Starting phenix.real_space_refine on Sat Jul 4 07:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhl_65070/07_2026/9vhl_65070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhl_65070/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vhl_65070/07_2026/9vhl_65070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhl_65070/07_2026/9vhl_65070.map" model { file = "/net/cci-nas-00/data/ceres_data/9vhl_65070/07_2026/9vhl_65070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhl_65070/07_2026/9vhl_65070.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.99, per 1000 atoms: 0.21 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: 1.82 Conformation dependent library (CDL) restraints added in 616.6 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: 2.12 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: 3.33 Time building geometry restraints manager: 2.35 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: 26926 3.77 - 7.54: 116 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: 2646 0.065 - 0.129: 324 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- 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= 0.553 Angle : 0.816 18.842 27075 Z= 0.568 Chirality : 0.047 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 0.00698 / 0.55 (19660) covalent geometry : angle 0.81545 / 0.57 (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 : 0.666 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: 0.5060 time to fit residues: 164.6757 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 : 0.660 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.161652 restraints weight = 19478.995| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.79 r_work: 0.4196 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19663 Z= 0.184 Angle : 0.685 8.193 27075 Z= 0.376 Chirality : 0.045 0.359 3045 Planarity : 0.005 0.055 3066 Dihedral : 20.332 163.980 3776 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.17 % Allowed : 22.11 % Favored : 72.71 % 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: -0.84 (0.19), residues: 2025 helix: 0.36 (0.18), residues: 844 sheet: -1.46 (0.29), residues: 328 loop : -1.00 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 533 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 0.007 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (19660) covalent geometry : angle 0.68419 / 0.38 (27071) SS BOND : bond 0.00865 / 0.44 ( 2) SS BOND : angle 2.56257 / 1.60 ( 4) hydrogen bonds : bond 0.05310 / 3.31 ( 830) hydrogen bonds : angle 5.42657 / 3.89 ( 2261) Misc. bond : bond 0.00244 / 0.13 ( 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 342 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 247 time to evaluate : 0.717 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: 0.6803 (m-80) cc_final: 0.6410 (m-80) REVERT: A 141 LYS cc_start: 0.6735 (mppt) cc_final: 0.6263 (mmtt) REVERT: A 142 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.4809 (m-70) REVERT: A 164 MET cc_start: 0.5802 (ptp) cc_final: 0.4779 (mtm) REVERT: A 304 MET cc_start: 0.6186 (mmm) cc_final: 0.5978 (mmt) REVERT: B 1 MET cc_start: 0.6658 (mmm) cc_final: 0.5622 (mpm) REVERT: B 6 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: B 83 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7236 (ttmt) REVERT: B 152 LYS cc_start: 0.6355 (mppt) cc_final: 0.5843 (pttm) REVERT: B 342 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5748 (pp) REVERT: B 396 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: B 436 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: C 67 ARG cc_start: 0.7150 (tpp-160) cc_final: 0.6905 (tmt90) REVERT: C 101 SER cc_start: 0.6233 (OUTLIER) cc_final: 0.6011 (m) REVERT: C 116 ASN cc_start: 0.7161 (m-40) cc_final: 0.6644 (m110) REVERT: C 125 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: C 184 ASP cc_start: 0.6909 (m-30) cc_final: 0.6558 (m-30) REVERT: C 251 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7744 (tptt) REVERT: C 320 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6813 (mttm) REVERT: C 342 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6271 (pt) REVERT: C 357 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7637 (mp) REVERT: D 87 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7589 (t0) REVERT: D 130 LEU cc_start: 0.7329 (mt) cc_final: 0.6936 (mm) REVERT: D 317 ILE cc_start: 0.8417 (mm) cc_final: 0.8194 (mt) REVERT: D 336 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.4713 (tmm) REVERT: D 415 SER cc_start: 0.7995 (t) cc_final: 0.7696 (p) REVERT: D 433 SER cc_start: 0.7732 (t) cc_final: 0.7503 (m) REVERT: D 455 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6708 (t0) REVERT: D 510 LEU cc_start: 0.8200 (mt) cc_final: 0.7827 (tt) REVERT: E 81 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7576 (mp0) REVERT: E 362 ARG cc_start: 0.6598 (mtm110) cc_final: 0.6286 (mtm110) REVERT: E 373 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.6208 (ttp-170) REVERT: E 414 ARG cc_start: 0.6945 (mpp-170) cc_final: 0.6615 (mpt-90) REVERT: E 465 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6237 (tp30) REVERT: E 475 ASN cc_start: 0.7459 (m-40) cc_final: 0.7050 (t0) REVERT: F 52 ARG cc_start: 0.6913 (ttm170) cc_final: 0.6554 (ttt90) REVERT: F 77 SER cc_start: 0.7568 (t) cc_final: 0.7332 (m) REVERT: F 125 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7909 (tt0) outliers start: 95 outliers final: 32 residues processed: 323 average time/residue: 0.4799 time to fit residues: 178.3300 Evaluate side-chains 260 