Starting phenix.real_space_refine on Fri Aug 7 04:29:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhl_65070/08_2026/9vhl_65070.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 120 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 11677 2.51 5 N 3348 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 19055 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2215 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3081 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 11, 'TRANS': 369} Chain breaks: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2705 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 11, 'TRANS': 324} Chain breaks: 3 Chain: "D" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3595 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1671 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 2 Chain: "G" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1483 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain breaks: 1 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 829 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 13, 'rna3p_pyr': 11} Link IDs: {'rna2p': 14, 'rna3p': 24} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 3.69, per 1000 atoms: 0.19 Number of scatterers: 19055 At special positions: 0 Unit cell: (97.232, 140.08, 145.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 120 15.00 Mg 1 11.99 O 3860 8.00 N 3348 7.00 C 11677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 48 " distance=2.04 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 697.9 milliseconds 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3902 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 20 sheets defined 46.8% alpha, 14.9% beta 27 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 86 removed outlier: 3.810A pdb=" N ASN A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 4.052A pdb=" N ILE A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.552A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.868A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.506A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.832A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.707A pdb=" N ALA B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.631A pdb=" N LEU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.993A 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 208 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.759A pdb=" N ALA B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 358 through 377 removed outlier: 3.934A pdb=" N VAL B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.646A pdb=" N ASN B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 119 removed outlier: 4.032A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 238 through 256 Processing helix chain 'C' and resid 310 through 326 Processing helix chain 'C' and resid 360 through 379 removed outlier: 4.033A pdb=" N LEU C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.910A pdb=" N THR C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) 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 97 through 119 removed outlier: 3.727A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.872A 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 208 Processing helix chain 'D' and resid 226 through 230 removed outlier: 3.737A pdb=" N TYR D 229 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 Processing helix chain 'D' and resid 311 through 326 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 379 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.623A pdb=" N GLY D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 417 removed outlier: 3.908A pdb=" N GLU D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 410 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU D 411 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 465 through 473 Processing helix chain 'D' and resid 487 through 499 Processing helix chain 'D' and resid 504 through 519 Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 99 through 118 removed outlier: 3.888A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 3.943A 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 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 238 through 254 Processing helix chain 'E' and resid 310 through 326 Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' 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 407 Processing helix chain 'E' and resid 408 through 411 removed outlier: 3.527A pdb=" N LEU E 411 " --> pdb=" O GLU E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 434 through 435 No H-bonds generated for 'chain 'E' and resid 434 through 435' Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 465 through 470 Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.941A pdb=" N HIS E 487 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP E 488 " --> pdb=" O ALA E 484 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY E 490 " --> pdb=" O SER E 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 494 " --> pdb=" O GLY E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 519 Processing helix chain 'E' and resid 522 through 544 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.619A pdb=" N LEU F 13 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 27 through 40 removed outlier: 4.090A pdb=" N VAL F 31 " --> pdb=" O ASP F 27 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 66 through 72 removed outlier: 6.541A pdb=" N TRP F 71 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER F 72 " --> pdb=" O PHE F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 133 through 147 Processing helix chain 'F' and resid 152 through 176 Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 177 through 180 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 201 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.521A pdb=" N ILE B 82 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 69 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 150 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS B 155 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.663A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 335 removed outlier: 4.081A pdb=" N LYS B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 83 removed outlier: 6.895A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR C 147 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 69 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER C 145 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 71 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP C 143 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP C 73 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 