Starting phenix.real_space_refine on Fri Aug 7 05:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.map" model { file = "/net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhe_65064/08_2026/9vhe_65064.cif" } resolution = 2.5 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= -0.001 sd= 0.070 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 50 5.16 5 C 11763 2.51 5 N 3377 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19207 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: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3139 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 12, 'TRANS': 376} 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: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3443 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 15, 'TRANS': 413} Chain breaks: 3 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: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1704 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} 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: "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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.72, per 1000 atoms: 0.19 Number of scatterers: 19207 At special positions: 0 Unit cell: (91.464, 137.608, 174.688, 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 50 16.00 P 120 15.00 Mg 1 11.99 O 3896 8.00 N 3377 7.00 C 11763 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 605.6 milliseconds 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3938 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 20 sheets defined 46.8% alpha, 14.1% beta 27 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.943A pdb=" N ILE A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 128 through 136 removed outlier: 3.511A pdb=" N PHE A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.747A 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 249 through 266 removed outlier: 4.295A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.608A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.505A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.820A pdb=" N GLU B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.885A pdb=" N LEU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.998A 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: 3.777A pdb=" N ALA B 228 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.739A pdb=" N VAL B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 4.048A 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: 3.586A pdb=" N ASN B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'C' and resid 99 through 119 removed outlier: 3.775A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.628A 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: 4.112A 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: 3.556A 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: 3.733A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.877A 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 removed outlier: 3.580A pdb=" N SER D 208 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.012A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 238 through 253 Processing helix chain 'D' and resid 311 through 326 removed outlier: 3.596A pdb=" N VAL D 326 " --> pdb=" O ILE D 322 " (cutoff:3.500A) 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: 3.774A pdb=" N GLY D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 417 removed outlier: 3.813A pdb=" N GLU D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 410 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 5.916A 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 434 through 435 No H-bonds generated for 'chain 'D' and resid 434 through 435' Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 465 through 473 Processing helix chain 'D' and resid 483 through 499 removed outlier: 3.850A pdb=" N HIS D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU D 489 " --> pdb=" O GLU D 485 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) 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: 4.433A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.096A 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 208 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 238 through 253 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 378 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 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 428 through 433 removed outlier: 3.913A pdb=" N LEU E 432 " --> pdb=" O SER E 428 " (cutoff:3.500A) 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 467 through 472 Processing helix chain 'E' and resid 483 through 499 removed outlier: 3.890A pdb=" N HIS E 487 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY E 490 " --> pdb=" O SER E 486 " (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 16 removed outlier: 4.147A pdb=" N ASP F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 92 through 97 removed outlier: 3.869A pdb=" N ASN F 96 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.814A pdb=" N ASP F 105 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 133 through 147 removed