Starting phenix.real_space_refine on Fri Aug 7 16:11:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.map" model { file = "/net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkz_65147/08_2026/9vkz_65147.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 72 5.16 5 C 13806 2.51 5 N 3870 2.21 5 O 4290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22056 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "C" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "D" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "F" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3645 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 442} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.22 Number of scatterers: 22056 At special positions: 0 Unit cell: (148.42, 141.86, 132.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 18 15.00 O 4290 8.00 N 3870 7.00 C 13806 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 24 sheets defined 50.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.687A pdb=" N GLY A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.829A pdb=" N ALA A 17 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 98 through 119 removed outlier: 3.769A pdb=" N TRP A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.583A pdb=" N GLN A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 257 through 277 removed outlier: 3.936A pdb=" N LYS A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 removed outlier: 5.288A pdb=" N SER A 281 " --> pdb=" O GLY A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 282 through 304 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 358 through 379 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 402 through 417 removed outlier: 4.056A pdb=" N GLU A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.828A pdb=" N GLY B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 removed outlier: 3.814A pdb=" N ALA B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.830A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.559A pdb=" N GLN B 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 257 through 276 removed outlier: 4.010A pdb=" N LYS B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 278 No H-bonds generated for 'chain 'B' and resid 277 through 278' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 304 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 358 through 379 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 417 removed outlier: 4.018A pdb=" N GLU B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.863A pdb=" N GLY C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 removed outlier: 3.794A pdb=" N ALA C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 49 Processing helix chain 'C' and resid 98 through 119 removed outlier: 3.815A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.551A pdb=" N ARG C 207 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 238 through 256 Processing helix chain 'C' and resid 257 through 277 removed outlier: 4.006A pdb=" N LYS C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 removed outlier: 5.262A pdb=" N SER C 281 " --> pdb=" O GLY C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 282 through 304 Processing helix chain 'C' and resid 310 through 326 Processing helix chain 'C' and resid 358 through 379 Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 402 through 417 removed outlier: 3.993A pdb=" N GLU C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE C 410 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 432 Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.687A pdb=" N GLY D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.829A pdb=" N ALA D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 49 Processing helix chain 'D' and resid 98 through 119 removed outlier: 3.768A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.583A pdb=" N GLN D 209 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 238 through 256 Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.936A pdb=" N LYS D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 281 removed outlier: 5.288A pdb=" N SER D 281 " --> pdb=" O GLY D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 281' Processing helix chain 'D' and resid 282 through 304 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 358 through 379 Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 402 through 417 removed outlier: 4.056A pdb=" N GLU D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE D 410 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU D 411 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.827A pdb=" N GLY E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 26 removed outlier: 3.814A pdb=" N ALA E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 49 Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.808A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 204 through 209 removed outlier: 3.561A pdb=" N GLN E 209 " --> pdb=" O GLU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 238 through 256 Processing helix chain 'E' and resid 257 through 276 removed outlier: 4.011A pdb=" N LYS E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 278 No H-bonds generated for 'chain 'E' and resid 277 through 278' Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 282 through 304 Processing helix chain 'E' and resid 310 through 326 Processing helix chain 'E' and resid 358 through 379 Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 402 through 417 removed outlier: 4.019A pdb=" N GLU E 408 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE E 410 " --> pdb=" O GLN E 406 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU E 411 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.865A pdb=" N GLY F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 26 removed outlier: 3.792A pdb=" N ALA F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 119 removed outlier: 3.821A pdb=" N TRP F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.561A pdb=" N ARG F 207 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 223 Processing helix chain 'F' and resid 224 through 230 Processing helix chain 'F' and resid 238 through 256 Processing helix chain 'F' and resid 257 through 277 removed outlier: 4.007A pdb=" N LYS F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY F 277 " --> pdb=" O ARG F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 281 removed outlier: 5.262A pdb=" N SER F 281 " --> pdb=" O GLY F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 281' Processing helix chain 'F' and resid 282 through 304 Processing helix chain 'F' and resid 310 through 326 Processing helix chain 'F' and resid 358 through 379 Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 402 through 417 removed outlier: 3.993A pdb=" N GLU F 408 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU F 411 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 438 No H-bonds generated for 'chain 'F' and resid 436 through 438' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 164 removed outlier: 4.770A pdb=" N LYS A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE A 150 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 148 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 149 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A 66 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 81 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.029A pdb=" N THR A 199 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 393 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 201 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP A 395 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR A 203 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 390 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE A 423 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 392 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR A 425 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 394 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ARG A 441 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 90 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 335 removed outlier: 4.116A pdb=" N LYS A 331 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 164 removed outlier: 4.772A pdb=" N LYS B 155 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 150 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 148 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B 81 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.031A pdb=" N THR B 199 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 393 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 201 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP B 395 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 203 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 335 removed outlier: 4.134A pdb=" N LYS B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 83 removed outlier: 5.444A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 68 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 163 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 148 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS C 155 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 203 removed outlier: 5.991A pdb=" N THR C 199 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 393 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA C 201 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP C 395 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR C 203 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 335 removed outlier: 4.102A pdb=" N LYS C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AB5, first strand: chain 'D' and resid 154 through 164 removed outlier: 4.771A pdb=" N LYS D 155 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE D 150 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 148 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 81 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.030A pdb=" N THR D 199 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 393 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 201 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP D 395 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR D 203 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 90 " --> pdb=" O ARG D 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 329 through 335 removed outlier: 4.121A pdb=" N LYS D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=AB9, first strand: chain 'E' and resid 154 through 164 removed outlier: 4.773A pdb=" N LYS E 155 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 148 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU E 81 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.030A pdb=" N THR E 199 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU E 393 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA E 201 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP E 395 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR E 203 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 90 " --> pdb=" O ARG E 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 329 through 335 removed outlier: 4.136A pdb=" N LYS E 331 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 52 Processing sheet with id=AC4, first strand: chain 'F' and resid 154 through 164 removed outlier: 4.794A pdb=" N LYS F 155 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE F 150 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE F 148 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 163 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE F 149 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU F 66 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU F 81 " --> pdb=" O SER F 452 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 199 through 203 removed outlier: 5.991A pdb=" N THR F 199 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU F 393 " --> pdb=" O THR F 199 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA F 201 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP F 395 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR F 203 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY F 390 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE F 423 " --> pdb=" O GLY F 390 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL F 392 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N THR F 425 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 394 " --> pdb=" O THR F 425 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG F 441 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F 90 " --> pdb=" O ARG F 441 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 329 through 335 removed outlier: 4.102A pdb=" N LYS F 331 " --> pdb=" O THR F 346 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3168 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: 4.17 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7436 1.34 - 1.46: 4507 1.46 - 1.58: 10341 1.58 - 1.69: 30 1.69 - 1.81: 126 Bond restraints: 22440 Sorted by residual: bond pdb=" O2B ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 1.529 1.469 0.060 2.20e-02 2.07e+03 7.39e+00 bond pdb=" O2B ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 1.529 1.469 0.060 2.20e-02 2.07e+03 7.37e+00 bond pdb=" O2B ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 1.529 1.469 0.060 2.20e-02 2.07e+03 7.35e+00 bond pdb=" O2B ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 1.529 1.470 0.059 2.20e-02 2.07e+03 7.23e+00 bond pdb=" O2B ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 1.529 1.470 0.059 2.20e-02 2.07e+03 7.20e+00 ... (remaining 22435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 29717 1.72 - 3.44: 493 3.44 - 5.16: 99 5.16 - 6.88: 10 6.88 - 8.60: 5 Bond angle restraints: 30324 Sorted by residual: angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 132.13 7.74 1.00e+00 1.00e+00 5.98e+01 