141 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.057A pdb=" N THR C 199 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 393 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 201 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 335 removed outlier: 4.438A pdb=" N LYS C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.551A pdb=" N THR D 147 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU D 69 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER D 145 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU D 71 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP D 143 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.280A pdb=" N THR D 199 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU D 393 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 201 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 329 through 337 removed outlier: 4.234A pdb=" N LYS D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 52 through 54 removed outlier: 3.892A pdb=" N GLU E 54 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 77 through 83 removed outlier: 6.275A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR E 147 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 148 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER E 156 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 83 removed outlier: 6.275A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.957A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.608A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR E 426 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL E 90 " --> pdb=" O ARG E 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC1, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AC2, first strand: chain 'F' and resid 118 through 120 764 hydrogen bonds defined for protein. 2127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3335 1.33 - 1.45: 5780 1.45 - 1.58: 10226 1.58 - 1.71: 240 1.71 - 1.84: 79 Bond restraints: 19660 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.235 0.296 1.20e-02 6.94e+03 6.10e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.237 0.294 1.20e-02 6.94e+03 6.00e+02 bond pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " ideal model delta sigma weight residual 1.531 1.240 0.291 1.20e-02 6.94e+03 5.86e+02 bond pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 1.444 1.292 0.152 1.10e-02 8.26e+03 1.90e+02 bond pdb=" C4' ATP E 601 " pdb=" O4' ATP E 601 " ideal model delta sigma weight residual 1.444 1.298 0.146 1.10e-02 8.26e+03 1.77e+02 ... (remaining 19655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 26924 3.77 - 7.54: 118 7.54 - 11.31: 16 11.31 - 15.07: 12 15.07 - 18.84: 1 Bond angle restraints: 27071 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.03 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.87 15.00 1.00e+00 1.00e+00 2.25e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 125.34 14.53 1.00e+00 1.00e+00 2.11e+02 angle pdb=" PA ATP E 601 " pdb=" O3A ATP E 601 " pdb=" PB ATP E 601 " ideal model delta sigma weight residual 136.83 123.26 13.57 1.00e+00 1.00e+00 1.84e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 124.73 12.10 1.00e+00 1.00e+00 1.47e+02 ... (remaining 27066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 10876 32.85 - 65.70: 829 65.70 - 98.55: 55 98.55 - 131.41: 4 131.41 - 164.26: 4 Dihedral angle restraints: 11768 sinusoidal: 5768 harmonic: 6000 Sorted by residual: dihedral pdb=" O4' U H 24 " pdb=" C1' U H 24 " pdb=" N1 U H 24 " pdb=" C2 U H 24 " ideal model delta sinusoidal sigma weight residual -160.00 4.26 -164.26 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U H 34 " pdb=" C1' U H 34 " pdb=" N1 U H 34 " pdb=" C2 U H 34 " ideal model delta sinusoidal sigma weight residual -160.00 -33.71 -126.29 1 1.50e+01 4.44e-03 6.79e+01 dihedral pdb=" CA ILE A 257 " pdb=" C ILE A 257 " pdb=" N LYS A 258 " pdb=" CA LYS A 258 " ideal model delta harmonic sigma weight residual 180.00 140.76 39.24 0 5.00e+00 4.00e-02 6.16e+01 ... (remaining 11765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2607 0.065 - 0.129: 363 0.129 - 0.194: 68 0.194 - 0.259: 3 0.259 - 0.324: 4 Chirality restraints: 3045 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.36 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PHE B 84 " pdb=" N PHE B 84 " pdb=" C PHE B 84 " pdb=" CB PHE B 84 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2' ATP E 601 " pdb=" C1' ATP E 601 " pdb=" C3' ATP E 601 " pdb=" O2' ATP E 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.39 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3042 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 82 " -0.044 2.00e-02 2.50e+03 9.06e-02 8.21e+01 pdb=" C ILE B 82 " 0.157 2.00e-02 2.50e+03 pdb=" O ILE B 82 " -0.060 2.00e-02 2.50e+03 pdb=" N LYS B 83 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 402 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO D 403 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 403 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 403 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 402 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO E 403 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 403 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 403 " 0.028 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 22 2.39 - 3.02: 11717 3.02 - 3.65: 29517 3.65 - 4.27: 47392 4.27 - 4.90: 75872 Nonbonded interactions: 164520 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.768 2.170 nonbonded pdb=" OD1 ASP C 395 " pdb="MG MG C 602 " model vdw 1.952 2.170 nonbonded pdb=" O3G ATP C 601 " pdb="MG MG C 602 " model vdw 2.041 2.170 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.231 2.432 nonbonded pdb=" O2' ATP B 601 " pdb=" O3' ATP B 601 " model vdw 2.251 2.432 ... (remaining 164515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 38 through 211 or resid 222 through 601)) selection = (chain 'E' and (resid 38 through 443 or resid 454 through 456 or resid 601)) } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.670 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.296 19663 Z= 0.554 Angle : 0.826 18.842 27075 Z= 0.581 Chirality : 0.049 0.324 3045 Planarity : 0.005 0.091 3066 Dihedral : 20.546 164.257 7860 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.12 % Allowed : 26.14 % Favored : 71.