Starting phenix.real_space_refine on Fri May 16 21:29:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_61064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_61064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_61064.map" model { file = "/net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_61064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j10_61064/05_2025/9j10_61064.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 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: 11.70, per 1000 atoms: 0.79 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.72 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: 4.49 Time building geometry restraints manager: 4.23 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: 5.660 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.420 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 255 HIS 0.006 0.002 HIS C 346 PHE 0.033 0.003 PHE C 319 TYR 0.020 0.002 TYR D 380 ARG 0.006 0.001 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.22482 ( 680) hydrogen bonds : angle 6.97228 ( 1824) covalent geometry : bond 0.00660 (15208) covalent geometry : angle 1.15977 (20596) *********************** 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 : 1.593 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: 0.8130 (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: 0.7496 (ttt180) REVERT: B 301 TYR cc_start: 0.8424 (t80) cc_final: 0.8173 (t80) REVERT: C 200 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7582 (tpt170) REVERT: C 301 TYR cc_start: 0.8468 (t80) cc_final: 0.8229 (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: 1.9329 time to fit residues: 268.6016 Evaluate side-chains 100 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 D 52 ASN D 62 ASN D 186 GLN D 350 GLN 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 = 0.4384 r_free = 0.4384 target = 0.176939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087137 restraints weight = 23673.842| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.75 r_work: 0.2759 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15208 Z= 0.195 Angle : 0.656 7.975 20596 Z= 0.350 Chirality : 0.045 0.174 2264 Planarity : 0.006 0.054 2552 Dihedral : 5.643 20.419 2000 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.68 % Allowed : 12.66 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 1764 helix: -0.93 (0.15), residues: 1008 sheet: -2.34 (0.57), residues: 80 loop : -1.79 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 255 HIS 0.007 0.001 HIS A 213 PHE 0.023 0.001 PHE C 319 TYR 0.014 0.002 TYR D 263 ARG 0.004 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.07590 ( 680) hydrogen bonds : angle 4.76491 ( 1824) covalent geometry : bond 0.00456 (15208) covalent geometry : angle 0.65560 (20596) *********************** 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 123 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.558 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: 0.8823 (pp20) cc_final: 0.8582 (pp20) REVERT: A 200 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7324 (ttt180) REVERT: A 323 MET cc_start: 0.8172 (mmp) cc_final: 0.7932 (mmp) REVERT: B 200 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7262 (ttt180) REVERT: B 204 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8759 (tt) REVERT: C 127 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.8026 (pmm-80) REVERT: C 200 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7420 (ttt180) REVERT: C 204 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8740 (tt) REVERT: C 312 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8956 (ttpp) REVERT: C 362 GLN cc_start: 0.8347 (tp-100) cc_final: 0.8133 (pm20) REVERT: D 200 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7321 (ttt180) outliers start: 11 outliers final: 4 residues processed: 122 average time/residue: 1.7172 time to fit residues: 225.8786 Evaluate side-chains 104 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 121 ARG Chi-restraints excluded: chain C residue 204 LEU 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 110 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 175 optimal weight: 50.