Starting phenix.real_space_refine on Thu Feb 5 18:00:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhl_65070/02_2026/9vhl_65070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhl_65070/02_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_65070/02_2026/9vhl_65070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhl_65070/02_2026/9vhl_65070.map" model { file = "/net/cci-nas-00/data/ceres_data/9vhl_65070/02_2026/9vhl_65070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhl_65070/02_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-2.0-5952/lib/python3.9/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: 5.01, per 1000 atoms: 0.26 Number of scatterers: 19055 At special positions: 0 Unit cell: (97.232, 140.08, 145.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 120 15.00 Mg 1 11.99 O 3860 8.00 N 3348 7.00 C 11677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 48 " distance=2.04 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 718.9 milliseconds 4050 Ramachandran restraints generated. 2025 Oldfield, 0 Emsley, 2025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3902 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 20 sheets defined 46.8% alpha, 14.9% beta 27 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 2.58 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: 3.80 Time building geometry restraints manager: 2.20 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: 26929 3.77 - 7.54: 113 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: 2681 0.065 - 0.129: 336 0.129 - 0.194: 21 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.300 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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= 0.510 Angle : 0.793 18.842 27075 Z= 0.508 Chirality : 0.044 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 covalent geometry : bond 0.00677 (19660) covalent geometry : angle 0.79295 (27071) SS BOND : bond 0.00597 ( 2) SS BOND : angle 2.18224 ( 4) hydrogen bonds : bond 0.13284 ( 830) hydrogen bonds : angle 6.56761 ( 2261) Misc. bond : bond 0.00425 ( 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 : 0.860 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: 0.5845 time to fit residues: 189.1661 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 : 0.707 ------------------------------------------------------------------------------- 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: 10.0000 chunk 77 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 67 HIS A 138 GLN C 218 ASN D 487 HIS E 400 HIS ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.199491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.163103 restraints weight = 19635.274| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.84 r_work: 0.4220 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19663 Z= 0.176 Angle : 0.650 8.587 27075 Z= 0.350 Chirality : 0.043 0.239 3045 Planarity : 0.005 0.068 3066 Dihedral : 20.152 162.904 3776 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.17 % Allowed : 22.00 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 2025 helix: 0.48 (0.18), residues: 838 sheet: -1.49 (0.28), residues: 338 loop : -0.87 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 221 TYR 0.019 0.002 TYR E 248 PHE 0.020 0.002 PHE B 113 TRP 0.016 0.001 TRP E 245 HIS 0.005 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00393 (19660) covalent geometry : angle 0.64985 (27071) SS BOND : bond 0.00659 ( 2) SS BOND : angle 1.81524 ( 4) hydrogen bonds : bond 0.04704 ( 830) hydrogen bonds : angle 5.20672 ( 2261) Misc. bond : bond 0.00402 ( 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 355 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 260 time to evaluate : 0.714 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: 0.6958 (m-80) cc_final: 0.6583 (m-80) REVERT: A 141 LYS cc_start: 0.6720 (mppt) cc_final: 0.6343 (mmtt) REVERT: A 142 HIS cc_start: 0.5530 (OUTLIER) cc_final: 0.4802 (m-70) REVERT: A 164 MET cc_start: 0.5899 (ptp) cc_final: 0.4843 (mtm) REVERT: B 1 MET cc_start: 0.6712 (mmm) cc_final: 0.6263 (mmm) REVERT: B 6 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: B 125 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6511 (mt0) REVERT: B 152 LYS cc_start: 0.6472 (mppt) cc_final: 0.6080 (pttm) REVERT: B 342 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5719 (pp) REVERT: B 396 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: B 436 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: C 116 ASN cc_start: 0.7086 (m-40) cc_final: 0.6649 (m110) REVERT: C 125 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: C 184 ASP cc_start: 0.6801 (m-30) cc_final: 0.6485 (m-30) REVERT: C 250 HIS cc_start: 0.7160 (t70) cc_final: 0.6877 (t70) REVERT: C 251 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7711 (tptt) REVERT: C 320 LYS cc_start: 0.7445 (mmmt) cc_final: 0.6928 (mttm) REVERT: D 130 LEU cc_start: 0.7262 (mt) cc_final: 0.6872 (mm) REVERT: D 141 TYR cc_start: 0.7714 (p90) cc_final: 0.7400 (p90) REVERT: D 172 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6842 (tpt170) REVERT: D 317 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8243 (mt) REVERT: D 336 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.4678 (tmm) REVERT: D 373 ARG cc_start: 0.6770 (ttp-110) cc_final: 0.6395 (ptm-80) REVERT: D 415 SER cc_start: 0.7987 (t) cc_final: 0.7714 (p) REVERT: D 433 SER cc_start: 0.7684 (t) cc_final: 0.7410 (m) REVERT: D 498 ASP cc_start: 0.7524 (t0) cc_final: 0.7219 (t0) REVERT: D 510 LEU cc_start: 0.8200 (mt) cc_final: 0.7873 (tt) REVERT: E 72 LYS cc_start: 0.7764 (mttt) cc_final: 0.7113 (tmmm) REVERT: E 81 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7656 (mp0) REVERT: E 163 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6540 (tpt-90) REVERT: E 389 ARG cc_start: 0.7829 (ptp-170) cc_final: 0.7408 (ptp-170) REVERT: E 475 ASN cc_start: 0.7469 (m-40) cc_final: 0.7087 (t0) REVERT: F 47 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: F 52 ARG cc_start: 0.6881 (ttm170) cc_final: 0.6561 (ttm-80) REVERT: F 125 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7408 (tp30) REVERT: F 142 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: F 147 PHE cc_start: 0.7433 (m-80) cc_final: 0.6899 (m-80) outliers start: 95 outliers final: 31 residues processed: 333 average time/residue: 0.5701 time to fit residues: 216.4319 Evaluate side-chains 257 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 125 GLN 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 436 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 317 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 419 ASN Chi-restraints excluded: chain D residue 426 THR 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 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 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 407 GLN C 139 ASN D 477 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 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 = 0.4786 r_free = 0.4786 target = 0.200870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.165974 restraints weight = 19930.942| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 3.03 r_work: 0.4243 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19663 Z= 0.197 Angle : 0.675 9.263 27075 Z= 0.361 Chirality : 0.044 0.315 3045 Planarity : 0.005 0.067 3066 Dihedral : 20.033 163.149 3750 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.75 % Allowed : 22.33 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.19), residues: 2025 helix: 0.50 (0.18), residues: 837 sheet: -1.45 (0.28), residues: 330 loop : -0.73 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 221 TYR 0.018 0.002 TYR B 21 PHE 0.023 0.002 PHE E 417 TRP 0.022 0.002 TRP E 245 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00446 (19660) covalent geometry : angle 0.67373 (27071) SS BOND : bond 0.02148 ( 2) SS BOND : angle 3.65992 ( 4) hydrogen bonds : bond 0.04868 ( 830) hydrogen bonds : angle 5.08738 ( 2261) Misc. bond : bond 0.00059 ( 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 373 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 249 time to evaluate : 0.725 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: 0.7161 (m-80) cc_final: 0.6813 (m-80) REVERT: A 102 ASN cc_start: 0.7773 (m-40) cc_final: 0.7200 (m110) REVERT: A 141 LYS cc_start: 0.6824 (mppt) cc_final: 0.6493 (mmtt) REVERT: A 142 HIS cc_start: 0.5521 (OUTLIER) cc_final: 0.4711 (m-70) REVERT: A 159 ILE cc_start: 0.7336 (mm) cc_final: 0.6856 (mt) REVERT: A 164 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5376 (mtm) REVERT: A 237 THR cc_start: 0.7547 (OUTLIER) cc_final: 0.7304 (p) REVERT: B 1 MET cc_start: 0.6773 (mmm) cc_final: 0.6243 (mmm) REVERT: B 6 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: B 125 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6461 (mt0) REVERT: B 152 LYS cc_start: 0.6693 (mppt) cc_final: 0.6254 (pttp) REVERT: B 342 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5760 (pp) REVERT: B 396 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: B 436 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: C 125 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: C 250 HIS cc_start: 0.7144 (t70) cc_final: 0.6897 (t70) REVERT: C 251 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7727 (tptt) REVERT: C 320 LYS cc_start: 0.7361 (mmmt) cc_final: 0.6835 (mttm) REVERT: D 140 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7629 (mtt180) REVERT: D 336 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.4749 (tmm) REVERT: D 377 MET cc_start: 0.6245 (mtm) cc_final: 0.5696 (mtp) REVERT: D 415 SER cc_start: 0.7927 (t) cc_final: 0.7632 (p) REVERT: D 433 SER cc_start: 0.7660 (t) cc_final: 0.7412 (m) REVERT: D 455 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6582 (t0) REVERT: D 465 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7200 (mm-30) REVERT: D 498 ASP cc_start: 0.7504 (t0) cc_final: 0.7257 (t0) REVERT: D 506 GLN cc_start: 0.7656 (mp10) cc_final: 0.7239 (mp10) REVERT: D 534 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6591 (mt) REVERT: E 72 LYS cc_start: 0.7802 (mttt) cc_final: 0.7080 (tmmm) REVERT: E 163 ARG cc_start: 0.7240 (tpp80) cc_final: 0.6527 (tpt-90) REVERT: E 373 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.6040 (ttp-170) REVERT: E 383 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: E 389 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7443 (ptp-170) REVERT: E 475 ASN cc_start: 0.7473 (m-40) cc_final: 0.7150 (t0) REVERT: E 506 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: F 125 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: F 147 PHE cc_start: 0.7146 (m-80) cc_final: 0.6927 (m-80) outliers start: 124 outliers final: 46 residues processed: 341 average time/residue: 0.4901 time to fit residues: 190.5312 Evaluate side-chains 290 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 227 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 125 GLN 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 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 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 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 C residue 411 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 534 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 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 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 48 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 198 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 48 GLN E 477 HIS ** 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 = 0.4801 r_free = 0.4801 target = 0.202607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.166518 restraints weight = 19748.616| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.85 r_work: 0.4273 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19663 Z= 0.140 Angle : 0.590 7.876 27075 Z= 0.318 Chirality : 0.041 0.262 3045 Planarity : 0.005 0.086 3066 Dihedral : 19.833 166.082 3748 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.10 % Allowed : 24.07 % Favored : 69.83 % 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: -0.27 (0.19), residues: 2025 helix: 0.79 (0.18), residues: 845 sheet: -1.24 (0.28), residues: 331 loop : -0.59 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 172 TYR 0.023 0.002 TYR D 141 PHE 0.024 0.002 PHE E 417 TRP 0.024 0.001 TRP E 245 HIS 0.003 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00309 (19660) covalent geometry : angle 0.58930 (27071) SS BOND : bond 0.01070 ( 2) SS BOND : angle 2.38797 ( 4) hydrogen bonds : bond 0.03916 ( 830) hydrogen bonds : angle 4.82621 ( 2261) Misc. bond : bond 0.00039 ( 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 373 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 261 time to evaluate : 0.676 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: 0.7220 (m-80) cc_final: 0.6847 (m-80) REVERT: A 102 ASN cc_start: 0.7825 (m-40) cc_final: 0.7266 (m110) REVERT: A 141 LYS cc_start: 0.6862 (mppt) cc_final: 0.6533 (mmtt) REVERT: A 142 HIS cc_start: 0.5539 (OUTLIER) cc_final: 0.4620 (m-70) REVERT: A 159 ILE cc_start: 0.7370 (mm) cc_final: 0.7135 (mt) REVERT: A 164 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5431 (mtm) REVERT: A 237 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 304 MET cc_start: 0.6249 (mmt) cc_final: 0.4739 (tmm) REVERT: B 1 MET cc_start: 0.6715 (mmm) cc_final: 0.5879 (mpp) REVERT: B 152 LYS cc_start: 0.6643 (mppt) cc_final: 0.6274 (pttm) REVERT: B 342 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5665 (pp) REVERT: B 396 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: C 119 LYS cc_start: 0.6348 (mmmt) cc_final: 0.5937 (mttm) REVERT: C 125 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: C 126 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7449 (ptm160) REVERT: C 250 HIS cc_start: 0.7075 (t70) cc_final: 0.6867 (t70) REVERT: C 251 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7678 (tptt) REVERT: C 320 LYS cc_start: 0.7381 (mmmt) cc_final: 0.6888 (mttm) REVERT: D 130 LEU cc_start: 0.7538 (mt) cc_final: 0.7064 (mm) REVERT: D 140 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7607 (mtt180) REVERT: D 172 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6998 (tpt170) REVERT: D 175 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: D 336 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4628 (tmm) REVERT: D 377 MET cc_start: 0.6302 (mtm) cc_final: 0.5718 (mtp) REVERT: D 415 SER cc_start: 0.7866 (t) cc_final: 0.7556 (p) REVERT: D 433 SER cc_start: 0.7558 (t) cc_final: 0.7233 (m) REVERT: D 465 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 533 ARG cc_start: 0.7919 (ptm160) cc_final: 0.7638 (ptm-80) REVERT: E 72 LYS cc_start: 0.7741 (mttt) cc_final: 0.7064 (tmmm) REVERT: E 230 SER cc_start: 0.8097 (m) cc_final: 0.7776 (t) REVERT: E 317 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5813 (mp) REVERT: E 389 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7470 (ptp-170) REVERT: E 475 ASN cc_start: 0.7455 (m-40) cc_final: 0.7087 (t0) REVERT: E 506 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5760 (mp10) REVERT: F 125 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7184 (tp30) outliers start: 112 outliers final: 36 residues processed: 346 average time/residue: 0.4961 time to fit residues: 196.0427 Evaluate side-chains 270 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 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 89 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 317 ILE 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 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 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 