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2025 helix: 0.09 (0.18), residues: 824 sheet: -1.80 (0.27), residues: 343 loop : -1.08 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 221 TYR 0.016 0.002 TYR C 246 PHE 0.019 0.001 PHE B 242 TRP 0.023 0.001 TRP E 333 HIS 0.005 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.55 (19660) covalent geometry : angle 0.82596 / 0.58 (27071) SS BOND : bond 0.00597 / 0.31 ( 2) SS BOND : angle 2.18224 / 1.37 ( 4) hydrogen bonds : bond 0.13284 / 8.74 ( 830) hydrogen bonds : angle 6.56761 / 4.77 ( 2261) Misc. bond : bond 0.00425 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7140 (m-80) cc_final: 0.6832 (m-80) REVERT: A 141 LYS cc_start: 0.6739 (mppt) cc_final: 0.6270 (mmtt) REVERT: A 142 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.4745 (m-70) REVERT: A 164 MET cc_start: 0.5798 (ptp) cc_final: 0.4938 (mtm) REVERT: B 1 MET cc_start: 0.6465 (mmm) cc_final: 0.5901 (mpm) REVERT: B 83 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7664 (mptt) REVERT: B 86 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: B 152 LYS cc_start: 0.6299 (mppt) cc_final: 0.5614 (pttm) REVERT: C 125 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: C 184 ASP cc_start: 0.6699 (m-30) cc_final: 0.6214 (m-30) REVERT: C 320 LYS cc_start: 0.7500 (mmmt) cc_final: 0.7078 (mttm) REVERT: D 87 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7705 (t0) REVERT: D 130 LEU cc_start: 0.7161 (mt) cc_final: 0.6758 (mm) REVERT: D 172 ARG cc_start: 0.7357 (tpt170) cc_final: 0.7075 (tpt170) REVERT: D 317 ILE cc_start: 0.8491 (mm) cc_final: 0.8270 (mp) REVERT: D 336 MET cc_start: 0.5598 (ppp) cc_final: 0.4738 (tmm) REVERT: D 371 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6839 (mt) REVERT: D 415 SER cc_start: 0.8038 (t) cc_final: 0.7764 (p) REVERT: D 433 SER cc_start: 0.8055 (t) cc_final: 0.7802 (m) REVERT: D 444 ASP cc_start: 0.8031 (m-30) cc_final: 0.6823 (t70) REVERT: D 495 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7557 (mt) REVERT: D 510 LEU cc_start: 0.8206 (mt) cc_final: 0.7749 (tt) REVERT: E 72 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7333 (ttpp) REVERT: E 162 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8152 (t) REVERT: E 170 GLU cc_start: 0.7872 (mp0) cc_final: 0.7672 (mp0) REVERT: E 315 LYS cc_start: 0.6130 (tttm) cc_final: 0.5320 (tptt) REVERT: E 362 ARG cc_start: 0.6608 (mtm110) cc_final: 0.6312 (mtm110) REVERT: E 383 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: E 389 ARG cc_start: 0.8112 (ptp-170) cc_final: 0.7551 (ttp-170) REVERT: E 414 ARG cc_start: 0.6845 (mpp-170) cc_final: 0.6604 (mpt-90) REVERT: E 465 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6299 (tp30) REVERT: E 475 ASN cc_start: 0.7535 (m-40) cc_final: 0.7102 (t0) outliers start: 39 outliers final: 15 residues processed: 284 average time/residue: 0.5171 time to fit residues: 168.3294 Evaluate side-chains 247 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 90 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN C 218 ASN D 487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.198137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.161341 restraints weight = 19485.483| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 2.85 r_work: 0.4190 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19663 Z= 0.182 Angle : 0.691 8.691 27075 Z= 0.376 Chirality : 0.046 0.340 3045 Planarity : 0.005 0.056 3066 Dihedral : 20.290 162.667 3776 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.17 % Allowed : 22.00 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.83 (0.19), residues: 2025 helix: 0.37 (0.18), residues: 844 sheet: -1.44 (0.29), residues: 328 loop : -0.99 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 221 TYR 0.021 0.002 TYR E 248 PHE 0.021 0.002 PHE B 242 TRP 0.021 0.002 TRP E 245 HIS 0.006 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (19660) covalent geometry : angle 0.69062 / 0.38 (27071) SS BOND : bond 0.00939 / 0.47 ( 2) SS BOND : angle 2.52618 / 1.56 ( 4) hydrogen bonds : bond 0.05235 / 3.25 ( 830) hydrogen bonds : angle 5.40421 / 3.88 ( 2261) Misc. bond : bond 0.00289 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 246 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6801 (m-80) cc_final: 0.6407 (m-80) REVERT: A 141 LYS cc_start: 0.6747 (mppt) cc_final: 0.6274 (mmtt) REVERT: A 142 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.4812 (m-70) REVERT: A 164 MET cc_start: 0.5800 (ptp) cc_final: 0.4792 (mtm) REVERT: B 1 MET cc_start: 0.6646 (mmm) cc_final: 0.5989 (mmm) REVERT: B 6 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: B 83 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7217 (ttmt) REVERT: B 152 LYS cc_start: 0.6357 (mppt) cc_final: 0.5823 (pttm) REVERT: B 342 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5742 (pp) REVERT: B 396 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: B 436 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: C 67 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6891 (tmt90) REVERT: C 101 SER cc_start: 0.6221 (OUTLIER) cc_final: 0.5991 (m) REVERT: C 116 ASN cc_start: 0.7147 (m-40) cc_final: 0.6626 (m110) REVERT: C 125 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: C 184 ASP cc_start: 0.6950 (m-30) cc_final: 0.6587 (m-30) REVERT: C 251 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7740 (tptt) REVERT: C 320 LYS cc_start: 0.7356 (mmmt) cc_final: 0.6788 (mttm) REVERT: C 357 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7638 (mp) REVERT: D 87 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7600 (t0) REVERT: D 130 LEU cc_start: 0.7318 (mt) cc_final: 0.6919 (mm) REVERT: D 317 ILE cc_start: 0.8416 (mm) cc_final: 0.8187 (mt) REVERT: D 336 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.4710 (tmm) REVERT: D 415 SER cc_start: 0.7984 (t) cc_final: 0.7679 (p) REVERT: D 433 SER cc_start: 0.7715 (t) cc_final: 0.7478 (m) REVERT: D 455 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6709 (t0) REVERT: D 510 LEU cc_start: 0.8200 (mt) cc_final: 0.7824 (tt) REVERT: E 81 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7563 (mp0) REVERT: E 362 ARG cc_start: 0.6582 (mtm110) cc_final: 0.6269 (mtm110) REVERT: E 373 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.6155 (ttp-170) REVERT: E 414 ARG cc_start: 0.6941 (mpp-170) cc_final: 0.6601 (mpt-90) REVERT: E 465 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6252 (tp30) REVERT: E 475 ASN cc_start: 0.7460 (m-40) cc_final: 0.7043 (t0) REVERT: F 52 ARG cc_start: 0.6911 (ttm170) cc_final: 0.6601 (ttt90) REVERT: F 77 SER cc_start: 0.7539 (t) cc_final: 0.7306 (m) REVERT: F 125 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7909 (tt0) outliers start: 95 outliers final: 32 residues processed: 321 average time/residue: 0.5409 time to fit residues: 198.8986 Evaluate side-chains 256 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS A 242 ASN B 407 GLN D 477 HIS D 517 HIS E 231 