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 59 HIS ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 350 GLN D 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.179157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090637 restraints weight = 23808.042| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.81 r_work: 0.2819 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15208 Z= 0.117 Angle : 0.555 6.696 20596 Z= 0.294 Chirality : 0.041 0.139 2264 Planarity : 0.005 0.055 2552 Dihedral : 5.027 17.178 2000 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.87 % Allowed : 13.40 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1764 helix: 0.26 (0.17), residues: 968 sheet: -1.17 (0.50), residues: 116 loop : -0.99 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 255 HIS 0.005 0.001 HIS A 354 PHE 0.023 0.001 PHE A 319 TYR 0.030 0.001 TYR A 351 ARG 0.008 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.05360 ( 680) hydrogen bonds : angle 4.31363 ( 1824) covalent geometry : bond 0.00260 (15208) covalent geometry : angle 0.55465 (20596) *********************** 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 117 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.588 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: 0.9120 (tpt) cc_final: 0.8868 (tpp) REVERT: A 189 GLU cc_start: 0.8812 (pp20) cc_final: 0.8565 (pp20) REVERT: A 200 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7246 (ttt180) REVERT: A 323 MET cc_start: 0.8342 (mmp) cc_final: 0.8069 (mmp) REVERT: B 200 ARG cc_start: 0.7624 (ttm170) cc_final: 0.7143 (ttt180) REVERT: B 204 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8812 (tt) REVERT: C 70 MET cc_start: 0.9050 (tpt) cc_final: 0.8805 (tpp) REVERT: C 127 ARG cc_start: 0.8500 (ptp-110) cc_final: 0.8059 (pmm-80) REVERT: C 200 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7178 (ttt180) REVERT: C 204 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8782 (tt) REVERT: C 362 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: D 127 ARG cc_start: 0.8471 (pmm-80) cc_final: 0.8220 (pmm-80) outliers start: 14 outliers final: 3 residues processed: 115 average time/residue: 1.6640 time to fit residues: 206.8086 Evaluate side-chains 105 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 362 GLN 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 115 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 151 optimal weight: 0.1980 chunk 121 optimal weight: 40.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 350 GLN D 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.180402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090966 restraints weight = 23454.718| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.37 r_work: 0.2829 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15208 Z= 0.109 Angle : 0.519 6.374 20596 Z= 0.276 Chirality : 0.041 0.154 2264 Planarity : 0.004 0.056 2552 Dihedral : 4.610 17.455 2000 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.30 % Allowed : 14.08 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1764 helix: 0.76 (0.17), residues: 972 sheet: -0.71 (0.54), residues: 108 loop : -0.75 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 255 HIS 0.004 0.001 HIS A 213 PHE 0.027 0.001 PHE C 319 TYR 0.015 0.001 TYR C 351 ARG 0.010 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 680) hydrogen bonds : angle 4.06033 ( 1824) covalent geometry : bond 0.00240 (15208) covalent geometry : angle 0.51899 (20596) *********************** 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 128 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.524 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: 0.9127 (tpt) cc_final: 0.8909 (tpp) REVERT: A 189 GLU cc_start: 0.8817 (pp20) cc_final: 0.8575 (pp20) REVERT: A 200 ARG cc_start: 0.7479 (ttm170) cc_final: 0.6985 (ttt180) REVERT: A 323 MET cc_start: 0.8441 (mmp) cc_final: 0.8176 (mmp) REVERT: A 362 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8673 (pm20) REVERT: B 51 HIS cc_start: 0.6252 (m-70) cc_final: 0.6004 (m-70) REVERT: B 200 ARG cc_start: 0.7600 (ttm170) cc_final: 0.7120 (ttt180) REVERT: B 204 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8880 (tt) REVERT: C 70 MET cc_start: 0.9088 (tpt) cc_final: 0.8858 (tpp) REVERT: C 127 ARG cc_start: 0.8487 (ptp-110) cc_final: 0.8058 (pmm-80) REVERT: C 200 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7068 (ttt180) REVERT: C 204 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8874 (tt) REVERT: C 335 LEU cc_start: 0.4972 (OUTLIER) cc_final: 0.4692 (mm) outliers start: 21 outliers final: 5 residues processed: 127 average time/residue: 1.5153 time to fit residues: 209.0410 Evaluate side-chains 107 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 HIS 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 167 optimal weight: 40.0000 chunk 148 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN D 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.084750 restraints weight = 23681.406| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.36 r_work: 0.2683 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15208 Z= 0.232 Angle : 0.622 9.508 20596 Z= 0.326 Chirality : 0.046 0.184 2264 Planarity : 0.005 0.057 2552 Dihedral : 4.811 17.413 2000 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1764 helix: 0.32 (0.17), residues: 1028 sheet: -0.66 (0.53), residues: 108 loop : -1.30 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 255 HIS 0.007 0.001 HIS B 213 PHE 0.022 0.002 PHE A 319 TYR 0.013 0.001 TYR B 263 ARG 0.009 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.07801 ( 680) hydrogen bonds : angle 4.29351 ( 1824) covalent geometry : bond 0.00567 (15208) covalent geometry : angle 0.62210 (20596) *********************** 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 129 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.665 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: 0.9143 (tpt) cc_final: 0.8938 (tpp) REVERT: A 189 GLU cc_start: 0.8876 (pp20) cc_final: 0.8582 (pp20) REVERT: A 200 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7230 (ttt180) REVERT: A 204 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8730 (tt) REVERT: A 362 GLN cc_start: 0.9092 (tp-100) cc_final: 0.8769 (pm20) REVERT: B 51 HIS cc_start: 0.6543 (m-70) cc_final: 0.6303 (m-70) REVERT: B 200 ARG cc_start: 0.7730 (ttm170) cc_final: 0.7255 (ttt180) REVERT: B 204 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 70 MET cc_start: 0.9127 (tpt) cc_final: 0.8916 (tpp) REVERT: C 127 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8140 (pmm-80) REVERT: C 200 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7204 (ttt180) REVERT: C 204 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (tt) REVERT: D 200 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7129 (ttt180) outliers start: 29 outliers final: 9 residues processed: 127 average time/residue: 1.5551 time to fit residues: 214.9831 Evaluate side-chains 105 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 354 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 57 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 121 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.179388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089013 restraints weight = 23621.382| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.29 r_work: 0.2782 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3221 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= 0.118 Angle : 0.548 9.510 20596 Z= 0.283 Chirality : 0.041 0.149 2264 Planarity : 0.004 0.057 2552 Dihedral : 4.513 19.692 2000 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 15.32 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1764 helix: 0.97 (0.17), residues: 976 sheet: -0.68 (0.51), residues: 108 loop : -0.65 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.005 0.001 HIS B 213 PHE 0.021 0.001 PHE A 319 TYR 0.016 0.001 TYR A 351 ARG 0.011 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 680) hydrogen bonds : angle 3.94557 ( 1824) covalent geometry : bond 0.00266 (15208) covalent geometry : angle 0.54824 (20596) *********************** 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 120 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9129 (tpt) cc_final: 0.8890 (tpp) REVERT: A 189 GLU cc_start: 0.8875 (pp20) cc_final: 0.8568 (pp20) REVERT: A 200 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7080 (ttt180) REVERT: A 362 GLN cc_start: 0.9033 (tp-100) cc_final: 0.8667 (pm20) REVERT: B 51 HIS cc_start: 0.6344 (m-70) cc_final: 0.6141 (m-70) REVERT: B 200 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7115 (ttt180) REVERT: B 204 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8797 (tt) REVERT: C 70 MET cc_start: 0.9145 (tpt) cc_final: 0.8932 (tpp) REVERT: C 127 ARG cc_start: 0.8497 (ptp-110) cc_final: 0.8052 (pmm-80) REVERT: C 200 ARG cc_start: 0.7566 (ttm170) cc_final: 0.7111 (tpt170) REVERT: C 204 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8789 (tt) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 1.5855 time to fit residues: 202.4558 Evaluate side-chains 105 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 51 HIS Chi-restraints excluded: chain C residue 204 LEU 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 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 30 optimal weight: 0.0770 chunk 15 optimal weight: 0.0970 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 172 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.091650 restraints weight = 23839.980| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.28 r_work: 0.2818 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15208 Z= 0.104 Angle : 0.534 7.844 20596 Z= 0.274 Chirality : 0.041 0.256 2264 Planarity : 0.004 0.057 2552 Dihedral : 4.279 23.229 2000 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.24 % Allowed : 15.94 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1764 helix: 1.17 (0.17), residues: 984 sheet: -0.68 (0.51), residues: 108 loop : -0.51 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 255 HIS 0.004 0.000 HIS C 213 PHE 0.020 0.001 PHE A 