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 A residue 281 LEU 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: 4.9990 chunk 99 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN E 231 GLN ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.200296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.165744 restraints weight = 19969.546| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.92 r_work: 0.4237 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 19663 Z= 0.259 Angle : 0.767 11.348 27075 Z= 0.416 Chirality : 0.049 0.353 3045 Planarity : 0.006 0.066 3066 Dihedral : 20.386 160.677 3754 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.70 % Allowed : 21.73 % Favored : 71.57 % 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: -1.02 (0.18), residues: 2025 helix: 0.13 (0.18), residues: 844 sheet: -1.64 (0.27), residues: 353 loop : -0.90 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 49 TYR 0.024 0.002 TYR D 141 PHE 0.026 0.003 PHE B 242 TRP 0.022 0.002 TRP E 245 HIS 0.007 0.002 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 (19660) covalent geometry : angle 0.76475 / 0.41 (27071) SS BOND : bond 0.03189 / 1.67 ( 2) SS BOND : angle 4.72017 / 3.08 ( 4) hydrogen bonds : bond 0.06045 / 3.71 ( 830) hydrogen bonds : angle 5.39253 / 3.84 ( 2261) Misc. bond : bond 0.00118 / 0.06 ( 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 358 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 235 time to evaluate : 0.691 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: 0.7095 (m-80) cc_final: 0.6777 (m-80) REVERT: A 141 LYS cc_start: 0.6829 (mppt) cc_final: 0.6392 (mmtt) REVERT: A 142 HIS cc_start: 0.5447 (OUTLIER) cc_final: 0.4699 (m-70) REVERT: A 164 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5105 (mtm) REVERT: A 237 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7350 (p) REVERT: B 1 MET cc_start: 0.6735 (mmm) cc_final: 0.6300 (mmm) REVERT: B 6 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: B 125 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6638 (mt0) REVERT: B 152 LYS cc_start: 0.6824 (mppt) cc_final: 0.6268 (pttm) REVERT: B 342 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5796 (pp) REVERT: B 396 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: B 436 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: C 101 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.6028 (m) REVERT: C 116 ASN cc_start: 0.7106 (m-40) cc_final: 0.6584 (m110) REVERT: C 125 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: C 184 ASP cc_start: 0.6990 (m-30) cc_final: 0.6614 (m-30) REVERT: C 250 HIS cc_start: 0.7122 (t70) cc_final: 0.6837 (t70) REVERT: C 251 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7757 (tptt) REVERT: C 320 LYS cc_start: 0.7391 (mmmt) cc_final: 0.6820 (mttm) REVERT: C 357 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7524 (mp) REVERT: D 87 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7622 (t0) REVERT: D 317 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8198 (mt) REVERT: D 336 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4686 (tmm) REVERT: D 415 SER cc_start: 0.8005 (t) cc_final: 0.7714 (p) REVERT: D 455 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6652 (t0) REVERT: D 510 LEU cc_start: 0.8355 (mt) cc_final: 0.7810 (tt) REVERT: E 72 LYS cc_start: 0.7850 (mttt) cc_final: 0.7119 (tmmm) REVERT: E 317 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6188 (mp) REVERT: E 362 ARG cc_start: 0.6709 (mtm110) cc_final: 0.6396 (mtm110) REVERT: E 373 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6185 (ttp-170) REVERT: E 383 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: E 414 ARG cc_start: 0.6953 (mpp-170) cc_final: 0.6658 (mpt-90) REVERT: E 475 ASN cc_start: 0.7545 (m-40) cc_final: 0.7128 (t0) REVERT: F 52 ARG cc_start: 0.6969 (ttm170) cc_final: 0.6764 (ttt90) REVERT: F 125 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7907 (tt0) outliers start: 123 outliers final: 56 residues processed: 327 average time/residue: 0.5283 time to fit residues: 197.7930 Evaluate side-chains 290 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 237 THR 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 224 GLU 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 432 LEU 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 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 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 70 THR 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 143 ASP 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 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: 5.9990 chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 242 ASN B 22 GLN E 241 HIS E 400 HIS E 535 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.203163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.168959 restraints weight = 19785.030| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 2.99 r_work: 0.4263 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19663 Z= 0.146 Angle : 0.633 9.709 27075 Z= 0.348 Chirality : 0.044 0.318 3045 Planarity : 0.005 0.057 3066 Dihedral : 20.298 161.596 3750 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.94 % Allowed : 23.47 % Favored : 70.59 % 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: -0.58 (0.19), residues: 2025 helix: 0.53 (0.18), residues: 846 sheet: -1.43 (0.28), residues: 348 loop : -0.72 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 180 TYR 0.027 0.002 TYR D 141 PHE 0.018 0.002 PHE B 242 TRP 0.025 0.001 TRP E 245 