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 141.86 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" C5' ATP B 501 " pdb=" O5' ATP B 501 " pdb=" PA ATP B 501 " ideal model delta sigma weight residual 121.27 117.00 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 141.07 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" C5' ATP A 501 " pdb=" O5' ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 121.27 117.45 3.82 1.00e+00 1.00e+00 1.46e+01 ... (remaining 30319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 12418 17.76 - 35.53: 1068 35.53 - 53.29: 214 53.29 - 71.05: 44 71.05 - 88.81: 26 Dihedral angle restraints: 13770 sinusoidal: 5832 harmonic: 7938 Sorted by residual: dihedral pdb=" CA ARG A 75 " pdb=" C ARG A 75 " pdb=" N ARG A 76 " pdb=" CA ARG A 76 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG C 75 " pdb=" C ARG C 75 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG F 75 " pdb=" C ARG F 75 " pdb=" N ARG F 76 " pdb=" CA ARG F 76 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 13767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2208 0.032 - 0.065: 827 0.065 - 0.097: 215 0.097 - 0.129: 129 0.129 - 0.161: 5 Chirality restraints: 3384 Sorted by residual: chirality pdb=" CB ILE E 254 " pdb=" CA ILE E 254 " pdb=" CG1 ILE E 254 " pdb=" CG2 ILE E 254 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB ILE B 254 " pdb=" CA ILE B 254 " pdb=" CG1 ILE B 254 " pdb=" CG2 ILE B 254 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 3381 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 28 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.97e+00 pdb=" N PRO C 29 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 28 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO F 29 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 29 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 29 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 28 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO D 29 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.018 5.00e-02 4.00e+02 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 124 2.40 - 3.02: 12699 3.02 - 3.65: 35456 3.65 - 4.27: 54529 4.27 - 4.90: 89784 Nonbonded interactions: 192592 Sorted by model distance: nonbonded pdb=" O ARG F 75 " pdb=" O3B ATP F 501 " model vdw 1.773 3.040 nonbonded pdb=" OG1 THR A 100 " pdb=" O1G ATP A 501 " model vdw 1.807 3.040 nonbonded pdb=" OG1 THR E 100 " pdb=" O1G ATP E 501 " model vdw 1.814 3.040 nonbonded pdb=" OG1 THR D 100 " pdb=" O3G ATP D 501 " model vdw 1.841 3.040 nonbonded pdb=" OG SER F 101 " pdb=" O2' ATP F 501 " model vdw 1.851 3.040 ... (remaining 192587 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.410 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.012 0.798 22447 Z= 1.146 Angle : 0.574 8.602 30324 Z= 0.338 Chirality : 0.040 0.161 3384 Planarity : 0.003 0.035 3912 Dihedral : 14.297 88.814 8622 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2724 helix: 1.52 (0.15), residues: 1230 sheet: 0.08 (0.26), residues: 396 loop : -0.43 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.019 0.002 TYR F 104 PHE 0.019 0.001 PHE F 364 TRP 0.014 0.001 TRP D 245 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (22440) covalent geometry : angle 0.57420 / 0.34 (30324) hydrogen bonds : bond 0.13959 / 9.17 ( 1124) hydrogen bonds : angle 4.88580 / 3.46 ( 3168) Misc. bond : bond 0.64382 / 34.68 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7945 (m-40) cc_final: 0.7573 (m110) REVERT: A 130 LEU cc_start: 0.8498 (mp) cc_final: 0.8284 (mp) REVERT: A 359 ASP cc_start: 0.7780 (m-30) cc_final: 0.7449 (m-30) REVERT: B 62 ASN cc_start: 0.7829 (m-40) cc_final: 0.7541 (m110) REVERT: B 116 ASN cc_start: 0.7722 (m-40) cc_final: 0.7512 (m-40) REVERT: B 289 MET cc_start: 0.0755 (mmm) cc_final: -0.0904 (ptm) REVERT: B 359 ASP cc_start: 0.7793 (m-30) cc_final: 0.7517 (m-30) REVERT: C 62 ASN cc_start: 0.8016 (m-40) cc_final: 0.7627 (m110) REVERT: C 136 ASP cc_start: 0.7004 (m-30) cc_final: 0.6638 (t0) REVERT: C 231 GLN cc_start: 0.7367 (mt0) cc_final: 0.6627 (tm-30) REVERT: C 289 MET cc_start: -0.1071 (mmm) cc_final: -0.2315 (ptm) REVERT: D 62 ASN cc_start: 0.7903 (m-40) cc_final: 0.7536 (m110) REVERT: D 130 LEU cc_start: 0.8532 (mp) cc_final: 0.8315 (mp) REVERT: D 359 ASP cc_start: 0.7788 (m-30) cc_final: 0.7425 (m-30) REVERT: E 62 ASN cc_start: 0.7826 (m-40) cc_final: 0.7533 (m110) REVERT: E 116 ASN cc_start: 0.7719 (m-40) cc_final: 0.7512 (m-40) REVERT: E 289 MET cc_start: 0.0727 (mmm) cc_final: -0.0920 (ptm) REVERT: E 359 ASP cc_start: 0.7806 (m-30) cc_final: 0.7524 (m-30) REVERT: F 62 ASN cc_start: 0.8009 (m-40) cc_final: 0.7581 (m110) REVERT: F 136 ASP cc_start: 0.7035 (m-30) cc_final: 0.6650 (t0) REVERT: F 231 GLN cc_start: 0.7358 (mt0) cc_final: 0.6612 (tm-30) REVERT: F 289 MET cc_start: -0.1071 (mmm) cc_final: -0.2320 (ptm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.7784 time to fit residues: 265.8394 Evaluate side-chains 214 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN B 218 ASN B 347 ASN B 427 HIS C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 HIS D 125 GLN E 218 ASN E 347 ASN E 427 HIS F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.202534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128150 restraints weight = 22180.769| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.15 r_work: 0.3218 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22447 Z= 0.195 Angle : 0.573 7.594 30324 Z= 0.308 Chirality : 0.043 0.155 3384 Planarity : 0.005 0.059 3912 Dihedral : 9.108 88.467 3186 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.93 % Allowed : 8.58 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2724 helix: 1.45 (0.14), residues: 1242 sheet: 0.16 (0.24), residues: 468 loop : -0.40 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 160 TYR 0.025 0.002 TYR F 104 PHE 0.032 0.002 PHE B 364 TRP 0.014 0.002 TRP A 245 HIS 0.007 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (22440) covalent geometry : angle 0.57337 / 0.31 (30324) hydrogen bonds : bond 0.04124 / 2.74 ( 1124) hydrogen bonds : angle 4.32263 / 3.05 ( 3168) Misc. bond : bond 0.00778 / 0.37 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7529 (m-40) cc_final: 0.7088 (m110) REVERT: A 82 ILE cc_start: 0.8739 (mt) cc_final: 0.8496 (mt) REVERT: A 116 ASN cc_start: 0.8078 (m-40) cc_final: 0.7818 (m-40) REVERT: A 136 ASP cc_start: 0.7505 (t0) cc_final: 0.7265 (t0) REVERT: A 140 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6911 (tpm-80) REVERT: A 311 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: B 62 ASN cc_start: 0.7581 (m-40) cc_final: 0.7259 (m110) REVERT: B 116 ASN cc_start: 0.8034 (m-40) cc_final: 0.7802 (m-40) REVERT: B 289 MET cc_start: 0.0393 (mmm) cc_final: -0.0972 (ptm) REVERT: C 81 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: C 83 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7944 (tmtt) REVERT: C 116 ASN cc_start: 0.8215 (m-40) cc_final: 0.7976 (m-40) REVERT: C 136 ASP cc_start: 0.7817 (m-30) cc_final: 0.7040 (t0) REVERT: C 204 ASN cc_start: 0.8683 (m110) cc_final: 0.8318 (m-40) REVERT: C 289 MET cc_start: -0.1503 (mmm) cc_final: -0.2315 (ptm) REVERT: D 62 ASN cc_start: 0.7544 (m-40) cc_final: 0.7103 (m110) REVERT: D 82 ILE cc_start: 0.8753 (mt) cc_final: 0.8490 (mt) REVERT: D 116 ASN cc_start: 0.8059 (m-40) cc_final: 0.7811 (m-40) REVERT: D 136 ASP cc_start: 0.7532 (t0) cc_final: 0.7300 (t0) REVERT: D 140 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6954 (tpm-80) REVERT: E 62 ASN cc_start: 0.7572 (m-40) cc_final: 0.7243 (m110) REVERT: E 83 LYS cc_start: 0.8154 (tptp) cc_final: 0.7901 (tptp) REVERT: E 116 ASN cc_start: 0.8077 (m-40) cc_final: 0.7832 (m-40) REVERT: E 289 MET cc_start: 0.0404 (mmm) cc_final: -0.0976 (ptm) REVERT: F 116 ASN cc_start: 0.8247 (m-40) cc_final: 0.8016 (m-40) REVERT: F 136 ASP cc_start: 0.7897 (m-30) cc_final: 0.7028 (t0) REVERT: F 289 MET cc_start: -0.1522 (mmm) cc_final: -0.2315 (ptm) outliers start: 47 outliers final: 16 residues processed: 291 average time/residue: 0.6422 time to fit residues: 212.0382 Evaluate side-chains 259 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 312 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 114 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 238 optimal weight: 0.6980 chunk 169 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS A 125 GLN B 51 HIS B 427 HIS C 51 HIS C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 125 GLN E 51 HIS E 427 HIS F 51 HIS F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.204698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130302 restraints weight = 22116.461| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.17 r_work: 0.3242 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22447 Z= 0.128 Angle : 0.501 7.151 30324 Z= 0.273 Chirality : 0.041 0.178 3384 Planarity : 0.004 0.042 3912 Dihedral : 8.669 89.095 3186 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.67 % Allowed : 11.49 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2724 helix: 1.62 (0.14), residues: 1242 sheet: -0.21 (0.26), residues: 396 loop : -0.28 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.022 0.002 TYR C 104 PHE 0.016 0.001 PHE C 364 TRP 0.011 0.001 TRP D 245 HIS 0.004 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22440) covalent geometry : angle 0.50101 / 0.27 (30324) hydrogen bonds : bond 0.03594 / 2.38 ( 1124) hydrogen bonds : angle 4.17595 / 2.94 ( 3168) Misc. bond : bond 0.00648 / 0.31 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 243 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7551 (m-40) cc_final: 0.7087 (m110) REVERT: A 116 ASN cc_start: 0.8111 (m-40) cc_final: 0.7838 (m-40) REVERT: A 136 ASP cc_start: 0.7352 (t0) cc_final: 0.7062 (t0) REVERT: A 140 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6918 (tpm-80) REVERT: A 298 GLU cc_start: 0.1621 (OUTLIER) cc_final: 0.0624 (tm-30) REVERT: A 311 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: B 62 ASN cc_start: 0.7618 (m-40) cc_final: 0.7289 (m110) REVERT: B 116 ASN cc_start: 0.8014 (m-40) cc_final: 0.7791 (m-40) REVERT: B 136 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7496 (t0) REVERT: B 140 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7129 (tpm-80) REVERT: B 163 ARG cc_start: 0.8433 (tpt-90) cc_final: 0.8148 (tpt-90) REVERT: B 206 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7729 (pt0) REVERT: B 289 MET cc_start: 0.0204 (mmm) cc_final: -0.1052 (ptm) REVERT: C 62 ASN cc_start: 0.7600 (m-40) cc_final: 0.7270 (m110) REVERT: C 83 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7985 (tmtt) REVERT: C 116 ASN cc_start: 0.8204 (m-40) cc_final: 0.7978 (m-40) REVERT: C 120 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7247 (mp0) REVERT: C 136 ASP cc_start: 0.7844 (m-30) cc_final: 0.6983 (t0) REVERT: C 289 MET cc_start: -0.1498 (mmm) cc_final: -0.2313 (ptm) REVERT: C 298 GLU cc_start: 0.1326 (OUTLIER) cc_final: 0.0987 (mm-30) REVERT: C 336 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.5202 (mpt) REVERT: D 62 ASN cc_start: 0.7557 (m-40) cc_final: 0.7097 (m110) REVERT: D 116 ASN cc_start: 0.8104 (m-40) cc_final: 0.7836 (m-40) REVERT: D 120 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7292 (mp0) REVERT: D 136 ASP cc_start: 0.7428 (t0) cc_final: 0.7153 (t0) REVERT: D 140 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6934 (tpm-80) REVERT: D 160 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7655 (ttp-110) REVERT: D 298 GLU cc_start: 0.1481 (OUTLIER) cc_final: 0.0578 (tm-30) REVERT: E 83 LYS cc_start: 0.8118 (tptp) cc_final: 0.7866 (tptp) REVERT: E 116 ASN cc_start: 0.8037 (m-40) cc_final: 0.7800 (m-40) REVERT: E 136 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7496 (t0) REVERT: E 140 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7157 (tpm-80) REVERT: E 163 ARG cc_start: 0.8442 (tpt-90) cc_final: 0.8154 (tpt-90) REVERT: E 206 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7723 (pt0) REVERT: E 289 MET cc_start: 0.0217 (mmm) cc_final: -0.1057 (ptm) REVERT: F 116 ASN cc_start: 0.8223 (m-40) cc_final: 0.7984 (m-40) REVERT: F 136 ASP cc_start: 0.7851 (m-30) cc_final: 0.6939 (t0) REVERT: F 204 ASN cc_start: 0.8582 (m-40) cc_final: 0.8333 (m110) REVERT: F 289 MET cc_start: -0.1508 (mmm) cc_final: -0.2314 (ptm) REVERT: F 298 GLU cc_start: 0.1335 (OUTLIER) cc_final: 0.0998 (mm-30) REVERT: F 336 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.5140 (mpt) outliers start: 65 outliers final: 28 residues processed: 283 average time/residue: 0.7131 time to fit residues: 227.6946 Evaluate side-chains 271 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 216 optimal weight: 0.7980 chunk 238 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 185 optimal weight: 7.9990 chunk 182 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 218 ASN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.204033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131023 restraints weight = 22124.283| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.13 r_work: 0.3245 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22447 Z= 0.130 Angle : 0.492 7.174 30324 Z= 0.268 Chirality : 0.040 0.174 3384 Planarity : 0.004 0.034 3912 Dihedral : 8.414 87.201 3186 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.96 % Allowed : 12.93 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.16), residues: 2724 helix: 1.74 (0.15), residues: 1242 sheet: -0.25 (0.26), residues: 396 loop : -0.22 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.021 0.002 TYR E 104 PHE 0.013 0.001 PHE F 242 TRP 0.011 0.001 TRP A 245 HIS 0.004 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (22440) covalent geometry : angle 0.49210 / 0.27 (30324) hydrogen bonds : bond 0.03476 / 2.30 ( 1124) hydrogen bonds : angle 4.08494 / 2.88 ( 3168) Misc. bond : bond 0.00656 / 0.31 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7547 (m-40) cc_final: 0.7114 (m110) REVERT: A 116 ASN