outlier: 3.685A pdb=" N ALA F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 176 removed outlier: 3.588A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 181 through 196 removed outlier: 4.046A pdb=" N ILE F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 201 through 210 removed outlier: 3.520A pdb=" N ALA F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) 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 81 through 82 removed outlier: 5.428A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.771A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.297A 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: 4.105A 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: 6.767A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C 147 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 69 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER C 145 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 71 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 143 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP C 73 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR C 141 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.596A pdb=" N ALA C 201 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR C 89 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 426 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE C 91 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 335 removed outlier: 4.475A pdb=" N LYS C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.546A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR D 147 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU D 69 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 145 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 71 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP D 143 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASP D 73 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR D 141 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.405A 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 335 removed outlier: 4.306A 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: 4.147A 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: 4.082A pdb=" N PHE E 77 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 79 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS E 72 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 81 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 70 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 83 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG E 68 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR E 147 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE E 148 " --> pdb=" O SER E 156 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER E 156 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 3.894A 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: 4.082A pdb=" N PHE E 77 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 79 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS E 72 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 81 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 70 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 83 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG E 68 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 11.047A 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: 6.814A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 5.943A 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 56 through 57 Processing sheet with id=AC2, first strand: chain 'F' and resid 118 through 120 739 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3034 1.32 - 1.45: 5997 1.45 - 1.58: 10463 1.58 - 1.72: 240 1.72 - 1.85: 80 Bond restraints: 19814 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 1.20e-02 6.94e+03 6.18e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.238 0.293 1.20e-02 6.94e+03 5.98e+02 bond pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " ideal model delta sigma weight residual 1.531 1.238 0.293 1.20e-02 6.94e+03 5.96e+02 bond pdb=" C4' ATP B 601 " pdb=" O4' ATP B 601 " ideal model delta sigma weight residual 1.444 1.294 0.150 1.10e-02 8.26e+03 1.85e+02 bond pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 1.444 1.295 0.149 1.10e-02 8.26e+03 1.84e+02 ... (remaining 19809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 27079 3.43 - 6.86: 164 6.86 - 10.29: 27 10.29 - 13.72: 6 13.72 - 17.15: 4 Bond angle restraints: 27280 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 139.87 122.72 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 123.27 16.60 1.00e+00 1.00e+00 2.76e+02 angle pdb=" PA ATP E 601 " pdb=" O3A ATP E 601 " pdb=" PB ATP E 601 " ideal model delta sigma weight residual 136.83 122.23 14.60 1.00e+00 1.00e+00 2.13e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 125.90 13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 123.33 13.50 1.00e+00 1.00e+00 1.82e+02 ... (remaining 27275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 11051 33.98 - 67.95: 755 67.95 - 101.93: 51 101.93 - 135.91: 5 135.91 - 169.89: 3 Dihedral angle restraints: 11865 sinusoidal: 5809 