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (19660) covalent geometry : angle 0.63208 / 0.35 (27071) SS BOND : bond 0.01089 / 0.56 ( 2) SS BOND : angle 2.85772 / 1.85 ( 4) hydrogen bonds : bond 0.04406 / 2.74 ( 830) hydrogen bonds : angle 5.06222 / 3.61 ( 2261) Misc. bond : bond 0.00070 / 0.04 ( 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 362 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 253 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7022 (m-80) cc_final: 0.6669 (m-80) REVERT: A 102 ASN cc_start: 0.7859 (m-40) cc_final: 0.7570 (m110) REVERT: A 141 LYS cc_start: 0.6702 (mppt) cc_final: 0.6355 (mmtt) REVERT: A 142 HIS cc_start: 0.5491 (OUTLIER) cc_final: 0.4723 (m-70) REVERT: A 164 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5132 (mtm) REVERT: A 237 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7358 (p) REVERT: B 1 MET cc_start: 0.6692 (mmm) cc_final: 0.6256 (mmm) REVERT: B 6 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: B 152 LYS cc_start: 0.6564 (mppt) cc_final: 0.6074 (pttm) REVERT: B 342 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5708 (pp) REVERT: B 396 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: B 436 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: C 116 ASN cc_start: 0.7039 (m-40) cc_final: 0.6486 (m110) REVERT: C 125 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7211 (mt0) REVERT: C 184 ASP cc_start: 0.6909 (m-30) cc_final: 0.6547 (m-30) REVERT: C 320 LYS cc_start: 0.7256 (mmmt) cc_final: 0.6768 (mttm) REVERT: D 87 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7543 (t0) REVERT: D 140 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7630 (mtt180) REVERT: D 172 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6922 (tpt170) REVERT: D 175 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: D 336 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4710 (tmm) REVERT: D 377 MET cc_start: 0.6310 (mtm) cc_final: 0.5682 (mtp) REVERT: D 415 SER cc_start: 0.7970 (t) cc_final: 0.7660 (p) REVERT: D 455 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6636 (t0) REVERT: D 465 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7171 (mm-30) REVERT: D 498 ASP cc_start: 0.7612 (t0) cc_final: 0.7175 (t0) REVERT: D 510 LEU cc_start: 0.8311 (mt) cc_final: 0.7730 (tt) REVERT: D 534 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6712 (mt) REVERT: E 72 LYS cc_start: 0.7714 (mttt) cc_final: 0.6964 (tmmm) REVERT: E 120 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: E 182 LEU cc_start: 0.7661 (tp) cc_final: 0.7434 (tp) REVERT: E 317 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.5819 (mp) REVERT: E 383 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: E 475 ASN cc_start: 0.7553 (m-40) cc_final: 0.7120 (t0) REVERT: E 506 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5708 (mp10) REVERT: F 125 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: F 142 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7381 (mp0) outliers start: 109 outliers final: 32 residues processed: 332 average time/residue: 0.4870 time to fit residues: 185.9724 Evaluate side-chains 259 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 237 THR 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 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 431 VAL 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 125 GLN 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 143 ASP 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 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 505 ASN Chi-restraints excluded: chain D residue 534 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 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 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 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: 5.9990 chunk 53 optimal weight: 0.3980 chunk 138 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS 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 = 0.4780 r_free = 0.4780 target = 0.200696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.165440 restraints weight = 19795.020| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.01 r_work: 0.4231 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 19663 Z= 0.192 Angle : 0.683 11.234 27075 Z= 0.370 Chirality : 0.045 0.411 3045 Planarity : 0.005 0.058 3066 Dihedral : 20.200 160.988 3746 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 6.48 % Allowed : 23.64 % Favored : 69.88 % 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: -0.64 (0.19), residues: 2025 helix: 0.48 (0.18), residues: 844 sheet: -1.48 (0.27), residues: 348 loop : -0.73 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 126 TYR 0.026 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 0.00426 / 0.19 (19660) covalent geometry : angle 0.68256 / 0.37 (27071) SS BOND : bond 0.01020 / 0.53 ( 2) SS BOND : angle 2.97465 / 1.92 ( 4) hydrogen bonds : bond 0.04966 / 3.06 ( 830) hydrogen bonds : angle 5.11552 / 3.63 ( 2261) Misc. bond : bond 0.00016 / 0.01 ( 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 343 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 224 time to evaluate : 0.670 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: 0.7181 (m-80) cc_final: 0.6836 (m-80) REVERT: A 141 LYS cc_start: 0.6738 (mppt) cc_final: 0.6400 (mmtt) REVERT: A 142 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4699 (m-70) REVERT: A 164 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5256 (mtm) REVERT: A 214 PHE cc_start: 0.6432 (m-10) cc_final: 0.6138 (m-80) REVERT: A 237 