319 TYR 0.014 0.001 TYR A 351 ARG 0.014 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 680) hydrogen bonds : angle 3.76291 ( 1824) covalent geometry : bond 0.00229 (15208) covalent geometry : angle 0.53415 (20596) *********************** 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 121 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9108 (tpt) cc_final: 0.8868 (tpp) REVERT: A 189 GLU cc_start: 0.8908 (pp20) cc_final: 0.8617 (pp20) REVERT: A 200 ARG cc_start: 0.7444 (ttm170) cc_final: 0.6938 (ttt180) REVERT: A 362 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8674 (pm20) REVERT: B 51 HIS cc_start: 0.6022 (m-70) cc_final: 0.5816 (m-70) REVERT: B 127 ARG cc_start: 0.8603 (mtm110) cc_final: 0.8344 (mtm110) REVERT: B 200 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7106 (ttt180) REVERT: B 204 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8876 (tt) REVERT: C 70 MET cc_start: 0.9099 (tpt) cc_final: 0.8845 (tpp) REVERT: C 200 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7066 (tpt170) outliers start: 20 outliers final: 9 residues processed: 118 average time/residue: 1.5889 time to fit residues: 203.1523 Evaluate side-chains 107 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 51 HIS 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 121 ARG Chi-restraints excluded: chain D residue 204 LEU 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 98 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 95 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.179126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089085 restraints weight = 23622.803| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.12 r_work: 0.2766 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3494 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= 0.130 Angle : 0.558 8.419 20596 Z= 0.287 Chirality : 0.042 0.195 2264 Planarity : 0.004 0.057 2552 Dihedral : 4.316 22.226 2000 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.18 % Allowed : 16.38 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1764 helix: 1.17 (0.17), residues: 980 sheet: -0.66 (0.51), residues: 108 loop : -0.48 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 255 HIS 0.007 0.001 HIS C 354 PHE 0.021 0.001 PHE C 319 TYR 0.012 0.001 TYR A 351 ARG 0.013 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 680) hydrogen bonds : angle 3.81195 ( 1824) covalent geometry : bond 0.00303 (15208) covalent geometry : angle 0.55752 (20596) *********************** 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 114 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9115 (tpt) cc_final: 0.8878 (tpp) REVERT: A 189 GLU cc_start: 0.8970 (pp20) cc_final: 0.8651 (pp20) REVERT: A 200 ARG cc_start: 0.7468 (ttm170) cc_final: 0.6941 (ttt180) REVERT: A 362 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8667 (pm20) REVERT: B 51 HIS cc_start: 0.6069 (m-70) cc_final: 0.5854 (m-70) REVERT: B 127 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8252 (pmm-80) REVERT: B 200 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7090 (ttt180) REVERT: B 204 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 70 MET cc_start: 0.9149 (tpt) cc_final: 0.8911 (tpp) REVERT: C 127 ARG cc_start: 0.8511 (ptp-110) cc_final: 0.8117 (ptp-110) REVERT: C 200 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7093 (tpt170) REVERT: C 320 ARG cc_start: 0.8105 (tmt170) cc_final: 0.7858 (tpt90) outliers start: 19 outliers final: 8 residues processed: 110 average time/residue: 1.6512 time to fit residues: 196.8232 Evaluate side-chains 104 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 51 HIS Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 121 ARG 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 156 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.175874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083935 restraints weight = 23523.427| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.19 r_work: 0.2682 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15208 Z= 0.298 Angle : 0.670 8.332 20596 Z= 0.351 Chirality : 0.049 0.197 2264 Planarity : 0.005 0.060 2552 Dihedral : 4.674 20.491 2000 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.36 % Allowed : 16.63 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1764 helix: 0.43 (0.16), residues: 1028 sheet: -1.70 (0.57), residues: 80 loop : -1.12 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 255 HIS 0.009 0.001 HIS B 213 PHE 0.022 0.002 PHE C 319 TYR 0.015 0.002 TYR C 258 ARG 0.013 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.08396 ( 680) hydrogen bonds : angle 4.15364 ( 1824) covalent geometry : bond 0.00735 (15208) covalent geometry : angle 0.66957 (20596) *********************** 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 