cc_start: 0.8090 (m-40) cc_final: 0.7824 (m-40) REVERT: A 136 ASP cc_start: 0.7376 (t0) cc_final: 0.7119 (t0) REVERT: A 140 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7113 (tpm-80) REVERT: A 298 GLU cc_start: 0.1590 (OUTLIER) cc_final: 0.0599 (tm-30) REVERT: A 311 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: B 62 ASN cc_start: 0.7666 (m-40) cc_final: 0.7437 (m-40) REVERT: B 116 ASN cc_start: 0.8018 (m-40) cc_final: 0.7777 (m-40) REVERT: B 140 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7144 (tpm-80) REVERT: B 163 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.7971 (tpt-90) REVERT: B 289 MET cc_start: 0.0184 (mmm) cc_final: -0.1133 (ptm) REVERT: C 83 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8011 (tmtt) REVERT: C 136 ASP cc_start: 0.7844 (m-30) cc_final: 0.7040 (t0) REVERT: C 289 MET cc_start: -0.1481 (mmm) cc_final: -0.2278 (ptm) REVERT: C 298 GLU cc_start: 0.1196 (OUTLIER) cc_final: 0.0792 (mm-30) REVERT: C 336 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.5250 (mpt) REVERT: D 62 ASN cc_start: 0.7578 (m-40) cc_final: 0.7141 (m110) REVERT: D 116 ASN cc_start: 0.8073 (m-40) cc_final: 0.7814 (m-40) REVERT: D 136 ASP cc_start: 0.7409 (t0) cc_final: 0.7158 (t0) REVERT: D 140 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7093 (tpm-80) REVERT: D 298 GLU cc_start: 0.1516 (OUTLIER) cc_final: 0.0520 (tm-30) REVERT: E 83 LYS cc_start: 0.8173 (tptp) cc_final: 0.7945 (tptp) REVERT: E 116 ASN cc_start: 0.8047 (m-40) cc_final: 0.7802 (m-40) REVERT: E 140 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7154 (tpm-80) REVERT: E 163 ARG cc_start: 0.8486 (tpt-90) cc_final: 0.7994 (tpt-90) REVERT: E 289 MET cc_start: 0.0155 (mmm) cc_final: -0.1141 (ptm) REVERT: F 68 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7403 (ttm170) REVERT: F 116 ASN cc_start: 0.8213 (m-40) cc_final: 0.8005 (m-40) REVERT: F 136 ASP cc_start: 0.7820 (m-30) cc_final: 0.6943 (t0) REVERT: F 204 ASN cc_start: 0.8574 (m-40) cc_final: 0.8199 (m110) REVERT: F 289 MET cc_start: -0.1460 (mmm) cc_final: -0.2269 (ptm) REVERT: F 298 GLU cc_start: 0.1232 (OUTLIER) cc_final: 0.0812 (mm-30) REVERT: F 336 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.5213 (mpt) outliers start: 72 outliers final: 32 residues processed: 282 average time/residue: 0.6227 time to fit residues: 200.8487 Evaluate side-chains 273 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 427 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 145 optimal weight: 0.5980 chunk 223 optimal weight: 0.0040 chunk 88 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 151 optimal weight: 0.0040 chunk 175 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 HIS ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 218 ASN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.212954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138635 restraints weight = 21408.129| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.15 r_work: 0.3263 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22447 Z= 0.108 Angle : 0.470 8.995 30324 Z= 0.254 Chirality : 0.040 0.181 3384 Planarity : 0.003 0.035 3912 Dihedral : 8.046 87.040 3186 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 14.74 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2724 helix: 1.84 (0.15), residues: 1242 sheet: -0.26 (0.26), residues: 396 loop : -0.22 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.021 0.002 TYR E 104 PHE 0.012 0.001 PHE C 242 TRP 0.010 0.001 TRP F 245 HIS 0.003 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (22440) covalent geometry : angle 0.47009 / 0.25 (30324) hydrogen bonds : bond 0.03300 / 2.18 ( 1124) hydrogen bonds : angle 4.04196 / 2.84 ( 3168) Misc. bond : bond 0.00576 / 0.28 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7488 (m-40) cc_final: 0.7045 (m110) REVERT: A 116 ASN cc_start: 0.8036 (m-40) cc_final: 0.7806 (m-40) REVERT: A 136 ASP cc_start: 0.7389 (t0) cc_final: 0.7067 (t0) REVERT: A 140 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7117 (tpm-80) REVERT: A 298 GLU cc_start: 0.1546 (OUTLIER) cc_final: 0.0529 (tm-30) REVERT: A 311 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: A 336 MET cc_start: 0.7086 (mpt) cc_final: 0.6781 (mmt) REVERT: B 116 ASN cc_start: 0.8001 (m-40) cc_final: 0.7750 (m-40) REVERT: B 140 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7106 (tpm-80) REVERT: B 163 ARG cc_start: 0.8514 (tpt-90) cc_final: 0.8277 (tpt-90) REVERT: B 206 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7779 (pt0) REVERT: B 289 MET cc_start: 0.0115 (mmm) cc_final: -0.1264 (ptm) REVERT: C 82 ILE cc_start: 0.8714 (mt) cc_final: 0.8399 (mt) REVERT: C 83 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7959 (tmtt) REVERT: C 136 ASP cc_start: 0.7911 (m-30) cc_final: 0.7005 (t0) REVERT: C 289 MET cc_start: -0.1566 (mmm) cc_final: -0.2212 (ptm) REVERT: C 298 GLU cc_start: 0.1228 (OUTLIER) cc_final: 0.0827 (mm-30) REVERT: D 62 ASN cc_start: 0.7563 (m-40) cc_final: 0.7119 (m110) REVERT: D 116 ASN cc_start: 0.8020 (m-40) cc_final: 0.7792 (m-40) REVERT: D 136 ASP cc_start: 0.7436 (t0) cc_final: 0.7129 (t0) REVERT: D 138 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: D 140 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7126 (tpm-80) REVERT: D 298 GLU cc_start: 0.1544 (OUTLIER) cc_final: 0.0493 (tm-30) REVERT: D 336 MET cc_start: 0.7107 (mpt) cc_final: 0.6809 (mmt) REVERT: E 83 LYS cc_start: 0.8147 (tptp) cc_final: 0.7925 (tptp) REVERT: E 116 ASN cc_start: 0.7976 (m-40) cc_final: 0.7749 (m-40) REVERT: E 140 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7180 (tpm-80) REVERT: E 163 ARG cc_start: 0.8514 (tpt-90) cc_final: 0.8280 (tpt-90) REVERT: E 206 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7768 (pt0) REVERT: E 289 MET cc_start: 0.0103 (mmm) cc_final: -0.1278 (ptm) REVERT: F 68 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7403 (ttm170) REVERT: F 116 ASN cc_start: 0.8174 (m-40) cc_final: 0.7770 (m-40) REVERT: F 136 ASP cc_start: 0.7869 (m-30) cc_final: 0.6977 (t0) REVERT: F 289 MET cc_start: -0.1568 (mmm) cc_final: -0.2209 (ptm) REVERT: F 298 GLU cc_start: 0.1252 (OUTLIER) cc_final: 0.0844 (mm-30) outliers start: 61 outliers final: 29 residues processed: 277 average time/residue: 0.6350 time to fit residues: 199.8642 Evaluate side-chains 269 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 178 optimal weight: 0.0370 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 152 optimal weight: 0.0870 chunk 48 optimal weight: 10.0000 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.210623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134927 restraints weight = 21470.148| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.20 r_work: 0.3174 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22447 Z= 0.138 Angle : 0.493 7.468 30324 Z= 0.266 Chirality : 0.040 0.177 3384 Planarity : 0.004 0.034 3912 Dihedral : 7.941 86.904 3186 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.87 % Allowed : 