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7341 (p) REVERT: A 244 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: B 1 MET cc_start: 0.6696 (mmm) cc_final: 0.6244 (mmm) REVERT: B 6 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: B 125 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: B 152 LYS cc_start: 0.6726 (mppt) cc_final: 0.6188 (pttm) REVERT: B 342 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5750 (pp) REVERT: B 396 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: B 436 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: C 116 ASN cc_start: 0.7058 (m-40) cc_final: 0.6508 (m110) REVERT: C 125 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: C 126 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7334 (ptm160) REVERT: C 143 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.5254 (t70) REVERT: C 184 ASP cc_start: 0.6893 (m-30) cc_final: 0.6555 (m-30) REVERT: C 250 HIS cc_start: 0.7035 (t70) cc_final: 0.6809 (t70) REVERT: C 251 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7681 (tptt) REVERT: C 320 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6743 (mttm) REVERT: D 87 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7500 (t0) REVERT: D 140 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7612 (mtt180) REVERT: D 175 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6068 (tm-30) REVERT: D 336 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4774 (tmm) REVERT: D 415 SER cc_start: 0.7921 (t) cc_final: 0.7603 (p) REVERT: D 455 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6624 (t0) REVERT: D 465 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7240 (mm-30) REVERT: D 498 ASP cc_start: 0.7584 (t0) cc_final: 0.7150 (t0) REVERT: D 534 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6774 (mt) REVERT: E 72 LYS cc_start: 0.7728 (mttt) cc_final: 0.7014 (tmmm) REVERT: E 182 LEU cc_start: 0.7626 (tp) cc_final: 0.7416 (tp) REVERT: E 317 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.5915 (mp) REVERT: E 373 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.6082 (ttp-170) REVERT: E 383 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: E 389 ARG cc_start: 0.7789 (ptp-170) cc_final: 0.7384 (ptp-170) REVERT: E 475 ASN cc_start: 0.7549 (m-40) cc_final: 0.7139 (t0) REVERT: F 125 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: F 172 TYR cc_start: 0.7156 (t80) cc_final: 0.6928 (t80) outliers start: 119 outliers final: 50 residues processed: 315 average time/residue: 0.5233 time to fit residues: 188.6836 Evaluate side-chains 275 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain A residue 244 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 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 431 VAL 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 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 143 ASP 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 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 143 ASP 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 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 427 HIS Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 537 MET 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 345 VAL 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 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 108 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN B 407 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.201011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.165323 restraints weight = 19713.786| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 3.16 r_work: 0.4229 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19663 Z= 0.146 Angle : 0.635 9.860 27075 Z= 0.346 Chirality : 0.043 0.341 3045 Planarity : 0.005 0.066 3066 Dihedral : 20.097 161.413 3746 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.45 % Allowed : 25.22 % Favored : 69.34 % 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: -0.46 (0.19), residues: 2025 helix: 0.63 (0.18), residues: 846 sheet: -1.35 (0.27), residues: 344 loop : -0.67 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.029 0.002 TYR D 141 PHE 0.027 0.002 PHE B 113 TRP 0.030 0.002 TRP E 245 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (19660) covalent geometry : angle 0.63437 / 0.35 (27071) SS BOND : bond 0.01027 / 0.53 ( 2) SS BOND : angle 2.70206 / 1.74 ( 4) hydrogen bonds : bond 0.04258 / 2.65 ( 830) hydrogen bonds : angle 4.98382 / 3.54 ( 2261) Misc. bond : bond 0.00012 / 0.01 ( 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 327 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 227 time to evaluate : 0.512 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: 0.7161 (m-80) cc_final: 0.6854 (m-80) REVERT: A 141 LYS cc_start: 0.6717 (mppt) cc_final: 0.6376 (mmtt) REVERT: A 142 HIS cc_start: 0.5499 (OUTLIER) cc_final: 0.4676 (m-70) REVERT: A 164 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5302 (mtm) REVERT: A 214 PHE cc_start: 0.6501 (m-10) cc_final: 0.6265 (m-80) REVERT: A 237 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7144 (p) REVERT: A 244 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: B 1 MET cc_start: 0.6714 (mmm) cc_final: 0.6170 (mmm) REVERT: B 6 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: B 152 LYS cc_start: 0.6620 (mppt) cc_final: 0.6109 (pttm) REVERT: B 223 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.5965 (mt-10) REVERT: B 342 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5723 (pp) REVERT: B 396 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: C 116 ASN cc_start: 0.7008 (m-40) cc_final: 0.6433 (m110) REVERT: C 125 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: C 126 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7408 (ptm160) REVERT: C 143 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5328 (t70) REVERT: C 184 ASP cc_start: 0.6882 (m-30) cc_final: 0.6588 (m-30) REVERT: C 244 GLU cc_start: 0.7142 (tt0) cc_final: 0.6748 (tt0) REVERT: C 250 HIS cc_start: 0.7093 (t70) cc_final: 0.6865 (t70) REVERT: C 320 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6854 (mttm) REVERT: D 87 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (t0) REVERT: D 140 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7597 (mtt180) REVERT: D 175 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: D 336 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.4784 (tmm) REVERT: D 415 SER cc_start: 0.7859 (t) cc_final: 0.7542 (p) REVERT: D 455 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6611 (t0) REVERT: D 465 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7236 (mm-30) REVERT: D 498 ASP cc_start: 0.7614 (t70) cc_final: 0.7191 (t0) REVERT: E 72 LYS cc_start: 0.7619 (mttt) cc_final: 0.6890 (tmmm) REVERT: E 182 LEU cc_start: 0.7612 (tp) cc_final: 0.7398 (tp) REVERT: E 230 SER cc_start: 0.8147 (m) cc_final: 0.7822 (t) REVERT: E 317 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5798 (mp) REVERT: E 383 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: E 389 ARG cc_start: 0.7800 (ptp-170) cc_final: 0.7222 (ptp-170) REVERT: E 475 ASN cc_start: 0.7523 (m-40) cc_final: 0.7109 (t0) REVERT: F 1 MET cc_start: 0.6832 (tpp) cc_final: 0.6582 (tpp) REVERT: F 125 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7296 (tp30) outliers start: 100 outliers final: 38 residues processed: 302 average time/residue: 0.4472 time to fit residues: 156.5562 Evaluate side-chains 270 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain A residue 244 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 223 GLU Chi-restraints excluded: chain B residue 224 GLU 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 375 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 SER 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 87 ASP 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 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 485 GLU 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 210 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN C 139 ASN E 48 GLN E 209 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 = 0.4771 r_free = 0.4771 target = 0.199513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.163668 restraints weight = 19761.520| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 3.17 r_work: 0.4208 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19663 Z= 0.177 Angle : 0.665 12.356 27075 Z= 0.361 Chirality : 0.044 0.394 3045 Planarity : 0.005 0.063 3066 Dihedral : 20.052 161.247 3745 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.66 % Allowed : 25.65 % 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: -0.52 (0.19), residues: 2025 helix: 0.58 (0.18), residues: 844 sheet: -1.43 (0.27), residues: 350 loop : -0.68 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 27 TYR 0.024 0.002 TYR D 248 PHE 0.023 0.002 PHE B 242 TRP 0.032 0.002 TRP E 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (19660) covalent geometry : angle 0.66505 / 0.36 (27071) SS BOND : bond 0.00589 / 0.29 ( 2) SS BOND : angle 1.35790 / 0.71 ( 4) hydrogen bonds : bond 0.04650 / 2.89 ( 830) hydrogen bonds : angle 5.05023 / 3.57 ( 2261) Misc. bond : bond 0.00010 / 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 335 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 231 time to evaluate : 0.712 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: 0.7186 (m-80) cc_final: 0.6880 (m-80) REVERT: A 141 LYS cc_start: 0.6772 (mppt) cc_final: 0.6451 (mmtt) REVERT: A 142 HIS cc_start: 0.5487 (OUTLIER) cc_final: 0.4613 (m-70) REVERT: A 164 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5402 (mtm) REVERT: A 214 PHE cc_start: 0.6543 (m-10) cc_final: 0.6225 (m-80) REVERT: A 237 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7129 (p) REVERT: B 1 MET cc_start: 0.6659 (mmm) cc_final: 0.6345 (mmm) REVERT: B 6 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: B 125 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6450 (mt0) REVERT: B 152 LYS cc_start: 0.6720 (mppt) cc_final: 0.6176 (pttm) REVERT: B 223 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6033 (mt-10) REVERT: B 342 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5740 (pp) REVERT: B 396 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6584 (mt-10) REVERT: B 436 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6942 (mm-30) REVERT: C 116 ASN cc_start: 0.6999 (m-40) cc_final: 0.6443 (m110) REVERT: C 125 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: C 126 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7448 (ptm160) REVERT: C 143 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5375 (t70) REVERT: C 250 HIS cc_start: 0.7057 (t70) cc_final: 0.6843 (t70) REVERT: C 251 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7687 (tptt) REVERT: C 320 LYS cc_start: 0.7339 (mmmt) cc_final: 0.6806 (mttm) REVERT: D 87 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7479 (t0) REVERT: D 140 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7556 (mtt180) REVERT: D 175 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: D 336 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4722 (tmm) REVERT: D 377 MET cc_start: 0.6340 (mtm) cc_final: 0.5675 (mtp) REVERT: D 415 SER cc_start: 0.7918 (t) cc_final: 0.7599 (p) REVERT: D 465 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 498 ASP cc_start: 0.7595 (t70) cc_final: 0.7176 (t0) REVERT: E 72 LYS cc_start: 0.7620 (mttt) cc_final: 0.6879 (tmmm) REVERT: E 182 LEU cc_start: 0.7612 (tp) cc_final: 0.7401 (tp) REVERT: E 317 ILE cc_start: 0.6613 (OUTLIER) cc_final: 0.5862 (mp) REVERT: E 383 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: E 389 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7230 (ptp-170) REVERT: E 475 ASN cc_start: 0.7513 (m-40) cc_final: 0.7123 (t0) REVERT: E 506 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: F 1 MET cc_start: 0.6845 (tpp) cc_final: 0.6627 (tpp) REVERT: F 53 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.6955 (mmm-85) REVERT: F 125 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7325 (tp30) outliers start: 104 outliers final: 48 residues processed: 311 average time/residue: 0.4528 time to fit residues: 162.9239 Evaluate side-chains 276 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 237 THR 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 223 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 323 CYS 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 431 VAL 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 143 ASP 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 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 87 ASP Chi-restraints excluded: chain D residue 145 SER 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 332 ILE 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 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 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 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 73 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 195 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 156 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.205318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.170540 restraints weight = 19825.601| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 3.01 r_work: 0.4297 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2475 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= 0.135 Angle : 0.633 12.235 27075 Z= 0.345 Chirality : 0.043 0.366 3045 Planarity : 0.005 0.062 3066 Dihedral : 19.962 162.106 3745 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 4.36 % Allowed : 27.07 % Favored : 68.57 % 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: -0.37 (0.19), residues: 2025 helix: 0.71 (0.18), residues: 846 sheet: -1.20 (0.28), residues: 339 loop : -0.68 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 126 TYR 0.032 0.002 TYR D 248 PHE 0.019 0.001 PHE F 147 TRP 0.038 0.002 TRP C 245 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (19660) covalent geometry : angle 0.63257 / 0.34 (27071) SS BOND : bond 0.00423 / 0.20 ( 2) SS BOND : angle 1.47612 / 0.75 ( 4) hydrogen bonds : bond 0.03967 / 2.48 ( 830) hydrogen bonds : angle 4.95545 / 3.50 ( 2261) Misc. bond : bond 0.00042 / 0.02 ( 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 309 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 229 time to evaluate : 0.702 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: 0.7208 (m-80) cc_final: 0.6952 (m-80) REVERT: A 141 LYS cc_start: 0.6740 (mppt) cc_final: 0.6445 (mmtt) REVERT: A 142 HIS cc_start: 0.5499 (OUTLIER) cc_final: 0.4557 (m-70) REVERT: A 164 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5815 (mtm) REVERT: A 237 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7227 (p) REVERT: B 1 MET cc_start: 0.6719 (mmm) cc_final: 0.5836 (mpp) REVERT: B 152 LYS cc_start: 0.6674 (mppt) cc_final: 0.6192 (pttm) REVERT: B 342 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5705 (pp) REVERT: B 396 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: C 116 ASN cc_start: 0.6958 (m-40) cc_final: 0.6393 (m110) REVERT: C 125 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7076 (mt0) REVERT: C 126 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7377 (ptm160) REVERT: C 244 GLU cc_start: 0.7241 (tt0) cc_final: 0.6871 (tt0) REVERT: C 320 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6775 (mttm) REVERT: D 87 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7390 (t0) REVERT: D 130 LEU cc_start: 0.7546 (mt) cc_final: 0.7041 (mm) REVERT: D 140 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7558 (mtt180) REVERT: D 175 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: D 336 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4707 (tmm) REVERT: D 377 MET cc_start: 0.6154 (mtm) cc_final: 0.5608 (mtp) REVERT: D 405 TRP cc_start: 0.6089 (t60) cc_final: 0.5216 (m-10) REVERT: D 415 SER cc_start: 0.7888 (t) cc_final: 0.7546 (p) REVERT: D 465 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7206 (mm-30) REVERT: D 498 ASP cc_start: 0.7548 (t70) cc_final: 0.7115 (t0) REVERT: D 510 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7798 (tt) REVERT: E 72 LYS cc_start: 0.7537 (mttt) cc_final: 0.6816 (tmmm) REVERT: E 182 LEU cc_start: 0.7618 (tp) cc_final: 0.7383 (tp) REVERT: E 230 SER cc_start: 0.8067 (m) cc_final: 0.7772 (t) REVERT: E 317 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.5795 (mp) REVERT: E 389 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7190 (ptp-170) REVERT: E 475 ASN cc_start: 0.7409 (m-40) cc_final: 0.7088 (t0) REVERT: F 53 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.7001 (mmm-85) REVERT: F 125 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: F 142 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7486 (mp0) outliers start: 80 outliers final: 35 residues processed: 288 average time/residue: 0.4705 time to fit residues: 156.8543 Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR 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 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 431 VAL 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 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 87 ASP 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 343 VAL 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 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 389 ARG Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 479 THR 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 142 GLU 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: 9.9990 chunk 155 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 419 ASN ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN F 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.197863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.163736 restraints weight = 20101.527| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 3.04 r_work: 0.4208 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 19663 Z= 0.338 Angle : 0.875 11.404 27075 Z= 0.469 Chirality : 0.054 0.414 3045 Planarity : 0.007 0.063 3066 Dihedral : 20.293 161.137 3745 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.50 % Allowed : 26.63 % Favored : 67.86 % 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: -1.18 (0.18), residues: 2025 helix: -0.08 (0.17), residues: 839 sheet: -1.69 (0.27), residues: 352 loop : -0.92 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 252 TYR 0.035 0.004 TYR C 141 PHE 0.034 0.003 PHE B 113 TRP 0.046 0.003 TRP C 245 HIS 0.009 0.002 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.34 (19660) covalent geometry : angle 0.87430 / 0.47 (27071) SS BOND : bond 0.01911 / 1.00 ( 2) SS BOND : angle 1.93236 / 1.13 ( 4) hydrogen bonds : bond 0.06984 / 4.27 ( 830) hydrogen bonds : angle 5.52763 / 3.87 ( 2261) Misc. bond : bond 0.00005 / 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 321 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 220 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.4002 (t80) cc_final: 0.3522 (m-80) REVERT: A 141 LYS cc_start: 0.6784 (mppt) cc_final: 0.6445 (mmtt) REVERT: A 142 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.4491 (m-70) REVERT: A 164 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.5716 (mtm) REVERT: A 237 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7235 (p) REVERT: B 1 MET cc_start: 0.6848 (mmm) cc_final: 0.6561 (mmm) REVERT: B 152 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6515 (pttp) REVERT: B 223 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6382 (mt-10) REVERT: B 342 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5837 (pp) REVERT: B 396 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 436 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: C 116 ASN cc_start: 0.7103 (m-40) cc_final: 0.6617 (m110) REVERT: C 125 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: C 126 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7591 (ptm160) REVERT: C 172 ARG cc_start: 0.6238 (mmt90) cc_final: 0.5727 (mmp-170) REVERT: C 223 GLU cc_start: 0.5807 (OUTLIER) cc_final: 0.5484 (tt0) REVERT: C 320 LYS cc_start: 0.7333 (mmmt) cc_final: 0.6813 (mttm) REVERT: D 175 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: D 336 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4762 (tmm) REVERT: D 415 SER cc_start: 0.8026 (t) cc_final: 0.7715 (p) REVERT: D 455 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6537 (t0) REVERT: D 465 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7355 (mm-30) REVERT: D 498 ASP cc_start: 0.7605 (t70) cc_final: 0.7145 (t0) REVERT: E 72 LYS cc_start: 0.7800 (mttt) cc_final: 0.7094 (tmmm) REVERT: E 225 ARG cc_start: 0.6561 (mtp180) cc_final: 0.5392 (mmt-90) REVERT: E 317 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6190 (mp) REVERT: E 373 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6154 (ttp-170) REVERT: E 389 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7492 (ptp-170) REVERT: E 475 ASN cc_start: 0.7439 (m-40) cc_final: 0.7094 (t0) REVERT: F 125 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7521 (mp0) REVERT: F 142 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 101 outliers final: 48 residues processed: 294 average time/residue: 0.5260 time to fit residues: 176.3544 Evaluate side-chains 275 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 A residue 237 THR Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 323 CYS 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 431 VAL Chi-restraints excluded: chain B residue 436 GLU 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 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 223 GLU 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 87 ASP Chi-restraints excluded: chain D residue 145 SER 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 343 VAL 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 373 ARG 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 E residue 531 LEU Chi-restraints excluded: chain F residue 31 VAL 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 130 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 128 optimal weight: 0.2980 chunk 208 