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 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 38 MET Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 60 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 48 GLN E 231 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.199359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.163497 restraints weight = 19716.386| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 3.16 r_work: 0.4210 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19663 Z= 0.187 Angle : 0.653 9.176 27075 Z= 0.350 Chirality : 0.043 0.299 3045 Planarity : 0.005 0.062 3066 Dihedral : 19.897 166.109 3746 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.81 % Allowed : 23.64 % Favored : 69.55 % 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: -0.38 (0.19), residues: 2025 helix: 0.63 (0.18), residues: 842 sheet: -1.27 (0.28), residues: 330 loop : -0.58 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 126 TYR 0.023 0.002 TYR B 21 PHE 0.021 0.002 PHE B 242 TRP 0.025 0.002 TRP E 245 HIS 0.006 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00425 (19660) covalent geometry : angle 0.65222 (27071) SS BOND : bond 0.01413 ( 2) SS BOND : angle 2.56003 ( 4) hydrogen bonds : bond 0.04597 ( 830) hydrogen bonds : angle 4.96262 ( 2261) Misc. bond : bond 0.00028 ( 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 363 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 238 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: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.7887 (m-40) cc_final: 0.7454 (m-40) REVERT: A 141 LYS cc_start: 0.6666 (mppt) cc_final: 0.6400 (mmtt) REVERT: A 142 HIS cc_start: 0.5483 (OUTLIER) cc_final: 0.4502 (m-70) REVERT: A 159 ILE cc_start: 0.7378 (mm) cc_final: 0.6840 (mt) REVERT: A 164 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5790 (mtm) REVERT: A 207 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 237 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7185 (p) REVERT: A 304 MET cc_start: 0.6334 (mmt) cc_final: 0.4799 (tmm) REVERT: B 125 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6510 (mt0) REVERT: B 152 LYS cc_start: 0.6788 (mppt) cc_final: 0.6429 (pttp) REVERT: B 342 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5834 (pp) REVERT: B 396 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: B 436 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: C 119 LYS cc_start: 0.6542 (mmmt) cc_final: 0.6052 (mtpp) REVERT: C 125 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: C 250 HIS cc_start: 0.7110 (t70) cc_final: 0.6899 (t70) REVERT: C 251 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7662 (tptt) REVERT: C 320 LYS cc_start: 0.7391 (mmmt) cc_final: 0.6881 (mttm) REVERT: D 130 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7350 (mt) REVERT: D 140 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7638 (mtt180) REVERT: D 175 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: D 336 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4588 (tmm) REVERT: D 415 SER cc_start: 0.7954 (t) cc_final: 0.7669 (p) REVERT: D 433 SER cc_start: 0.7572 (t) cc_final: 0.7278 (m) REVERT: D 455 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6625 (t0) REVERT: E 72 LYS cc_start: 0.7842 (mttt) cc_final: 0.7138 (tmmm) REVERT: E 317 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.5938 (mp) REVERT: E 373 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.6021 (ttp-170) REVERT: E 389 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7489 (ptp-170) REVERT: E 475 ASN cc_start: 0.7529 (m-40) cc_final: 0.7174 (t0) REVERT: E 506 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: F 125 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7356 (tp30) outliers start: 125 outliers final: 52 residues processed: 336 average time/residue: 0.5588 time to fit residues: 214.0832 Evaluate side-chains 287 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 258 LYS Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 38 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 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 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 130 LEU 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 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 431 VAL 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 520 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 249 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 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 87 TRP Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 407 GLN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 48 GLN ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.198342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.162805 restraints weight = 19565.016| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.73 r_work: 0.4218 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19663 Z= 0.173 Angle : 0.654 10.444 27075 Z= 0.348 Chirality : 0.043 0.308 3045 Planarity : 0.005 0.058 3066 Dihedral : 19.893 168.009 3745 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.88 % Allowed : 25.11 % Favored : 69.01 % 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: 0.68 (0.18), residues: 838 sheet: -1.27 (0.28), residues: 336 loop : -0.61 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 126 TYR 0.024 0.002 TYR D 141 PHE 0.021 0.002 PHE B 113 TRP 0.028 0.002 TRP E 245 HIS 0.005 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00389 (19660) covalent geometry : angle 0.65359 (27071) SS BOND : bond 0.01408 ( 2) SS BOND : angle 1.50288 ( 4) hydrogen bonds : bond 0.04257 ( 830) hydrogen bonds : angle 4.94793 ( 2261) Misc. bond : bond 0.00019 ( 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 339 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 231 time to evaluate : 0.575 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: 0.7174 (m-80) cc_final: 0.6928 (m-80) REVERT: A 102 ASN cc_start: 0.7879 (m-40) cc_final: 0.7389 (m-40) REVERT: A 141 LYS cc_start: 0.6737 (mppt) cc_final: 0.6500 (mmtt) REVERT: A 164 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5748 (mtm) REVERT: A 170 ARG cc_start: 0.6782 (mtt-85) cc_final: 0.6513 (mmm-85) REVERT: A 237 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7290 (p) REVERT: A 301 LEU cc_start: 0.7387 (tt) cc_final: 0.7175 (pp) REVERT: A 304 MET cc_start: 0.6410 (mmt) cc_final: 0.4864 (tmm) REVERT: B 1 MET cc_start: 0.6810 (mmm) cc_final: 0.6582 (mmm) REVERT: B 125 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6521 (mt0) REVERT: B 152 LYS cc_start: 0.6783 (mppt) cc_final: 0.6439 (pttp) REVERT: B 396 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: B 436 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: C 119 LYS cc_start: 0.6454 (mmmt) cc_final: 0.5880 (mttm) REVERT: C 125 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: C 187 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7267 (ttp-110) REVERT: C 250 HIS cc_start: 0.7110 (t70) cc_final: 0.6903 (t70) REVERT: C 320 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6918 (mttm) REVERT: C 357 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7648 (mp) REVERT: D 140 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7513 (mtt180) REVERT: D 175 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6110 (tm-30) REVERT: D 377 MET cc_start: 0.6192 (mtm) cc_final: 0.5648 (mtp) REVERT: D 415 SER cc_start: 0.7905 (t) cc_final: 0.7632 (p) REVERT: D 433 SER cc_start: 0.7495 (t) cc_final: 0.7236 (m) REVERT: E 72 LYS cc_start: 0.7793 (mttt) cc_final: 0.7090 (tmmm) REVERT: E 230 SER cc_start: 0.8130 (m) cc_final: 0.7849 (t) REVERT: E 317 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.5867 (mp) REVERT: E 389 ARG cc_start: 0.7906 (ptp-170) cc_final: 0.7511 (ptp-170) REVERT: E 416 VAL cc_start: 0.6441 (p) cc_final: 0.6214 (m) REVERT: E 475 ASN cc_start: 0.7401 (m-40) cc_final: 0.7109 (t0) REVERT: E 506 GLN cc_start: 0.6153 (OUTLIER) cc_final: 0.5793 (mp10) REVERT: F 125 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: F 147 PHE cc_start: 0.7088 (m-80) cc_final: 0.6875 (m-80) outliers start: 108 outliers final: 48 residues processed: 314 average time/residue: 0.4939 time to fit residues: 177.1669 Evaluate side-chains 272 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 237 THR 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 161 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU 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 125 GLN Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 143 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 355 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU 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 249 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 194 ASN A 242 ASN D 475 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** F 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.203554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.168294 restraints weight = 19626.842| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 2.87 r_work: 0.4290 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19663 Z= 0.136 Angle : 0.628 12.485 27075 Z= 0.331 Chirality : 0.041 0.323 3045 Planarity : 0.004 0.057 3066 Dihedral : 19.743 171.233 3743 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.12 % Allowed : 26.25 % Favored : 68.63 % 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: -0.17 (0.19), residues: 2025 helix: 0.84 (0.18), residues: 844 sheet: -1.10 (0.28), residues: 336 loop : -0.55 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 126 TYR 0.024 0.001 TYR D 141 PHE 0.017 0.001 PHE B 242 TRP 0.023 0.001 TRP E 245 HIS 0.006 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00301 (19660) covalent geometry : angle 0.62790 (27071) SS BOND : bond 0.01444 ( 2) SS BOND : angle 1.81158 ( 4) hydrogen bonds : bond 0.03722 ( 830) hydrogen bonds : angle 4.81391 ( 2261) Misc. bond : bond 0.00020 ( 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 334 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 240 time to evaluate : 0.603 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: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7191 (m-80) cc_final: 0.6949 (m-80) REVERT: A 102 ASN cc_start: 0.7881 (m-40) cc_final: 0.7355 (m-40) REVERT: A 164 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5715 (mtm) REVERT: A 170 ARG cc_start: 0.6741 (mtt-85) cc_final: 0.6449 (mmm-85) REVERT: A 258 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.4970 (ttpt) REVERT: A 304 MET cc_start: 0.6367 (mmt) cc_final: 0.4850 (tmm) REVERT: B 152 LYS cc_start: 0.6803 (mppt) cc_final: 0.6477 (pttm) REVERT: B 396 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: B 436 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: C 119 LYS cc_start: 0.6338 (mmmt) cc_final: 0.5919 (pptt) REVERT: C 125 GLN cc_start: 0.7614 (mp-120) cc_final: 0.7281 (mt0) REVERT: C 126 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7530 (ptm160) REVERT: C 187 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7285 (ttp-110) REVERT: C 320 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6887 (mttm) REVERT: C 357 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7642 (mp) REVERT: D 140 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7562 (mtt180) REVERT: D 175 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6080 (tm-30) REVERT: D 405 TRP cc_start: 0.5992 (t60) cc_final: 0.5260 (m-10) REVERT: D 415 SER cc_start: 0.7929 (t) cc_final: 0.7605 (p) REVERT: D 433 SER cc_start: 0.7403 (t) cc_final: 0.7056 (m) REVERT: D 533 ARG cc_start: 0.7988 (ptm-80) cc_final: 0.7766 (ptm-80) REVERT: E 72 LYS cc_start: 0.7734 (mttt) cc_final: 0.7054 (tmmm) REVERT: E 230 SER cc_start: 0.8033 (m) cc_final: 0.7770 (t) REVERT: E 317 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.5849 (mp) REVERT: E 389 ARG cc_start: 0.7819 (ptp-170) cc_final: 0.7502 (ptp-170) REVERT: E 416 VAL cc_start: 0.6385 (p) cc_final: 0.6170 (m) REVERT: E 475 ASN cc_start: 0.7336 (m-40) cc_final: 0.7007 (t0) REVERT: E 506 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5781 (mp10) REVERT: F 53 ARG cc_start: 0.7123 (mmt90) cc_final: 0.6825 (mmm-85) REVERT: F 125 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 94 outliers final: 46 residues processed: 314 average time/residue: 0.5272 time to fit residues: 188.3215 Evaluate side-chains 271 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 3 LYS 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 161 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 VAL 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 317 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 475 ASN Chi-restraints excluded: chain D residue 505 ASN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 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 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 38 MET Chi-restraints excluded: chain F residue 47 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 195 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 171 optimal weight: 0.0980 chunk 202 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.204555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.168834 restraints weight = 19598.729| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 2.91 r_work: 0.4301 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19663 Z= 0.133 Angle : 0.630 14.192 27075 Z= 0.331 Chirality : 0.041 0.325 3045 Planarity : 0.004 0.058 3066 Dihedral : 19.599 174.144 3739 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.36 % Allowed : 27.61 % Favored : 68.03 % 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: -0.05 (0.19), residues: 2025 helix: 0.96 (0.18), residues: 843 sheet: -0.97 (0.28), residues: 336 loop : -0.53 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 126 TYR 0.026 0.002 TYR D 248 PHE 0.022 0.001 PHE B 113 TRP 0.031 0.001 TRP C 245 HIS 0.009 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00297 (19660) covalent geometry : angle 0.62967 (27071) SS BOND : bond 0.01144 ( 2) SS BOND : angle 1.45827 ( 4) hydrogen bonds : bond 0.03670 ( 830) hydrogen bonds : angle 4.75120 ( 2261) Misc. bond : bond 0.00029 ( 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 319 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.724 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: symmetry clash REVERT: A 29 TYR cc_start: 0.7235 (m-80) cc_final: 0.6964 (m-80) REVERT: A 164 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5377 (mtm) REVERT: A 170 ARG cc_start: 0.6734 (mtt-85) cc_final: 0.6405 (mmm-85) REVERT: A 258 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.4975 (ttpt) REVERT: B 125 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6434 (mt0) REVERT: B 152 LYS cc_start: 0.6783 (mppt) cc_final: 0.6409 (pttm) REVERT: B 396 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6221 (mt-10) REVERT: C 119 LYS cc_start: 0.6372 (mmmt) cc_final: 0.5994 (pptt) REVERT: C 125 GLN cc_start: 0.7571 (mp-120) cc_final: 0.7229 (mt0) REVERT: C 315 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5605 (ptpt) REVERT: C 320 LYS cc_start: 0.7346 (mmmt) cc_final: 0.6935 (mttm) REVERT: C 357 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7622 (mp) REVERT: D 140 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7594 (mtt180) REVERT: D 336 MET cc_start: 0.5469 (pp-130) cc_final: 0.4939 (mtt) REVERT: D 405 TRP cc_start: 0.5957 (t60) cc_final: 0.5279 (m-10) REVERT: D 415 SER cc_start: 0.7978 (t) cc_final: 0.7614 (p) REVERT: D 433 SER cc_start: 0.7293 (t) cc_final: 0.6978 (m) REVERT: E 72 LYS cc_start: 0.7640 (mttt) cc_final: 0.6950 (tmmm) REVERT: E 230 SER cc_start: 0.8035 (m) cc_final: 0.7779 (t) REVERT: E 317 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.5903 (mp) REVERT: E 