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.198864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.164224 restraints weight = 20039.662| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.90 r_work: 0.4221 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 19663 Z= 0.302 Angle : 0.837 12.908 27075 Z= 0.447 Chirality : 0.053 0.403 3045 Planarity : 0.006 0.070 3066 Dihedral : 20.412 158.202 3754 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 7.57 % Allowed : 21.30 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.24 (0.18), residues: 2025 helix: -0.07 (0.17), residues: 843 sheet: -1.76 (0.27), residues: 351 loop : -1.02 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 49 TYR 0.022 0.003 TYR D 141 PHE 0.028 0.003 PHE B 242 TRP 0.022 0.003 TRP E 245 HIS 0.009 0.002 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (19660) covalent geometry : angle 0.83410 / 0.45 (27071) SS BOND : bond 0.00394 / 0.19 ( 2) SS BOND : angle 5.50890 / 3.59 ( 4) hydrogen bonds : bond 0.06724 / 4.10 ( 830) hydrogen bonds : angle 5.52216 / 3.92 ( 2261) Misc. bond : bond 0.00146 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 239 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7041 (pmt-80) cc_final: 0.6832 (ppt90) REVERT: A 102 ASN cc_start: 0.7812 (m-40) cc_final: 0.7497 (m-40) REVERT: A 141 LYS cc_start: 0.6859 (mppt) cc_final: 0.6402 (mmtt) REVERT: A 142 HIS cc_start: 0.5469 (OUTLIER) cc_final: 0.4721 (m-70) REVERT: A 164 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5238 (mtm) REVERT: A 237 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7368 (p) REVERT: B 1 MET cc_start: 0.6720 (mmm) cc_final: 0.6386 (mmm) REVERT: B 6 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: B 125 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6682 (mt0) REVERT: B 152 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6308 (pttp) REVERT: B 342 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5854 (pp) REVERT: B 396 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: B 436 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: C 101 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.6031 (m) REVERT: C 116 ASN cc_start: 0.7165 (m-40) cc_final: 0.6657 (m110) REVERT: C 125 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: C 184 ASP cc_start: 0.6994 (m-30) cc_final: 0.6619 (m-30) REVERT: C 250 HIS cc_start: 0.7142 (t70) cc_final: 0.6862 (t70) REVERT: C 251 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7760 (tptt) REVERT: C 320 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6840 (mttm) REVERT: C 357 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 87 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7659 (t0) REVERT: D 175 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6108 (tm-30) REVERT: D 317 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 336 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.4729 (tmm) REVERT: D 415 SER cc_start: 0.7996 (t) cc_final: 0.7696 (p) REVERT: D 444 ASP cc_start: 0.8396 (m-30) cc_final: 0.8119 (m-30) REVERT: D 455 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6627 (t0) REVERT: E 72 LYS cc_start: 0.7893 (mttt) cc_final: 0.7158 (tmmm) REVERT: E 317 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6241 (mp) REVERT: E 362 ARG cc_start: 0.6744 (mtm110) cc_final: 0.6439 (mtm110) REVERT: E 373 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6233 (ttp-170) REVERT: E 383 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: E 414 ARG cc_start: 0.7097 (mpp-170) cc_final: 0.6801 (mpt-90) REVERT: E 475 ASN cc_start: 0.7564 (m-40) cc_final: 0.7158 (t0) REVERT: F 125 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7917 (tt0) outliers start: 139 outliers final: 63 residues processed: 342 average time/residue: 0.5520 time to fit residues: 215.9799 Evaluate side-chains 292 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 207 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 143 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 198 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN E 241 HIS E 400 HIS E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.203564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.169343 restraints weight = 19796.206| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 2.98 r_work: 0.4278 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19663 Z= 0.158 Angle : 0.658 8.059 27075 Z= 0.358 Chirality : 0.045 0.276 3045 Planarity : 0.005 0.059 3066 Dihedral : 20.300 158.906 3750 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 6.10 % Allowed : 23.86 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.71 (0.19), residues: 2025 helix: 0.41 (0.18), residues: 846 sheet: -1.47 (0.27), residues: 345 loop : -0.79 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 225 TYR 0.027 0.002 TYR D 141 PHE 0.023 0.002 PHE D 149 TRP 0.025 0.002 TRP E 245 HIS 0.006 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (19660) covalent geometry : angle 0.65727 / 0.36 (27071) SS BOND : bond 0.01099 / 0.57 ( 2) SS BOND : angle 2.89051 / 1.87 ( 4) hydrogen bonds : bond 0.04548 / 2.82 ( 830) hydrogen bonds : angle 5.11160 / 3.63 ( 2261) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 252 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.6941 (m-80) cc_final: 0.6637 (m-80) REVERT: A 102 ASN cc_start: 0.7832 (m-40) cc_final: 0.7483 (m-40) REVERT: A 141 LYS cc_start: 0.6712 (mppt) cc_final: 0.6353 (mmtt) REVERT: A 142 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.4666 (m-70) REVERT: A 164 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5257 (mtm) REVERT: A 304 MET cc_start: 0.6164 (mmt) cc_final: 0.4600 (tmm) REVERT: B 1 MET cc_start: 0.6692 (mmm) cc_final: 0.6269 (mmm) REVERT: B 6 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: B 152 LYS cc_start: 0.6545 (mppt) cc_final: 0.6119 (pttm) REVERT: B 342 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5746 (pp) REVERT: B 396 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: B 436 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: C 116 ASN cc_start: 0.7048 (m-40) cc_final: 0.6515 (m110) REVERT: C 125 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7252 (mt0) REVERT: C 126 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7615 (ptm160) REVERT: C 184 ASP cc_start: 0.6924 (m-30) cc_final: 0.6574 (m-30) REVERT: C 250 HIS cc_start: 0.7031 (t70) cc_final: 0.6758 (t70) REVERT: C 320 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6829 (mttm) REVERT: D 87 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7548 (t0) REVERT: D 140 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7542 (mtt180) REVERT: D 336 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4784 (tmm) REVERT: D 415 SER