15.02 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2724 helix: 1.82 (0.15), residues: 1242 sheet: 0.05 (0.24), residues: 480 loop : -0.21 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.021 0.002 TYR E 141 PHE 0.014 0.001 PHE C 242 TRP 0.010 0.001 TRP F 245 HIS 0.006 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (22440) covalent geometry : angle 0.49316 / 0.27 (30324) hydrogen bonds : bond 0.03449 / 2.28 ( 1124) hydrogen bonds : angle 4.08963 / 2.87 ( 3168) Misc. bond : bond 0.00678 / 0.32 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7439 (m-40) cc_final: 0.6986 (m110) REVERT: A 116 ASN cc_start: 0.8081 (m-40) cc_final: 0.7821 (m-40) REVERT: A 136 ASP cc_start: 0.7449 (t0) cc_final: 0.7107 (t0) REVERT: A 140 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7116 (tpm-80) REVERT: A 298 GLU cc_start: 0.1409 (OUTLIER) cc_final: 0.0418 (tm-30) REVERT: A 311 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: A 336 MET cc_start: 0.7023 (mpt) cc_final: 0.6544 (mmt) REVERT: B 62 ASN cc_start: 0.7573 (m-40) cc_final: 0.7164 (m-40) REVERT: B 116 ASN cc_start: 0.7962 (m-40) cc_final: 0.7673 (m-40) REVERT: B 140 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7222 (tpm-80) REVERT: B 163 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8231 (tpt-90) REVERT: B 206 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7764 (pt0) REVERT: B 289 MET cc_start: 0.0014 (mmm) cc_final: -0.1233 (ptm) REVERT: C 83 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7895 (tmtt) REVERT: C 136 ASP cc_start: 0.7917 (m-30) cc_final: 0.6974 (t0) REVERT: C 289 MET cc_start: -0.1779 (mmm) cc_final: -0.2394 (ptm) REVERT: C 298 GLU cc_start: 0.1178 (OUTLIER) cc_final: 0.0266 (tm-30) REVERT: D 62 ASN cc_start: 0.7498 (m-40) cc_final: 0.7057 (m110) REVERT: D 116 ASN cc_start: 0.8061 (m-40) cc_final: 0.7808 (m-40) REVERT: D 136 ASP cc_start: 0.7513 (t0) cc_final: 0.7154 (t0) REVERT: D 140 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7125 (tpm-80) REVERT: D 298 GLU cc_start: 0.1388 (OUTLIER) cc_final: 0.0391 (tm-30) REVERT: D 336 MET cc_start: 0.7048 (mpt) cc_final: 0.6585 (mmt) REVERT: E 83 LYS cc_start: 0.8120 (tptp) cc_final: 0.7899 (tptp) REVERT: E 116 ASN cc_start: 0.7937 (m-40) cc_final: 0.7653 (m-40) REVERT: E 140 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7081 (tpm-80) REVERT: E 163 ARG cc_start: 0.8467 (tpt-90) cc_final: 0.8198 (tpt-90) REVERT: E 206 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7672 (pt0) REVERT: E 289 MET cc_start: -0.0018 (mmm) cc_final: -0.1255 (ptm) REVERT: F 62 ASN cc_start: 0.7556 (m-40) cc_final: 0.7269 (m110) REVERT: F 68 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: F 82 ILE cc_start: 0.8730 (mt) cc_final: 0.8349 (mt) REVERT: F 116 ASN cc_start: 0.8031 (m-40) cc_final: 0.7715 (m-40) REVERT: F 136 ASP cc_start: 0.7851 (m-30) cc_final: 0.6939 (t0) REVERT: F 289 MET cc_start: -0.1791 (mmm) cc_final: -0.2388 (ptm) REVERT: F 298 GLU cc_start: 0.1201 (OUTLIER) cc_final: 0.0814 (mm-30) outliers start: 70 outliers final: 36 residues processed: 290 average time/residue: 0.6186 time to fit residues: 203.9105 Evaluate side-chains 282 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 91 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 0.0000 chunk 157 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.211356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136590 restraints weight = 21432.437| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.14 r_work: 0.3209 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22447 Z= 0.126 Angle : 0.482 7.633 30324 Z= 0.260 Chirality : 0.040 0.163 3384 Planarity : 0.003 0.037 3912 Dihedral : 7.793 87.283 3186 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.96 % Allowed : 15.64 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 2724 helix: 1.85 (0.15), residues: 1242 sheet: -0.26 (0.26), residues: 408 loop : -0.24 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.021 0.002 TYR B 141 PHE 0.013 0.001 PHE C 242 TRP 0.010 0.001 TRP A 245 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22440) covalent geometry : angle 0.48246 / 0.26 (30324) hydrogen bonds : bond 0.03364 / 2.22 ( 1124) hydrogen bonds : angle 4.08936 / 2.86 ( 3168) Misc. bond : bond 0.00634 / 0.30 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7459 (m-40) cc_final: 0.7006 (m110) REVERT: A 116 ASN cc_start: 0.8144 (m-40) cc_final: 0.7862 (m-40) REVERT: A 136 ASP cc_start: 0.7405 (t0) cc_final: 0.7071 (t0) REVERT: A 138 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: A 140 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7169 (tpm-80) REVERT: A 160 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7263 (ttm110) REVERT: A 298 GLU cc_start: 0.1371 (OUTLIER) cc_final: 0.0321 (tm-30) REVERT: A 311 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: A 336 MET cc_start: 0.7013 (mpt) cc_final: 0.6489 (mmt) REVERT: B 62 ASN cc_start: 0.7615 (m-40) cc_final: 0.7367 (m110) REVERT: B 116 ASN cc_start: 0.7945 (m-40) cc_final: 0.7674 (m-40) REVERT: B 140 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7263 (tpm-80) REVERT: B 163 ARG cc_start: 0.8500 (tpt-90) cc_final: 0.8223 (tpt-90) REVERT: B 206 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7820 (pt0) REVERT: B 289 MET cc_start: 0.0067 (mmm) cc_final: -0.1282 (ptm) REVERT: C 83 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7947 (tmtt) REVERT: C 136 ASP cc_start: 0.7866 (m-30) cc_final: 0.6962 (t0) REVERT: C 289 MET cc_start: -0.1656 (mmm) cc_final: -0.2336 (ptm) REVERT: C 298 GLU cc_start: 0.1209 (OUTLIER) cc_final: 0.0291 (tm-30) REVERT: C 336 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6727 (mmt) REVERT: D 62 ASN cc_start: 0.7476 (m-40) cc_final: 0.7017 (m110) REVERT: D 116 ASN cc_start: 0.8122 (m-40) cc_final: 0.7819 (m-40) REVERT: D 136 ASP cc_start: 0.7432 (t0) cc_final: 0.7103 (t0) REVERT: D 140 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7166 (tpm-80) REVERT: D 298 GLU cc_start: 0.1353 (OUTLIER) cc_final: 0.0321 (tm-30) REVERT: D 336 MET cc_start: 0.6997 (mpt) cc_final: 0.6491 (mmt) REVERT: E 83 LYS cc_start: 0.8151 (tptp) cc_final: 0.7951 (tptp) REVERT: E 116 ASN cc_start: 0.7995 (m-40) cc_final: 0.7718 (m-40) REVERT: E 140 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7290 (tpm-80) REVERT: E 163 ARG cc_start: 0.8506 (tpt-90) cc_final: 0.8229 (tpt-90) REVERT: E 206 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7804 (pt0) REVERT: E 289 MET cc_start: 0.0024 (mmm) cc_final: -0.1304 (ptm) REVERT: F 62 ASN cc_start: 0.7610 (m-40) cc_final: 0.7342 (m110) REVERT: F 68 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: F 82 ILE cc_start: 0.8739 (mt) cc_final: 0.8362 (mt) REVERT: F 136 ASP cc_start: 0.7817 (m-30) cc_final: 0.6924 (t0) REVERT: F 289 MET cc_start: -0.1671 (mmm) cc_final: -0.2332 (ptm) REVERT: F 298 GLU cc_start: 0.1226 (OUTLIER) cc_final: 0.0290 (tm-30) REVERT: F 336 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6672 (mmt) outliers start: 