HIS 0.009 0.001 HIS D 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.30 (15208) covalent geometry : angle 0.67534 / 0.35 (20596) hydrogen bonds : bond 0.08513 / 5.54 ( 680) hydrogen bonds : angle 4.24694 / 2.95 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9116 (tpt) cc_final: 0.8911 (tpp) REVERT: A 200 ARG cc_start: 0.7784 (ttm170) cc_final: 0.7285 (ttt180) REVERT: A 324 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 362 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8709 (pm20) REVERT: B 127 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8240 (pmm-80) REVERT: B 200 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7281 (ttt180) REVERT: C 70 MET cc_start: 0.9128 (tpt) cc_final: 0.8922 (tpp) REVERT: C 127 ARG cc_start: 0.8467 (ptp-110) cc_final: 0.8152 (ptp-110) REVERT: C 200 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7264 (ttt180) REVERT: C 402 LEU cc_start: 0.2436 (OUTLIER) cc_final: 0.2158 (tp) REVERT: D 200 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7224 (ttt180) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.7874 time to fit residues: 100.8314 Evaluate side-chains 115 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 402 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 172 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 100 optimal weight: 0.0030 chunk 150 optimal weight: 0.4980 chunk 33 optimal weight: 20.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.178883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087989 restraints weight = 23879.872| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.22 r_work: 0.2775 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15208 Z= 0.121 Angle : 0.571 9.420 20596 Z= 0.297 Chirality : 0.042 0.216 2264 Planarity : 0.004 0.059 2552 Dihedral : 4.538 21.456 2000 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.18 % Allowed : 16.56 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1764 helix: 0.97 (0.17), residues: 984 sheet: -1.68 (0.57), residues: 80 loop : -0.52 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 127 TYR 0.014 0.001 TYR C 351 PHE 0.021 0.001 PHE A 319 TRP 0.011 0.001 TRP A 255 HIS 0.011 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15208) covalent geometry : angle 0.57102 / 0.30 (20596) hydrogen bonds : bond 0.05305 / 3.47 ( 680) hydrogen bonds : angle 3.92719 / 2.75 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9154 (tpt) cc_final: 0.8926 (tpp) REVERT: A 200 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7114 (ttt180) REVERT: A 324 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8285 (p0) REVERT: A 362 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8655 (pm20) REVERT: B 127 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8169 (pmm-80) REVERT: B 189 GLU cc_start: 0.8925 (pp20) cc_final: 0.8682 (pp20) REVERT: B 200 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7091 (ttt180) REVERT: C 70 MET cc_start: 0.9136 (tpt) cc_final: 0.8923 (tpp) REVERT: C 127 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.8174 (ptp-110) REVERT: C 200 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7195 (ttt180) REVERT: C 402 LEU cc_start: 0.2254 (OUTLIER) cc_final: 0.1979 (tp) REVERT: D 200 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7028 (ttt180) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.7911 time to fit residues: 99.3926 Evaluate side-chains 113 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 402 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 chunk 174 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086153 restraints weight = 23551.517| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.30 r_work: 0.2729 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15208 Z= 0.163 Angle : 0.598 7.712 20596 Z= 0.313 Chirality : 0.043 0.202 2264 Planarity : 0.004 0.059 2552 Dihedral : 4.557 23.417 2000 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.36 % Allowed : 16.44 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1764 helix: 0.95 (0.17), residues: 980 sheet: -1.62 (0.58), residues: 80 loop : -0.46 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 127 TYR 0.014 0.001 TYR A 351 PHE 0.022 0.001 PHE C 319 TRP 0.011 0.001 TRP A 255 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (15208) covalent geometry : angle 0.59759 / 0.31 (20596) hydrogen bonds : bond 0.06540 / 4.28 ( 680) hydrogen bonds : angle 3.98430 / 2.78 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9140 (tpt) cc_final: 0.8914 (tpp) REVERT: A 200 ARG cc_start: 0.7624 (ttm170) cc_final: 0.7170 (ttt180) REVERT: A 324 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8270 (p0) REVERT: A 362 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8667 (pm20) REVERT: B 127 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8166 (pmm-80) REVERT: B 200 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7175 (ttt180) REVERT: C 127 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: C 200 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7218 (ttt180) REVERT: C 402 LEU cc_start: 0.2272 (OUTLIER) cc_final: 0.2006 (tp) REVERT: D 200 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7044 (ttt180) outliers start: 22 outliers final: 14 residues processed: 117 average time/residue: 0.7763 time to fit residues: 98.4143 Evaluate side-chains 115 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 354 HIS Chi-restraints excluded: chain D residue 402 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 83 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 73 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 0.0980 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN C 354 HIS D 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.179594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088987 restraints weight = 23785.011| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.31 r_work: 0.2791 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15208 Z= 0.116 Angle : 0.559 7.662 20596 Z= 0.291 Chirality : 0.041 0.194 2264 Planarity : 0.004 0.061 2552 Dihedral : 4.394 23.888 2000 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.18 % Allowed : 16.69 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1764 helix: 1.12 (0.17), residues: 980 sheet: -1.62 (0.58), residues: 80 loop : -0.44 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 127 TYR 0.014 0.001 TYR A 351 PHE 0.019 0.001 PHE A 319 TRP 0.010 0.001 TRP D 255 HIS 0.003 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15208) covalent geometry : angle 0.55871 / 0.29 (20596) hydrogen bonds : bond 0.04939 / 3.24 ( 680) hydrogen bonds : angle 3.80191 / 2.66 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10308.23 seconds wall clock time: 175 minutes 16.52 seconds (10516.52 seconds total)