cc_start: 0.8019 (t) cc_final: 0.7727 (p) REVERT: D 455 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6570 (t0) REVERT: D 498 ASP cc_start: 0.7621 (t0) cc_final: 0.7193 (t0) REVERT: D 510 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7853 (tt) REVERT: E 72 LYS cc_start: 0.7762 (mttt) cc_final: 0.7069 (tmmm) REVERT: E 120 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6837 (tt0) REVERT: E 182 LEU cc_start: 0.7722 (tp) cc_final: 0.7501 (tp) REVERT: E 317 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.5893 (mp) REVERT: E 383 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: E 414 ARG cc_start: 0.6877 (mpp-170) cc_final: 0.6600 (mpt-90) REVERT: E 475 ASN cc_start: 0.7547 (m-40) cc_final: 0.7130 (t0) REVERT: F 125 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: F 147 PHE cc_start: 0.7306 (m-80) cc_final: 0.6890 (m-80) outliers start: 112 outliers final: 35 residues processed: 333 average time/residue: 0.5347 time to fit residues: 204.6431 Evaluate side-chains 264 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 60 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 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 = 0.4778 r_free = 0.4778 target = 0.200588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.165355 restraints weight = 19793.132| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.99 r_work: 0.4229 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19663 Z= 0.183 Angle : 0.690 10.692 27075 Z= 0.370 Chirality : 0.046 0.381 3045 Planarity : 0.005 0.059 3066 Dihedral : 20.218 158.333 3746 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.32 % Allowed : 24.51 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.68 (0.19), residues: 2025 helix: 0.41 (0.18), residues: 844 sheet: -1.42 (0.27), residues: 346 loop : -0.76 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 163 TYR 0.025 0.002 TYR D 141 PHE 0.025 0.002 PHE B 242 TRP 0.028 0.002 TRP E 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (19660) covalent geometry : angle 0.68914 / 0.37 (27071) SS BOND : bond 0.01073 / 0.55 ( 2) SS BOND : angle 2.71832 / 1.72 ( 4) hydrogen bonds : bond 0.04879 / 3.01 ( 830) hydrogen bonds : angle 5.11870 / 3.63 ( 2261) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 230 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7035 (m-80) cc_final: 0.6723 (m-80) REVERT: A 141 LYS cc_start: 0.6751 (mppt) cc_final: 0.6410 (mmtt) REVERT: A 142 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.4641 (m-70) REVERT: A 164 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5427 (mtm) REVERT: A 214 PHE cc_start: 0.6536 (m-10) cc_final: 0.6201 (m-80) REVERT: B 1 MET cc_start: 0.6750 (mmm) cc_final: 0.6287 (mmm) REVERT: B 6 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: B 125 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6547 (mt0) REVERT: B 152 LYS cc_start: 0.6645 (mppt) cc_final: 0.6151 (pttm) REVERT: B 342 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5773 (pp) REVERT: B 396 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: B 436 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 116 ASN cc_start: 0.7075 (m-40) cc_final: 0.6536 (m110) REVERT: C 119 LYS cc_start: 0.6474 (mmmt) cc_final: 0.5977 (mttm) REVERT: C 125 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: C 184 ASP cc_start: 0.6879 (m-30) cc_final: 0.6563 (m-30) REVERT: C 244 GLU cc_start: 0.7190 (tt0) cc_final: 0.6799 (tt0) REVERT: C 250 HIS cc_start: 0.7081 (t70) cc_final: 0.6828 (t70) REVERT: C 251 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7684 (tptt) REVERT: C 320 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6719 (mttm) REVERT: D 87 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7509 (t0) REVERT: D 140 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7613 (mtt180) REVERT: D 336 MET cc_start: 0.5446 (OUTLIER) cc_final: 0.4809 (tmm) REVERT: D 415 SER cc_start: 0.7944 (t) cc_final: 0.7623 (p) REVERT: D 455 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6600 (t0) REVERT: D 465 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7229 (mm-30) REVERT: D 498 ASP cc_start: 0.7602 (t0) cc_final: 0.7157 (t0) REVERT: E 72 LYS cc_start: 0.7717 (mttt) cc_final: 0.6999 (tmmm) REVERT: E 182 LEU cc_start: 0.7662 (tp) cc_final: 0.7455 (tp) REVERT: E 317 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.5907 (mp) REVERT: E 383 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: E 389 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7407 (ptp-170) REVERT: E 414 ARG cc_start: 0.6906 (mpp-170) cc_final: 0.6639 (mpt-90) REVERT: E 475 ASN cc_start: 0.7542 (m-40) cc_final: 0.7136 (t0) REVERT: F 125 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: F 142 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7563 (mp0) outliers start: 116 outliers final: 44 residues processed: 321 average time/residue: 0.5332 time to fit residues: 196.6466 Evaluate side-chains 268 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A 194 ASN B 407 GLN E 48 GLN E 209 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.201723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.166718 restraints weight = 19742.664| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 2.97 r_work: 0.4250 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19663 Z= 0.160 Angle : 0.657 8.804 27075 Z= 0.354 Chirality : 0.044 0.303 3045 Planarity : 0.005 0.068 3066 Dihedral : 20.083 158.129 3746 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.72 % Allowed : 25.16 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.56 (0.19), residues: 2025 helix: 0.51 (0.18), residues: 846 sheet: -1.42 (0.27), residues: 350 loop : -0.67 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.027 0.002 TYR D 141 PHE 0.029 0.002 PHE B 113 TRP 0.032 0.002 TRP E 245 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (19660) covalent geometry : angle 0.65582 / 0.35 (27071) SS BOND : bond 0.01985 / 1.04 ( 2) SS BOND : angle 2.82590 / 1.81 ( 4) hydrogen bonds : bond 0.04424 / 2.76 ( 830) hydrogen bonds : angle 5.02590 / 3.56 ( 2261) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 235 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7074 (m-80) cc_final: 0.6703 (m-80) REVERT: A 141 LYS cc_start: 0.6682 (mppt) cc_final: 0.6376 (mmtt) REVERT: A 142 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.4584 (m-70) REVERT: A 164 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5432 (mtm) REVERT: A 214 PHE cc_start: 0.6479 (m-10) cc_final: 0.6157 (m-80) REVERT: B 1 MET cc_start: 0.6750 (mmm) cc_final: 0.6375 (mmm) REVERT: B 6 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: B 10 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7333 (mmtp) REVERT: B 125 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6491 (mt0) REVERT: B 152 LYS cc_start: 0.6639 (mppt) cc_final: 0.6155 (pttm) REVERT: B 342 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5769 (pp) REVERT: B 396 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: B 436 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: C 116 ASN cc_start: 0.6995 (m-40) cc_final: 0.6429 (m110) REVERT: C 119 LYS cc_start: 0.6567 (mmmt) cc_final: 0.6007 (mttm) REVERT: C 125 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7130 (mt0) REVERT: C 126 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7574 (ptm160) REVERT: C 184 ASP cc_start: 0.6867 (m-30) cc_final: 0.6584 (m-30) REVERT: C 250 HIS cc_start: 0.7075 (t70) cc_final: 0.6841 (t70) REVERT: C 320 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6867 (mttm) REVERT: D 140 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7615 (mtt180) REVERT: D 172 ARG cc_start: 0.7309 (tpt170) cc_final: 0.7095 (tpt-90) REVERT: D 175 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: D 336 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.4756 (tmm) REVERT: D 415 SER cc_start: 0.7925 (t) cc_final: 0.7613 (p) REVERT: D 455 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6616 (t0) REVERT: D 465 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7197 (mm-30) REVERT: D 498 ASP cc_start: 0.7640 (t0) cc_final: 0.7208 (t0) REVERT: E 72 LYS cc_start: 0.7650 (mttt) cc_final: 0.6925 (tmmm) REVERT: E 182 LEU cc_start: 0.7660 (tp) cc_final: 0.7457 (tp) REVERT: E 317 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.5817 (mp) REVERT: E 383 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: E 389 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7443 (ptp-170) REVERT: E 414 ARG cc_start: 0.6921 (mpp-170) cc_final: 0.6651 (mpt-90) REVERT: E 475 ASN cc_start: 0.7509 (m-40) cc_final: 0.7117 (t0) REVERT: E 506 GLN cc_start: 0.6106 (OUTLIER) cc_final: 0.5703 (mp10) REVERT: F 1 MET cc_start: 0.6806 (tpp) cc_final: 0.6575 (tpp) REVERT: F 52 ARG cc_start: 0.6386 (ttt90) cc_final: 0.6091 (ttt90) REVERT: F 125 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: F 142 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7571 (mp0) outliers start: 105 outliers final: 46 residues processed: 315 average time/residue: 0.5154 time to fit residues: 187.1463 Evaluate side-chains 273 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 202 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN D 475 ASN D 517 HIS E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** 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 = 0.4792 r_free = 0.4792 target = 0.202088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.166360 restraints weight = 19743.213| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.15 r_work: 0.4241 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19663 Z= 0.142 Angle : 0.641 10.282 27075 Z= 0.346 Chirality : 0.043 0.340 3045 Planarity : 0.005 0.066 3066 Dihedral : 19.956 160.351 3743 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.79 % Allowed : 26.53 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 2025 helix: 0.65 (0.18), residues: 848 sheet: -1.35 (0.27), residues: 351 loop : -0.61 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.028 0.002 TYR D 141 PHE 0.022 0.002 PHE E 417 TRP 0.032 0.002 TRP E 245 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19660) covalent geometry : angle 0.64016 / 0.35 (27071) SS BOND : bond 0.01425 / 0.74 ( 2) SS BOND : angle 1.90714 / 1.11 ( 4) hydrogen bonds : bond 0.04132 / 2.57 ( 830) hydrogen bonds : angle 4.94078 / 3.50 ( 2261) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 227 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7107 (m-80) cc_final: 0.6762 (m-80) REVERT: A 141 LYS cc_start: 0.6768 (mppt) cc_final: 0.6422 (mmtt) REVERT: A 142 HIS cc_start: 0.5513 (OUTLIER) cc_final: 0.4595 (m-70) REVERT: A 164 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5517 (mtm) REVERT: A 214 PHE cc_start: 0.6439 (m-10) cc_final: 0.6112 (m-80) REVERT: B 1 MET cc_start: 0.6686 (mmm) cc_final: 0.6374 (mmm) REVERT: B 6 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: B 10 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7445 (mmtp) REVERT: B 152 LYS cc_start: 0.6581 (mppt) cc_final: 0.6137 (pttm) REVERT: B 342 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5713 (pp) REVERT: B 396 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6418 (mt-10) REVERT: C 67 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6901 (tmt90) REVERT: C 116 ASN cc_start: 0.7008 (m-40) cc_final: 0.6395 (m110) REVERT: C 119 LYS cc_start: 0.6421 (mmmt) cc_final: 0.5984 (mtpp) REVERT: C 125 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: C 126 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7424 (ptm160) REVERT: C 184 ASP cc_start: 0.6864 (m-30) cc_final: 0.6584 (m-30) REVERT: C 244 GLU cc_start: 0.7201 (tt0) cc_final: 0.6806 (tt0) REVERT: C 250 HIS cc_start: 0.7060 (t70) cc_final: 0.6857 (t70) REVERT: C 251 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7666 (tptt) REVERT: C 320 LYS cc_start: 0.7331 (mmmt) cc_final: 0.6820 (mttm) REVERT: D 140 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7590 (mtt180) REVERT: D 175 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: D 336 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.4777 (tmm) REVERT: D 377 MET cc_start: 0.6117 (mtm) cc_final: 0.5603 (mtp) REVERT: D 415 SER cc_start: 0.7886 (t) cc_final: 0.7532 (p) REVERT: D 465 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7150 (mm-30) REVERT: D 498 ASP cc_start: 0.7574 (t70) cc_final: 0.7133 (t0) REVERT: E 72 LYS cc_start: 0.7601 (mttt) cc_final: 0.6854 (tmmm) REVERT: E 182 LEU cc_start: 0.7622 (tp) cc_final: 0.7417 (tp) REVERT: E 230 SER cc_start: 0.8073 (m) cc_final: 0.7791 (t) REVERT: E 317 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.5750 (mp) REVERT: E 383 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: E 389 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7435 (ptp-170) REVERT: E 414 ARG cc_start: 0.6911 (mtp180) cc_final: 0.6662 (mpt-90) REVERT: E 475 ASN cc_start: 0.7472 (m-40) cc_final: 0.7111 (t0) REVERT: E 506 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.5633 (mp10) REVERT: F 1 MET cc_start: 0.6892 (tpp) cc_final: 0.6684 (tpp) REVERT: F 53 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: F 125 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7265 (tp30) outliers start: 88 outliers final: 41 residues processed: 297 average time/residue: 0.5000 time to fit residues: 169.4965 Evaluate side-chains 273 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 217 