harmonic: 6056 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 9.89 -169.89 1 1.50e+01 4.44e-03 8.47e+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 -26.74 -133.26 1 1.50e+01 4.44e-03 7.19e+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 180.00 139.34 40.66 0 5.00e+00 4.00e-02 6.61e+01 ... (remaining 11862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2599 0.062 - 0.124: 380 0.124 - 0.186: 78 0.186 - 0.248: 3 0.248 - 0.310: 5 Chirality restraints: 3065 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.40e+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 -2.38 -0.30 2.00e-01 2.50e+01 2.30e+00 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 -2.38 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 3062 not shown) Planarity restraints: 3098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.205 9.50e-02 1.11e+02 9.20e-02 5.50e+00 pdb=" NE ARG A 27 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 82 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C ILE B 82 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 82 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS B 83 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 402 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO E 403 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 403 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 403 " 0.028 5.00e-02 4.00e+02 ... (remaining 3095 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2089 2.74 - 3.28: 19764 3.28 - 3.82: 33896 3.82 - 4.36: 42644 4.36 - 4.90: 67259 Nonbonded interactions: 165652 Sorted by model distance: nonbonded pdb=" O2' ATP B 601 " pdb=" O3' ATP B 601 " model vdw 2.205 2.432 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.220 2.432 nonbonded pdb=" O MET E 336 " pdb=" OG1 THR E 337 " model vdw 2.224 3.040 nonbonded pdb=" O ASN F 102 " pdb=" OD1 ASN F 102 " model vdw 2.306 3.040 nonbonded pdb=" O LYS B 83 " pdb=" C PHE B 84 " model vdw 2.333 3.270 ... (remaining 165647 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 42 through 48 or resid 62 through 211 or resid 222 through \ 253 or resid 310 through 456)) selection = (chain 'D' and (resid 42 through 211 or resid 222 through 452 or resid 529 throu \ gh 530)) selection = (chain 'E' and (resid 42 through 48 or resid 62 through 253 or resid 310 through \ 452 or resid 529 through 530)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.630 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 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 0.298 19816 Z= 0.544 Angle : 0.786 17.151 27284 Z= 0.558 Chirality : 0.049 0.310 3065 Planarity : 0.005 0.092 3098 Dihedral : 20.250 169.887 7921 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.00 % Allowed : 23.96 % Favored : 74.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.34 (0.19), residues: 2044 helix: -0.10 (0.18), residues: 835 sheet: -1.81 (0.28), residues: 337 loop : -1.13 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 221 TYR 0.018 0.001 TYR B 104 PHE 0.028 0.001 PHE B 84 TRP 0.018 0.001 TRP B 245 HIS 0.011 0.001 HIS E 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.54 (19814) covalent geometry : angle 0.78482 / 0.56 (27280) SS BOND : bond 0.01153 / 0.55 ( 2) SS BOND : angle 2.89918 / 1.76 ( 4) hydrogen bonds : bond 0.14064 / 9.05 ( 809) hydrogen bonds : angle 6.62709 / 4.66 ( 2207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.6914 (pmt170) cc_final: 0.5519 (tpt170) REVERT: A 131 ILE cc_start: 0.7249 (mt) cc_final: 0.6625 (mm) REVERT: A 164 MET cc_start: 0.5861 (ptp) cc_final: 0.5583 (pmm) REVERT: B 173 ASP cc_start: 0.6639 (t70) cc_final: 0.6350 (t70) REVERT: C 125 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.6894 (mt0) REVERT: E 68 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7319 (ttm-80) REVERT: E 72 LYS cc_start: 0.7950 (mtpt) cc_final: 0.6767 (tmmt) REVERT: E 129 GLU cc_start: 0.7922 (pt0) cc_final: 0.7527 (pt0) REVERT: E 140 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6828 (mmm160) REVERT: E 161 LEU cc_start: 0.7595 (tp) cc_final: 0.7157 (mp) REVERT: E 170 GLU cc_start: 0.8037 (mp0) cc_final: 0.6944 (tm-30) REVERT: E 175 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6001 (tm-30) REVERT: E 246 TYR cc_start: 0.4463 (m-10) cc_final: 0.4211 (m-80) REVERT: E 329 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6817 (tt) REVERT: E 442 GLU cc_start: 0.8032 (pt0) cc_final: 0.7676 (pm20) REVERT: E 542 ASN cc_start: 0.7597 (t0) cc_final: 0.6934 (t0) REVERT: F 1 MET cc_start: 0.1964 (ptm) cc_final: 0.1063 (ptm) REVERT: F 171 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5255 (mm-30) REVERT: F 195 LYS cc_start: 0.5724 (ttmt) cc_final: 0.5498 (mmmt) outliers start: 37 outliers final: 22 residues processed: 285 average time/residue: 0.4978 time to fit residues: 161.2842 Evaluate side-chains 247 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 495 LEU 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 249 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain F residue 87 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 218 ASN C 314 GLN D 241 HIS D 250 HIS ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS E 487 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 113 ASN F 164 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.203836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.160163 restraints weight = 17659.282| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 1.77 r_work: 0.4267 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19816 Z= 0.165 Angle : 0.671 10.737 27284 Z= 0.365 Chirality : 0.044 0.233 3065 Planarity : 0.005 0.056 3098 Dihedral : 20.171 169.187 3798 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 5.29 % Allowed : 20.13 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 2044 helix: 0.19 (0.18), residues: 846 sheet: -1.64 (0.29), residues: 325 loop : -1.05 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 221 TYR 0.023 0.002 TYR B 65 PHE 0.019 0.002 PHE A 136 TRP 0.018 0.002 TRP E 333 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (19814) covalent geometry : angle 0.66983 / 0.36 (27280) SS BOND : bond 0.00839 / 0.41 ( 2) SS BOND : angle 2.64708 / 1.65 ( 4) hydrogen bonds : bond 0.05152 / 3.36 ( 809) hydrogen bonds : angle 5.29439 / 3.73 ( 2207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 254 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.7454 (mt) cc_final: 0.6892 (mm) REVERT: A 164 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.6041 (pmm) REVERT: B 1 MET cc_start: 0.6890 (pmm) cc_final: 0.6616 (pmm) REVERT: B 396 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6207 (mt-10) REVERT: C 125 GLN cc_start: 0.7632 (mp-120) cc_final: 0.7005 (mt0) REVERT: C 398 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6027 (pm20) REVERT: C 399 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.3937 (tt) REVERT: E 68 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7099 (ttm-80) REVERT: E 72 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6530 (tmmt) REVERT: E 129 GLU cc_start: 0.7800 (pt0) cc_final: 0.7435 (pt0) REVERT: E 140 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6860 (mmm160) REVERT: E 161 LEU cc_start: 0.7512 (tp) cc_final: 0.7082 (mp) REVERT: E 170 GLU cc_start: 0.7999 (mp0) cc_final: 0.7000 (tm-30) REVERT: E 175 GLU cc_start: 0.6599 (tm-30) cc_final: 0.5764 (tm-30) REVERT: E 241 HIS cc_start: 0.6274 (m90) cc_final: 0.5303 (t-170) REVERT: E 246 TYR cc_start: 0.4242 (m-10) cc_final: 0.4024 (m-80) REVERT: E 329 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.6881 (tt) REVERT: E 336 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.5274 (tpp) REVERT: E 356 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.4677 (mm-40) REVERT: E 442 GLU cc_start: 0.7931 (pt0) cc_final: 0.7729 (pm20) REVERT: E 472 GLN cc_start: 0.6481 (mm-40) cc_final: 0.5860 (mt0) REVERT: E 497 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6467 (mp) REVERT: E 542 ASN cc_start: 0.7579 (t0) cc_final: 0.6954 (t0) REVERT: F 1 MET cc_start: -0.0744 (ptm) cc_final: -0.2396 (ptm) REVERT: F 106 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7751 (mt) REVERT: F 108 LYS cc_start: 0.7321 (ttpt) cc_final: 0.6187 (mmmt) outliers start: 98 outliers final: 40 residues processed: 321 average time/residue: 0.4758 time to fit residues: 174.2621 Evaluate side-chains 277 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 68 ARG 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 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 GLN Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 74 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN B 62 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 421 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN F 169 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.198128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.156934 restraints weight = 17667.920| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.92 r_work: 0.4112 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19816 Z= 0.248 Angle : 0.740 12.019 27284 Z= 0.400 Chirality : 0.047 0.194 3065 Planarity : 0.006 0.061 3098 Dihedral : 20.194 170.076 3783 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.05 % Rotamer: Outliers : 6.48 % Allowed : 20.89 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2044 helix: -0.10 (0.17), residues: 852 sheet: -1.56 (0.29), residues: 315 loop : -1.14 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 27 TYR 0.024 0.003 TYR F 93 PHE 0.031 0.003 PHE D 150 TRP 0.020 0.002 TRP E 245 HIS 0.007 0.002 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (19814) covalent geometry : angle 0.73894 / 0.40 (27280) SS BOND : bond 0.00969 / 0.47 ( 2) SS BOND : angle 3.01411 / 1.79 ( 4) hydrogen bonds : bond 0.06194 / 3.93 ( 809) hydrogen bonds : angle 5.24347 / 3.70 ( 2207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 244 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6902 (ptm) cc_final: 0.6592 (ptp) REVERT: A 131 ILE cc_start: 0.7479 (mt) cc_final: 0.6915 (mm) REVERT: A 297 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: B 1 MET cc_start: 0.7085 (pmm) cc_final: 0.6842 (pmm) REVERT: B 7 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.5454 (mtp180) REVERT: B 248 TYR cc_start: 0.6149 (m-10) cc_final: 0.5943 (m-10) REVERT: B 336 