389 ARG cc_start: 0.7822 (ptp-170) cc_final: 0.7561 (ptp-170) REVERT: E 416 VAL cc_start: 0.6411 (p) cc_final: 0.6188 (m) REVERT: E 475 ASN cc_start: 0.7332 (m-40) cc_final: 0.6956 (t0) REVERT: E 506 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5781 (mp10) REVERT: F 53 ARG cc_start: 0.7010 (mmt90) cc_final: 0.6736 (mmm-85) REVERT: F 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7309 (mp0) outliers start: 80 outliers final: 39 residues processed: 301 average time/residue: 0.4990 time to fit residues: 172.2112 Evaluate side-chains 266 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 3 LYS 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 120 GLU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 343 VAL 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 509 GLU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 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 420 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 125 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 202 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 235 HIS B 4 GLN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS E 472 GLN ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN F 54 HIS F 141 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.195445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.159921 restraints weight = 19776.537| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.78 r_work: 0.4179 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 19663 Z= 0.240 Angle : 0.749 12.801 27075 Z= 0.393 Chirality : 0.046 0.344 3045 Planarity : 0.006 0.093 3066 Dihedral : 19.894 170.538 3737 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.47 % Allowed : 28.10 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2025 helix: 0.40 (0.18), residues: 851 sheet: -1.24 (0.27), residues: 348 loop : -0.66 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 27 TYR 0.024 0.002 TYR F 45 PHE 0.025 0.002 PHE B 443 TRP 0.045 0.002 TRP C 245 HIS 0.010 0.002 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00554 (19660) covalent geometry : angle 0.74786 (27071) SS BOND : bond 0.01484 ( 2) SS BOND : angle 2.67385 ( 4) hydrogen bonds : bond 0.04942 ( 830) hydrogen bonds : angle 5.11468 ( 2261) Misc. bond : bond 0.00027 ( 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 298 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 216 time to evaluate : 0.732 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 164 MET cc_start: 0.6515 (ptp) cc_final: 0.5635 (mtm) REVERT: A 170 ARG cc_start: 0.6794 (mtt-85) cc_final: 0.6494 (mmm-85) REVERT: B 152 LYS cc_start: 0.6695 (mppt) cc_final: 0.6421 (pttp) REVERT: B 396 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: B 436 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: C 116 ASN cc_start: 0.6912 (m-40) cc_final: 0.6365 (m110) REVERT: C 125 GLN cc_start: 0.7659 (mp-120) cc_final: 0.7257 (mt0) REVERT: C 126 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7590 (ptm160) REVERT: C 251 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7673 (tptt) REVERT: C 315 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5486 (ptpt) REVERT: C 320 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6882 (mttm) REVERT: C 357 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7629 (mp) REVERT: D 140 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7527 (mtt180) REVERT: D 336 MET cc_start: 0.5519 (pp-130) cc_final: 0.4968 (mtm) REVERT: D 404 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7847 (mmmm) REVERT: D 415 SER cc_start: 0.7909 (t) cc_final: 0.7516 (p) REVERT: D 433 SER cc_start: 0.7552 (t) cc_final: 0.7302 (m) REVERT: D 455 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6485 (t0) REVERT: E 72 LYS cc_start: 0.7768 (mttt) cc_final: 0.7031 (tmmm) REVERT: E 241 HIS cc_start: 0.7152 (m-70) cc_final: 0.6817 (m90) REVERT: E 317 ILE cc_start: 0.6613 (OUTLIER) cc_final: 0.5810 (mp) REVERT: E 389 ARG cc_start: 0.7863 (ptp-170) cc_final: 0.7490 (ptp-170) REVERT: E 416 VAL cc_start: 0.6405 (p) cc_final: 0.6180 (m) REVERT: E 475 ASN cc_start: 0.7408 (m-40) cc_final: 0.6983 (t0) REVERT: E 506 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5774 (mp10) REVERT: F 53 ARG cc_start: 0.7202 (mmt90) cc_final: 0.6960 (mmt90) REVERT: F 125 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7384 (mp0) outliers start: 82 outliers final: 42 residues processed: 285 average time/residue: 0.5854 time to fit residues: 189.6095 Evaluate side-chains 263 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 3 LYS 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 353 THR Chi-restraints excluded: chain B residue 364 PHE 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 90 VAL Chi-restraints excluded: chain C residue 100 THR 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 315 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 404 LYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE 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 420 ILE Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain F residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 19 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 GLN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.201353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.166370 