72 outliers final: 40 residues processed: 283 average time/residue: 0.6817 time to fit residues: 219.2155 Evaluate side-chains 284 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 73 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 241 HIS B 241 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 241 HIS ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 241 HIS E 241 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 241 HIS ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.209187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133399 restraints weight = 21151.400| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.18 r_work: 0.3131 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22447 Z= 0.183 Angle : 0.528 7.758 30324 Z= 0.283 Chirality : 0.042 0.178 3384 Planarity : 0.004 0.040 3912 Dihedral : 8.104 86.937 3186 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.00 % Allowed : 15.68 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.16), residues: 2724 helix: 1.73 (0.15), residues: 1242 sheet: -0.06 (0.24), residues: 468 loop : -0.29 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 160 TYR 0.021 0.002 TYR E 141 PHE 0.015 0.001 PHE F 242 TRP 0.011 0.001 TRP D 245 HIS 0.007 0.002 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (22440) covalent geometry : angle 0.52771 / 0.28 (30324) hydrogen bonds : bond 0.03659 / 2.41 ( 1124) hydrogen bonds : angle 4.20734 / 2.95 ( 3168) Misc. bond : bond 0.00801 / 0.38 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 235 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7339 (m-40) cc_final: 0.6862 (m110) REVERT: A 116 ASN cc_start: 0.8055 (m-40) cc_final: 0.7774 (m-40) REVERT: A 136 ASP cc_start: 0.7466 (t0) cc_final: 0.7113 (t0) REVERT: A 140 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7132 (tpm-80) REVERT: A 160 ARG cc_start: 0.7598 (ttp-110) cc_final: 0.7199 (ttm110) REVERT: A 298 GLU cc_start: 0.1265 (OUTLIER) cc_final: 0.0262 (tm-30) REVERT: A 311 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: B 62 ASN cc_start: 0.7478 (m-40) cc_final: 0.7178 (m110) REVERT: B 83 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7898 (tptp) REVERT: B 116 ASN cc_start: 0.7896 (m-40) cc_final: 0.7601 (m-40) REVERT: B 120 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7252 (mp0) REVERT: B 140 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7193 (tpm-80) REVERT: B 163 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.8084 (tpt-90) REVERT: B 206 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7575 (pt0) REVERT: B 289 MET cc_start: -0.0053 (mmm) cc_final: -0.1308 (ptm) REVERT: C 83 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7833 (tmtt) REVERT: C 136 ASP cc_start: 0.7981 (m-30) cc_final: 0.6999 (t0) REVERT: C 204 ASN cc_start: 0.8678 (m110) cc_final: 0.8300 (m-40) REVERT: C 289 MET cc_start: -0.1666 (mmm) cc_final: -0.2212 (ptm) REVERT: C 298 GLU cc_start: 0.1170 (OUTLIER) cc_final: 0.0291 (tt0) REVERT: D 62 ASN cc_start: 0.7386 (m-40) cc_final: 0.6927 (m110) REVERT: D 116 ASN cc_start: 0.8031 (m-40) cc_final: 0.7726 (m-40) REVERT: D 136 ASP cc_start: 0.7515 (t0) cc_final: 0.7161 (t0) REVERT: D 138 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: D 140 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7082 (tpm-80) REVERT: D 160 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.7192 (ttm110) REVERT: D 298 GLU cc_start: 0.1228 (OUTLIER) cc_final: 0.0260 (tm-30) REVERT: E 116 ASN cc_start: 0.7917 (m-40) cc_final: 0.7619 (m-40) REVERT: E 140 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7205 (tpm-80) REVERT: E 163 ARG cc_start: 0.8451 (tpt-90) cc_final: 0.8086 (tpt-90) REVERT: E 289 MET cc_start: -0.0162 (mmm) cc_final: -0.1359 (ptm) REVERT: F 68 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7190 (ttm170) REVERT: F 82 ILE cc_start: 0.8671 (mt) cc_final: 0.8282 (mt) REVERT: F 136 ASP cc_start: 0.7844 (m-30) cc_final: 0.6890 (t0) REVERT: F 289 MET cc_start: -0.1679 (mmm) cc_final: -0.2210 (ptm) REVERT: F 298 GLU cc_start: 0.1180 (OUTLIER) cc_final: 0.0292 (tt0) REVERT: F 331 LYS cc_start: 0.8788 (tttt) cc_final: 0.8244 (ttpm) outliers start: 73 outliers final: 38 residues processed: 286 average time/residue: 0.6861 time to fit residues: 222.9793 Evaluate side-chains 283 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 261 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 125 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.208635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132853 restraints weight = 21309.884| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.18 r_work: 0.3125 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22447 Z= 0.187 Angle : 0.535 7.892 30324 Z= 0.287 Chirality : 0.042 0.189 3384 Planarity : 0.004 0.046 3912 Dihedral : 8.190 89.161 3186 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 15.89 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2724 helix: 1.68 (0.15), residues: 1242 sheet: -0.10 (0.24), residues: 468 loop : -0.33 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.021 0.002 TYR E 104 PHE 0.015 0.001 PHE F 242 TRP 0.011 0.001 TRP B 245 HIS 0.009 0.002 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (22440) covalent geometry : angle 0.53524 / 0.29 (30324) hydrogen bonds : bond 0.03662 / 2.41 ( 1124) hydrogen bonds : angle 4.23764 / 2.96 ( 3168) Misc. bond : bond 0.00799 / 0.38 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 247 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7360 (m-40) cc_final: 0.6890 (m110) REVERT: A 116 ASN cc_start: 0.8048 (m-40) cc_final: 0.7756 (m-40) REVERT: A 136 ASP cc_start: 0.7507 (t0) cc_final: 0.7166 (t0) REVERT: A 140 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7057 (tpm-80) REVERT: A 298 GLU cc_start: 0.1250 (OUTLIER) cc_final: 0.0249 (tm-30) REVERT: A 311 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: B 62 ASN cc_start: 0.7464 (m-40) cc_final: 0.7162 (m110) REVERT: B 83 LYS cc_start: 0.8234 (tmtt) cc_final: 0.7867 (tptp) REVERT: B 116 ASN cc_start: 0.7906 (m-40) cc_final: 0.7596 (m-40) REVERT: B 120 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7242 (mp0) REVERT: B 129 GLU cc_start: 0.8146 (pm20) cc_final: 0.7545 (pm20) REVERT: B 140 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7155 (tpm-80) REVERT: B 206 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7562 (pt0) REVERT: B 289 MET cc_start: -0.0139 (mmm) cc_final: -0.1349 (ptm) REVERT: C 83 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7830 (tmtt) REVERT: C 136 ASP cc_start: 0.7970 (m-30) cc_final: 0.7000 (t0) REVERT: C 204 ASN cc_start: 0.8685 (m110) cc_final: 0.8236 (m-40) REVERT: C 226 PHE cc_start: 0.7863 (m-10) cc_final: 0.7588 (m-10) REVERT: C 289 MET cc_start: -0.1589 (mmm) cc_final: -0.2180 (ptm) REVERT: D 62 ASN cc_start: 0.7358 (m-40) cc_final: 0.6866 (m110) REVERT: D 116 ASN cc_start: 0.8042 (m-40) cc_final: 0.7754 (m-40) REVERT: D 136 ASP cc_start: 0.7510 (t0) cc_final: 0.7171 (t0) REVERT: D 