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.202762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.168261 restraints weight = 19923.989| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 3.01 r_work: 0.4269 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19663 Z= 0.154 Angle : 0.698 11.716 27075 Z= 0.377 Chirality : 0.045 0.357 3045 Planarity : 0.005 0.059 3066 Dihedral : 20.123 162.919 3745 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.94 % Allowed : 29.52 % Favored : 67.54 % 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: -0.62 (0.19), residues: 2025 helix: 0.43 (0.18), residues: 841 sheet: -1.39 (0.27), residues: 346 loop : -0.68 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 126 TYR 0.036 0.002 TYR D 248 PHE 0.024 0.002 PHE E 417 TRP 0.053 0.002 TRP C 245 HIS 0.004 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (19660) covalent geometry : angle 0.69701 / 0.38 (27071) SS BOND : bond 0.02699 / 1.42 ( 2) SS BOND : angle 2.71679 / 1.71 ( 4) hydrogen bonds : bond 0.04353 / 2.69 ( 830) hydrogen bonds : angle 5.13124 / 3.60 ( 2261) Misc. bond : bond 0.00021 / 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 277 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LYS cc_start: 0.6698 (mppt) cc_final: 0.6423 (mmtt) REVERT: A 142 HIS cc_start: 0.5487 (OUTLIER) cc_final: 0.4458 (m-70) REVERT: A 164 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5506 (mtm) REVERT: A 170 ARG cc_start: 0.6787 (mtt-85) cc_final: 0.6455 (mmm-85) REVERT: A 207 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: A 237 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7212 (p) REVERT: A 301 LEU cc_start: 0.7486 (tt) cc_final: 0.7234 (pp) REVERT: B 1 MET cc_start: 0.6818 (mmm) cc_final: 0.6525 (mmm) REVERT: B 152 LYS cc_start: 0.6745 (mppt) cc_final: 0.6255 (pttm) REVERT: B 342 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5820 (pp) REVERT: B 396 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6582 (mt-10) REVERT: C 116 ASN cc_start: 0.7029 (m-40) cc_final: 0.6485 (m110) REVERT: C 125 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: C 172 ARG cc_start: 0.6332 (mmt90) cc_final: 0.5841 (mmp-170) REVERT: C 320 LYS cc_start: 0.7338 (mmmt) cc_final: 0.6854 (mttm) REVERT: D 87 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7418 (t0) REVERT: D 175 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: D 336 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.4736 (tmm) REVERT: D 405 TRP cc_start: 0.5998 (t60) cc_final: 0.5184 (m-10) REVERT: D 415 SER cc_start: 0.8004 (t) cc_final: 0.7693 (p) REVERT: D 465 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 498 ASP cc_start: 0.7529 (t70) cc_final: 0.7083 (t0) REVERT: E 72 LYS cc_start: 0.7568 (mttt) cc_final: 0.6839 (tmmm) REVERT: E 182 LEU cc_start: 0.7613 (tp) cc_final: 0.7383 (tp) REVERT: E 230 SER cc_start: 0.8075 (m) cc_final: 0.7789 (t) REVERT: E 317 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.5746 (mp) REVERT: E 389 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7266 (ptp-170) REVERT: E 414 ARG cc_start: 0.6817 (mtp180) cc_final: 0.6570 (mpt-90) REVERT: E 475 ASN cc_start: 0.7428 (m-40) cc_final: 0.7133 (t0) REVERT: E 506 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5703 (mp10) REVERT: F 125 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7320 (tp30) REVERT: F 142 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (mp0) outliers start: 54 outliers final: 33 residues processed: 259 average time/residue: 0.4869 time to fit residues: 144.6447 Evaluate side-chains 255 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 A residue 237 THR Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 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 431 VAL 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 393 LEU Chi-restraints excluded: chain D residue 87 ASP 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 343 VAL 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 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 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 531 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 142 GLU 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 100 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS ** 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 102 ASN F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.195591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.160762 restraints weight = 20233.326| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.11 r_work: 0.4176 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 19663 Z= 0.340 Angle : 0.884 12.482 27075 Z= 0.472 Chirality : 0.054 0.390 3045 Planarity : 0.007 0.061 3066 Dihedral : 20.393 162.952 3745 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.19 % Allowed : 28.43 % Favored : 67.37 % 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: -1.30 (0.18), residues: 2025 helix: -0.19 (0.17), residues: 842 sheet: -1.72 (0.27), residues: 353 loop : -1.00 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 252 TYR 0.028 0.003 TYR A 185 PHE 0.039 0.003 PHE B 443 TRP 0.066 0.004 TRP C 245 HIS 0.008 0.002 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.34 (19660) covalent geometry : angle 0.88335 / 0.47 (27071) SS BOND : bond 0.02273 / 1.19 ( 2) SS BOND : angle 2.63556 / 1.60 ( 4) hydrogen bonds : bond 0.06933 / 4.26 ( 830) hydrogen bonds : angle 5.56134 / 3.90 ( 2261) Misc. bond : bond 0.00031 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6768.20 seconds wall clock time: 116 minutes 6.39 seconds (6966.39 seconds total)