restraints weight = 19637.642| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.93 r_work: 0.4260 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3446 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= 0.147 Angle : 0.671 12.780 27075 Z= 0.351 Chirality : 0.042 0.323 3045 Planarity : 0.005 0.056 3066 Dihedral : 19.596 174.341 3737 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.61 % Allowed : 30.50 % Favored : 66.88 % 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: -0.29 (0.19), residues: 2025 helix: 0.67 (0.18), residues: 845 sheet: -1.07 (0.28), residues: 346 loop : -0.55 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 221 TYR 0.033 0.002 TYR D 248 PHE 0.024 0.002 PHE B 113 TRP 0.050 0.002 TRP C 245 HIS 0.021 0.001 HIS E 427 Details of bonding type rmsd covalent geometry : bond 0.00333 (19660) covalent geometry : angle 0.66998 (27071) SS BOND : bond 0.01291 ( 2) SS BOND : angle 2.73428 ( 4) hydrogen bonds : bond 0.03868 ( 830) hydrogen bonds : angle 4.90570 ( 2261) Misc. bond : bond 0.00029 ( 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 285 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.804 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: 0.7250 (m-80) cc_final: 0.6977 (m-80) REVERT: A 164 MET cc_start: 0.6476 (ptp) cc_final: 0.5417 (mtm) REVERT: A 170 ARG cc_start: 0.6751 (mtt-85) cc_final: 0.6417 (mmm-85) REVERT: A 297 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7625 (mp0) REVERT: A 304 MET cc_start: 0.6726 (mmt) cc_final: 0.4961 (tmm) REVERT: B 152 LYS cc_start: 0.6739 (mppt) cc_final: 0.6445 (pttm) REVERT: B 396 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: C 116 ASN cc_start: 0.6810 (m-40) cc_final: 0.6426 (m110) REVERT: C 119 LYS cc_start: 0.6395 (mmmt) cc_final: 0.6075 (mtpp) REVERT: C 125 GLN cc_start: 0.7574 (mp-120) cc_final: 0.7212 (mt0) REVERT: C 126 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7536 (ptm160) REVERT: C 315 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5469 (ptpt) REVERT: C 320 LYS cc_start: 0.7344 (mmmt) cc_final: 0.6930 (mttm) REVERT: C 357 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7615 (mp) REVERT: D 140 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7587 (mtt180) REVERT: D 336 MET cc_start: 0.5424 (pp-130) cc_final: 0.4931 (mtt) REVERT: D 405 TRP cc_start: 0.5938 (t60) cc_final: 0.5246 (m-10) REVERT: D 415 SER cc_start: 0.7936 (t) cc_final: 0.7566 (p) REVERT: D 433 SER cc_start: 0.7404 (t) cc_final: 0.7143 (m) REVERT: E 72 LYS cc_start: 0.7709 (mttt) cc_final: 0.6998 (tmmm) REVERT: E 230 SER cc_start: 0.8075 (m) cc_final: 0.7785 (t) REVERT: E 241 HIS cc_start: 0.7050 (m-70) cc_final: 0.6733 (m90) REVERT: E 317 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.5886 (mp) REVERT: E 389 ARG cc_start: 0.7835 (ptp-170) cc_final: 0.7542 (ptp-170) REVERT: E 475 ASN cc_start: 0.7439 (m-40) cc_final: 0.7030 (t0) REVERT: E 506 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5767 (mp10) REVERT: F 125 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7418 (mp0) outliers start: 48 outliers final: 34 residues processed: 273 average time/residue: 0.5750 time to fit residues: 178.6814 Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 195 ILE 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 353 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 90 VAL 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 315 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 240 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 520 ILE Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 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 420 ILE Chi-restraints excluded: chain E residue 427 HIS 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 38 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 90 CYS 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: 7.9990 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 194 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 ASN E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.200356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.165678 restraints weight = 19699.002| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.88 r_work: 0.4251 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19663 Z= 0.168 Angle : 0.699 12.012 27075 Z= 0.366 Chirality : 0.043 0.356 3045 Planarity : 0.005 0.059 3066 Dihedral : 19.571 175.387 3737 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.00 % Allowed : 30.12 % Favored : 66.88 % 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: -0.35 (0.19), residues: 2025 helix: 0.57 (0.18), residues: 851 sheet: -1.05 (0.28), residues: 341 loop : -0.56 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 221 TYR 0.024 0.002 TYR D 141 PHE 0.018 0.002 PHE B 242 TRP 0.056 0.002 TRP C 245 HIS 0.007 0.001 HIS E 427 Details of bonding type rmsd covalent geometry : bond 0.00385 (19660) covalent geometry : angle 0.69874 (27071) SS BOND : bond 0.01397 ( 2) SS BOND : angle 2.52298 ( 4) hydrogen bonds : bond 0.04162 ( 830) hydrogen bonds : angle 4.94922 ( 2261) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.64 seconds wall clock time: 126 minutes 22.08 seconds (7582.08 seconds total)