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 195 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 133 optimal weight: 0.0670 chunk 126 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.199216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.164112 restraints weight = 19810.641| |-----------------------------------------------------------------------------| r_work (start): 0.4439 rms_B_bonded: 2.62 r_work: 0.4228 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19663 Z= 0.179 Angle : 0.675 9.776 27075 Z= 0.363 Chirality : 0.045 0.328 3045 Planarity : 0.005 0.061 3066 Dihedral : 19.979 158.604 3743 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.61 % Allowed : 25.98 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.50 (0.19), residues: 2025 helix: 0.53 (0.18), residues: 847 sheet: -1.36 (0.27), residues: 348 loop : -0.62 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 126 TYR 0.026 0.002 TYR D 248 PHE 0.027 0.002 PHE B 113 TRP 0.036 0.002 TRP C 245 HIS 0.006 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (19660) covalent geometry : angle 0.67488 / 0.36 (27071) SS BOND : bond 0.01629 / 0.85 ( 2) SS BOND : angle 1.92672 / 1.13 ( 4) hydrogen bonds : bond 0.04641 / 2.89 ( 830) hydrogen bonds : angle 5.03775 / 3.55 ( 2261) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 222 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7292 (m-80) cc_final: 0.6988 (m-80) REVERT: A 81 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7052 (p0) REVERT: A 141 LYS cc_start: 0.6768 (mppt) cc_final: 0.6461 (mmtt) REVERT: A 142 HIS cc_start: 0.5532 (OUTLIER) cc_final: 0.4623 (m-70) REVERT: A 164 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5663 (mtm) REVERT: A 214 PHE cc_start: 0.6501 (m-10) cc_final: 0.6290 (m-10) REVERT: A 301 LEU cc_start: 0.7430 (tt) cc_final: 0.7150 (pp) REVERT: B 1 MET cc_start: 0.6774 (mmm) cc_final: 0.6486 (mmm) REVERT: B 6 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: B 10 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7419 (mmtp) REVERT: B 152 LYS cc_start: 0.6793 (mppt) cc_final: 0.6269 (pttm) REVERT: B 342 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5781 (pp) REVERT: B 396 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: B 436 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: C 116 ASN cc_start: 0.7053 (m-40) cc_final: 0.6483 (m110) REVERT: C 119 LYS cc_start: 0.6521 (mmmt) cc_final: 0.6047 (mttm) REVERT: C 125 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: C 126 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7588 (ptm160) REVERT: C 223 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5518 (tt0) REVERT: C 251 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (tptt) REVERT: C 320 LYS cc_start: 0.7458 (mmmt) cc_final: 0.6932 (mttm) REVERT: D 140 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7711 (mtt180) REVERT: D 175 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: D 336 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4753 (tmm) REVERT: D 377 MET cc_start: 0.6337 (mtm) cc_final: 0.5784 (mtp) REVERT: D 405 TRP cc_start: 0.6204 (t60) cc_final: 0.5334 (m-10) REVERT: D 415 SER cc_start: 0.7958 (t) cc_final: 0.7619 (p) REVERT: D 465 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 498 ASP cc_start: 0.7552 (t70) cc_final: 0.7124 (t0) REVERT: E 72 LYS cc_start: 0.7743 (mttt) cc_final: 0.7016 (tmmm) REVERT: E 230 SER cc_start: 0.8213 (m) cc_final: 0.7886 (t) REVERT: E 317 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.5943 (mp) REVERT: E 375 MET cc_start: 0.6913 (ttm) cc_final: 0.6600 (ttm) REVERT: E 383 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: E 389 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7601 (ptp-170) REVERT: E 475 ASN cc_start: 0.7610 (m-40) cc_final: 0.7205 (t0) REVERT: E 506 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5687 (mp10) REVERT: F 125 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7427 (tp30) outliers start: 103 outliers final: 53 residues processed: 301 average time/residue: 0.5230 time to fit residues: 180.6955 Evaluate side-chains 281 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.0040 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 89 ASN E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 535 ASN ** 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 = 0.4764 r_free = 0.4764 target = 0.198711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.163919 restraints weight = 19945.824| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 3.02 r_work: 0.4216 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 19663 Z= 0.228 Angle : 0.746 10.743 27075 Z= 0.397 Chirality : 0.048 0.368 3045 Planarity : 0.005 0.059 3066 Dihedral : 20.085 159.256 3743 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.23 % Allowed : 26.85 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 2025 helix: 0.31 (0.18), residues: 846 sheet: -1.60 (0.27), residues: 353 loop : -0.72 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.032 0.002 TYR D 248 PHE 0.026 0.002 PHE B 242 TRP 0.048 0.002 TRP C 245 HIS 0.006 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (19660) covalent geometry : angle 0.74521 / 0.40 (27071) SS BOND : bond 0.01491 / 0.78 ( 2) SS BOND : angle 1.95329 / 1.19 ( 4) hydrogen bonds : bond 0.05288 / 3.28 ( 830) hydrogen bonds : angle 5.19288 / 3.65 ( 2261) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 218 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7127 (p0) REVERT: A 141 LYS cc_start: 0.6778 (mppt) cc_final: 0.6483 (mmtt) REVERT: A 142 HIS cc_start: 0.5486 (OUTLIER) cc_final: 0.4474 (m-70) REVERT: A 164 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5686 (mtm) REVERT: A 214 PHE cc_start: 0.6606 (m-10) cc_final: 0.6384 (m-10) REVERT: A 301 LEU cc_start: 0.7467 (tt) cc_final: 0.7194 (pp) REVERT: B 1 MET cc_start: 0.6853 (mmm) cc_final: 0.6568 (mmm) REVERT: B 6 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: B 10 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7471 (mmtp) REVERT: B 138 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6678 (tp30) REVERT: B 152 LYS cc_start: 0.6817 (mppt) cc_final: 0.6391 (pttm) REVERT: B 342 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5838 (pp) REVERT: B 396 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: B 436 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: C 116 ASN cc_start: 0.7012 (m-40) cc_final: 0.6499 (m110) REVERT: C 119 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6098 (mttm) REVERT: C 125 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: C 143 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5314 (t70) REVERT: C 172 ARG cc_start: 0.6266 (mmt90) cc_final: 