138 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: D 140 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7078 (tpm-80) REVERT: D 160 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7167 (ttm110) REVERT: D 298 GLU cc_start: 0.1226 (OUTLIER) cc_final: 0.0250 (tm-30) REVERT: E 116 ASN cc_start: 0.7927 (m-40) cc_final: 0.7633 (m-40) REVERT: E 140 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7179 (tpm-80) REVERT: E 163 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8075 (tpt-90) REVERT: E 206 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7561 (pt0) REVERT: E 289 MET cc_start: -0.0177 (mmm) cc_final: -0.1358 (ptm) REVERT: F 68 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7163 (ttm170) REVERT: F 82 ILE cc_start: 0.8637 (mt) cc_final: 0.8241 (mt) REVERT: F 136 ASP cc_start: 0.7843 (m-30) cc_final: 0.6885 (t0) REVERT: F 226 PHE cc_start: 0.7848 (m-10) cc_final: 0.7582 (m-10) REVERT: F 289 MET cc_start: -0.1592 (mmm) cc_final: -0.2177 (ptm) REVERT: F 298 GLU cc_start: 0.1192 (OUTLIER) cc_final: 0.0331 (tt0) REVERT: F 331 LYS cc_start: 0.8771 (tttt) cc_final: 0.8220 (ttpm) outliers start: 67 outliers final: 44 residues processed: 288 average time/residue: 0.6848 time to fit residues: 224.2624 Evaluate side-chains 298 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 0.9980 chunk 263 optimal weight: 0.0470 chunk 217 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 268 optimal weight: 0.0970 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 overall best weight: 0.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 241 HIS ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 241 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.213130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138959 restraints weight = 21354.136| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.18 r_work: 0.3227 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22447 Z= 0.105 Angle : 0.472 8.195 30324 Z= 0.254 Chirality : 0.040 0.177 3384 Planarity : 0.003 0.035 3912 Dihedral : 7.627 87.278 3186 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.38 % Allowed : 16.38 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 2724 helix: 1.89 (0.15), residues: 1242 sheet: -0.40 (0.26), residues: 396 loop : -0.31 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.020 0.002 TYR E 141 PHE 0.011 0.001 PHE C 242 TRP 0.011 0.001 TRP A 245 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (22440) covalent geometry : angle 0.47245 / 0.25 (30324) hydrogen bonds : bond 0.03238 / 2.14 ( 1124) hydrogen bonds : angle 4.09307 / 2.86 ( 3168) Misc. bond : bond 0.00545 / 0.26 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.7381 (m-40) cc_final: 0.6926 (m110) REVERT: A 116 ASN cc_start: 0.8093 (m-40) cc_final: 0.7791 (m-40) REVERT: A 136 ASP cc_start: 0.7480 (t0) cc_final: 0.7157 (t0) REVERT: A 140 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7081 (tpm-80) REVERT: A 298 GLU cc_start: 0.1262 (OUTLIER) cc_final: 0.0192 (tm-30) REVERT: A 311 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: A 336 MET cc_start: 0.7017 (mpt) cc_final: 0.6434 (mmt) REVERT: B 62 ASN cc_start: 0.7461 (m-40) cc_final: 0.7148 (m110) REVERT: B 83 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7879 (tptp) REVERT: B 116 ASN cc_start: 0.7960 (m-40) cc_final: 0.7674 (m-40) REVERT: B 140 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7036 (tpm-80) REVERT: B 163 ARG cc_start: 0.8452 (tpt-90) cc_final: 0.8143 (tpt-90) REVERT: B 206 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7681 (pt0) REVERT: B 289 MET cc_start: -0.0083 (mmm) cc_final: -0.1184 (ptm) REVERT: C 83 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7909 (tmtt) REVERT: C 136 ASP cc_start: 0.7930 (m-30) cc_final: 0.6965 (t0) REVERT: C 226 PHE cc_start: 0.7729 (m-10) cc_final: 0.7459 (m-10) REVERT: C 289 MET cc_start: -0.1674 (mmm) cc_final: -0.2304 (ptm) REVERT: C 336 MET cc_start: 0.7062 (mpt) cc_final: 0.6559 (mmt) REVERT: D 62 ASN cc_start: 0.7424 (m-40) cc_final: 0.6959 (m110) REVERT: D 116 ASN cc_start: 0.8073 (m-40) cc_final: 0.7766 (m-40) REVERT: D 136 ASP cc_start: 0.7489 (t0) cc_final: 0.7185 (t0) REVERT: D 138 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: D 140 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7090 (tpm-80) REVERT: D 298 GLU cc_start: 0.1217 (OUTLIER) cc_final: 0.0195 (tm-30) REVERT: D 336 MET cc_start: 0.7000 (mpt) cc_final: 0.6404 (mmt) REVERT: E 83 LYS cc_start: 0.8218 (tmtt) cc_final: 0.7970 (tptp) REVERT: E 140 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7173 (tpm-80) REVERT: E 163 ARG cc_start: 0.8466 (tpt-90) cc_final: 0.8154 (tpt-90) REVERT: E 206 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7716 (pt0) REVERT: E 289 MET cc_start: -0.0187 (mmm) cc_final: -0.1217 (ptm) REVERT: F 62 ASN cc_start: 0.7456 (m-40) cc_final: 0.7178 (m110) REVERT: F 68 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7292 (ttm170) REVERT: F 82 ILE cc_start: 0.8669 (mt) cc_final: 0.8273 (mt) REVERT: F 136 ASP cc_start: 0.7868 (m-30) cc_final: 0.6926 (t0) REVERT: F 226 PHE cc_start: 0.7721 (m-10) cc_final: 0.7467 (m-10) REVERT: F 289 MET cc_start: -0.1668 (mmm) cc_final: -0.2312 (ptm) REVERT: F 298 GLU cc_start: 0.1185 (OUTLIER) cc_final: 0.0264 (tm-30) REVERT: F 336 MET cc_start: 0.7024 (mpt) cc_final: 0.6517 (mmt) outliers start: 58 outliers final: 37 residues processed: 280 average time/residue: 0.6689 time to fit residues: 213.0455 Evaluate side-chains 277 residues out of total 2436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 382 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 298 GLU Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 427 HIS Chi-restraints excluded: chain F residue 432 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 57 optimal weight: 4.9990 chunk 133 optimal weight: 0.4980 chunk 134 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.212758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138152 restraints weight = 21395.399| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.15 r_work: 0.3257 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22447 Z= 0.110 Angle : 0.474 8.056 30324 Z= 0.254 Chirality : 0.040 0.187 3384 Planarity : 0.003 0.035 3912 Dihedral : 7.570 89.718 3186 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.30 % Allowed : 16.63 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2724 helix: 1.94 (0.15), residues: 1242 sheet: -0.38 (0.26), residues: 408 loop : -0.28 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.022 0.002 TYR B 141 PHE 0.012 0.001 PHE E 242 TRP 0.011 0.001 TRP C 245 HIS 0.005 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22440) covalent geometry : angle 0.47364 / 0.25 (30324) hydrogen bonds : bond 0.03244 / 2.14 ( 1124) hydrogen bonds : angle 4.03355 / 2.82 ( 3168) Misc. bond : bond 0.00590 / 0.28 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9445.65 seconds wall clock time: 161 minutes 19.38 seconds (9679.38 seconds total)