112 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8945 (pp20) cc_final: 0.8626 (pp20) REVERT: A 200 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7195 (ttt180) REVERT: A 362 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8676 (pm20) REVERT: B 51 HIS cc_start: 0.6440 (m-70) cc_final: 0.6239 (m-70) REVERT: B 200 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7231 (ttt180) REVERT: B 204 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8691 (tt) REVERT: C 70 MET cc_start: 0.9129 (tpt) cc_final: 0.8927 (tpp) REVERT: C 127 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8164 (ptp-110) REVERT: C 200 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7225 (ttt180) REVERT: D 200 ARG cc_start: 0.7666 (ttm170) cc_final: 0.7202 (ttt180) outliers start: 22 outliers final: 11 residues processed: 109 average time/residue: 1.6097 time to fit residues: 190.1643 Evaluate side-chains 101 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain B residue 204 LEU 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 175 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 121 ARG Chi-restraints excluded: chain D residue 175 LEU 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: 7.9990 chunk 32 optimal weight: 30.0000 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 HIS D 354 HIS 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 = 0.178712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087874 restraints weight = 23767.541| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.13 r_work: 0.2763 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3585 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= 0.132 Angle : 0.575 7.536 20596 Z= 0.298 Chirality : 0.042 0.171 2264 Planarity : 0.004 0.062 2552 Dihedral : 4.442 23.778 2000 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.74 % Allowed : 17.18 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1764 helix: 1.05 (0.17), residues: 972 sheet: -1.62 (0.57), residues: 80 loop : -0.63 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 255 HIS 0.004 0.001 HIS D 213 PHE 0.027 0.001 PHE C 319 TYR 0.014 0.001 TYR A 351 ARG 0.015 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 680) hydrogen bonds : angle 3.84581 ( 1824) covalent geometry : bond 0.00308 (15208) covalent geometry : angle 0.57481 (20596) ********************** 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 109 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.8958 (pp20) cc_final: 0.8617 (pp20) REVERT: A 200 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7027 (ttt180) REVERT: A 362 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8641 (pm20) REVERT: B 51 HIS cc_start: 0.6209 (m-70) cc_final: 0.6008 (m-70) REVERT: B 127 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8069 (pmm-80) REVERT: B 200 ARG cc_start: 0.7666 (ttm170) cc_final: 0.7141 (ttt180) REVERT: B 204 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 70 MET cc_start: 0.9150 (tpt) cc_final: 0.8942 (tpp) REVERT: C 127 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8150 (ptp-110) REVERT: C 200 ARG cc_start: 0.7614 (ttm170) cc_final: 0.7143 (tpt170) REVERT: D 134 ARG cc_start: 0.8778 (mtp-110) cc_final: 0.8488 (ptp-110) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 1.6216 time to fit residues: 189.5383 Evaluate side-chains 106 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 51 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 121 ARG 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 168 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 0.0170 chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 162 optimal weight: 8.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.177497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086493 restraints weight = 23657.140| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.11 r_work: 0.2725 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15208 Z= 0.177 Angle : 0.598 7.306 20596 Z= 0.313 Chirality : 0.044 0.173 2264 Planarity : 0.005 0.058 2552 Dihedral : 4.513 23.052 2000 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.74 % Allowed : 17.37 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1764 helix: 0.93 (0.17), residues: 980 sheet: -1.56 (0.58), residues: 80 loop : -0.62 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 255 HIS 0.006 0.001 HIS A 213 PHE 0.025 0.001 PHE C 319 TYR 0.014 0.001 TYR A 351 ARG 0.015 0.000 ARG B 127 Details of bonding type rmsd hydrogen bonds : bond 0.06751 ( 680) hydrogen bonds : angle 3.94051 ( 1824) covalent geometry : bond 0.00427 (15208) covalent geometry : angle 0.59758 (20596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20139.31 seconds wall clock time: 345 minutes 5.97 seconds (20705.97 seconds total)