0.5739 (mmp-170) REVERT: C 223 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5407 (tt0) REVERT: C 251 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7607 (tptt) REVERT: C 320 LYS cc_start: 0.7417 (mmmt) cc_final: 0.6895 (mttm) REVERT: D 140 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7605 (mtt180) REVERT: D 175 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6213 (tm-30) REVERT: D 336 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.4687 (tmm) REVERT: D 415 SER cc_start: 0.8030 (t) cc_final: 0.7713 (p) REVERT: D 455 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6539 (t0) REVERT: D 465 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 498 ASP cc_start: 0.7543 (t70) cc_final: 0.7111 (t0) REVERT: E 72 LYS cc_start: 0.7736 (mttt) cc_final: 0.6949 (tmmm) REVERT: E 317 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.5903 (mp) REVERT: E 375 MET cc_start: 0.6975 (ttm) cc_final: 0.6745 (ttm) REVERT: E 383 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: E 389 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7494 (ptp-170) REVERT: E 475 ASN cc_start: 0.7431 (m-40) cc_final: 0.7062 (t0) REVERT: F 1 MET cc_start: 0.6728 (tpp) cc_final: 0.6398 (tpp) REVERT: F 125 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7282 (tp30) outliers start: 96 outliers final: 52 residues processed: 291 average time/residue: 0.4928 time to fit residues: 164.9079 Evaluate side-chains 279 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 209 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 191 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.202773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.168174 restraints weight = 19843.329| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.99 r_work: 0.4270 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19663 Z= 0.146 Angle : 0.671 10.117 27075 Z= 0.358 Chirality : 0.044 0.339 3045 Planarity : 0.005 0.059 3066 Dihedral : 19.971 159.549 3743 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.65 % Allowed : 28.59 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.19), residues: 2025 helix: 0.50 (0.18), residues: 848 sheet: -1.39 (0.27), residues: 350 loop : -0.59 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 126 TYR 0.034 0.002 TYR D 248 PHE 0.020 0.001 PHE D 149 TRP 0.057 0.002 TRP C 245 HIS 0.004 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (19660) covalent geometry : angle 0.67091 / 0.36 (27071) SS BOND : bond 0.01445 / 0.75 ( 2) SS BOND : angle 1.73510 / 1.02 ( 4) hydrogen bonds : bond 0.04164 / 2.60 ( 830) hydrogen bonds : angle 5.01423 / 3.53 ( 2261) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 231 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7095 (p0) REVERT: A 141 LYS cc_start: 0.6741 (mppt) cc_final: 0.6456 (mmtt) REVERT: A 164 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5582 (mtm) REVERT: A 170 ARG cc_start: 0.6787 (mtt-85) cc_final: 0.6462 (mmm-85) REVERT: A 214 PHE cc_start: 0.6421 (m-10) cc_final: 0.6081 (m-80) REVERT: A 301 LEU cc_start: 0.7302 (tt) cc_final: 0.7035 (pp) REVERT: A 304 MET cc_start: 0.6571 (mmt) cc_final: 0.4794 (tmm) REVERT: B 1 MET cc_start: 0.6793 (mmm) cc_final: 0.6527 (mmm) REVERT: B 6 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: B 10 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7250 (mmtp) REVERT: B 138 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6564 (tp30) REVERT: B 152 LYS cc_start: 0.6655 (mppt) cc_final: 0.6219 (pttm) REVERT: B 342 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5793 (pp) REVERT: B 396 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: C 116 ASN cc_start: 0.7013 (m-40) cc_final: 0.6462 (m110) REVERT: C 119 LYS cc_start: 0.6444 (mmmt) cc_final: 0.6024 (mttm) REVERT: C 125 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: C 126 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7551 (ptm160) REVERT: C 172 ARG cc_start: 0.6328 (mmt90) cc_final: 0.5810 (mmp-170) REVERT: C 320 LYS cc_start: 0.7292 (mmmt) cc_final: 0.6787 (mttm) REVERT: D 140 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7542 (mtt180) REVERT: D 175 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: D 336 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4661 (tmm) REVERT: D 377 MET cc_start: 0.6265 (mtm) cc_final: 0.5702 (mtp) REVERT: D 405 TRP cc_start: 0.5997 (t60) cc_final: 0.5197 (m-10) REVERT: D 415 SER cc_start: 0.7952 (t) cc_final: 0.7641 (p) REVERT: D 465 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7229 (mm-30) REVERT: D 498 ASP cc_start: 0.7505 (t70) cc_final: 0.7064 (t0) REVERT: E 72 LYS cc_start: 0.7603 (mttt) cc_final: 0.6889 (tmmm) REVERT: E 230 SER cc_start: 0.8083 (m) cc_final: 0.7795 (t) REVERT: E 317 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.5754 (mp) REVERT: E 389 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7292 (ptp-170) REVERT: E 414 ARG cc_start: 0.6944 (mtp180) cc_final: 0.6725 (mpt-90) REVERT: E 475 ASN cc_start: 0.7419 (m-40) cc_final: 0.7050 (t0) REVERT: F 125 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7243 (tp30) outliers start: 67 outliers final: 35 residues processed: 277 average time/residue: 0.4777 time to fit residues: 151.6998 Evaluate side-chains 263 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 250 HIS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 389 ARG Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 55 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 475 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.203706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.169180 restraints weight = 19937.312| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 2.99 r_work: 0.4284 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19663 Z= 0.141 Angle : 0.670 11.387 27075 Z= 0.356 Chirality : 0.043 0.339 3045 Planarity : 0.005 0.059 3066 Dihedral : 19.874 161.640 3741 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.10 % Allowed : 29.47 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.40 (0.19), residues: 2025 helix: 0.60 (0.18), residues: 848 sheet: -1.24 (0.27), residues: 350 loop : -0.57 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 53 TYR 0.026 0.002 TYR D 141 PHE 0.026 0.002 PHE B 113 TRP 0.063 0.002 TRP C 245 HIS 0.007 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19660) covalent geometry : angle 0.66978 / 0.36 (27071) SS BOND : bond 0.01243 / 0.65 ( 2) SS BOND : angle 1.64890 / 0.96 ( 4) hydrogen bonds : bond 0.04080 / 2.54 ( 830) hydrogen bonds : angle 4.93378 / 3.48 ( 2261) Misc. bond : bond 0.00023 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7283.95 seconds wall clock time: 124 minutes 50.11 seconds (7490.11 seconds total)