MET cc_start: 0.6573 (mtm) cc_final: 0.6370 (mtm) REVERT: B 396 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 408 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5322 (pp20) REVERT: C 125 GLN cc_start: 0.7623 (mp-120) cc_final: 0.7145 (mt0) REVERT: C 336 MET cc_start: 0.7051 (ptm) cc_final: 0.6842 (ptt) REVERT: C 398 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6034 (pm20) REVERT: C 399 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4591 (tp) REVERT: D 45 ASP cc_start: 0.4589 (OUTLIER) cc_final: 0.4374 (t0) REVERT: E 68 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7348 (ttp-110) REVERT: E 72 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6521 (tmmt) REVERT: E 119 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6401 (ptpt) REVERT: E 129 GLU cc_start: 0.7770 (pt0) cc_final: 0.7403 (pt0) REVERT: E 140 ARG cc_start: 0.7233 (mmm160) cc_final: 0.7032 (mmm160) REVERT: E 161 LEU cc_start: 0.7553 (tp) cc_final: 0.7114 (mp) REVERT: E 170 GLU cc_start: 0.7977 (mp0) cc_final: 0.7029 (tm-30) REVERT: E 175 GLU cc_start: 0.6787 (tm-30) cc_final: 0.5960 (tm-30) REVERT: E 311 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6326 (mt-10) REVERT: E 356 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.4341 (mm-40) REVERT: E 442 GLU cc_start: 0.7942 (pt0) cc_final: 0.7624 (pm20) REVERT: E 542 ASN cc_start: 0.7539 (t0) cc_final: 0.6865 (t0) REVERT: F 1 MET cc_start: -0.0940 (ptm) cc_final: -0.2323 (ptm) REVERT: F 38 MET cc_start: 0.1962 (OUTLIER) cc_final: 0.1187 (ptt) REVERT: F 106 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7616 (mp) REVERT: F 108 LYS cc_start: 0.7329 (ttpt) cc_final: 0.6183 (mmmt) REVERT: F 142 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7041 (mm-30) REVERT: F 195 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5730 (ttpt) outliers start: 120 outliers final: 65 residues processed: 331 average time/residue: 0.5177 time to fit residues: 194.6734 Evaluate side-chains 299 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 219 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 356 GLN Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 195 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.200814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.156419 restraints weight = 17475.136| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.82 r_work: 0.4224 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19816 Z= 0.171 Angle : 0.660 11.454 27284 Z= 0.359 Chirality : 0.044 0.258 3065 Planarity : 0.005 0.062 3098 Dihedral : 20.179 171.560 3781 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 6.85 % Allowed : 20.94 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2044 helix: 0.11 (0.17), residues: 850 sheet: -1.41 (0.29), residues: 319 loop : -1.02 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 59 TYR 0.030 0.002 TYR F 93 PHE 0.023 0.002 PHE D 150 TRP 0.025 0.002 TRP E 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (19814) covalent geometry : angle 0.65970 / 0.36 (27280) SS BOND : bond 0.00864 / 0.42 ( 2) SS BOND : angle 2.62008 / 1.54 ( 4) hydrogen bonds : bond 0.04806 / 3.15 ( 809) hydrogen bonds : angle 5.06012 / 3.57 ( 2207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 243 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.7421 (mt) cc_final: 0.6860 (mm) REVERT: A 141 LYS cc_start: 0.5977 (mppt) cc_final: 0.5437 (mptt) REVERT: A 230 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: B 1 MET cc_start: 0.7002 (pmm) cc_final: 0.6734 (pmm) REVERT: B 238 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6714 (mmm160) REVERT: B 248 TYR cc_start: 0.6170 (m-10) cc_final: 0.5935 (m-10) REVERT: B 342 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6617 (pp) REVERT: B 408 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5301 (pp20) REVERT: C 125 GLN cc_start: 0.7526 (mp-120) cc_final: 0.7032 (mt0) REVERT: C 399 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4178 (tt) REVERT: D 45 ASP cc_start: 0.4568 (OUTLIER) cc_final: 0.4283 (t0) REVERT: E 68 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7206 (ttm-80) REVERT: E 72 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6485 (tmmt) REVERT: E 119 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6342 (ptpt) REVERT: E 129 GLU cc_start: 0.7863 (pt0) cc_final: 0.7441 (pt0) REVERT: E 130 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7573 (mt) REVERT: E 132 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: E 140 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6540 (mmm160) REVERT: E 161 LEU cc_start: 0.7544 (tp) cc_final: 0.7116 (mp) REVERT: E 170 GLU cc_start: 0.7987 (mp0) cc_final: 0.7040 (tm-30) REVERT: E 175 GLU cc_start: 0.6815 (tm-30) cc_final: 0.5894 (tm-30) REVERT: E 320 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6984 (mmtm) REVERT: E 336 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5336 (tpp) REVERT: E 358 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.6885 (t) REVERT: E 442 GLU cc_start: 0.7948 (pt0) cc_final: 0.7620 (pm20) REVERT: E 497 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6434 (mp) REVERT: E 542 ASN cc_start: 0.7556 (t0) cc_final: 0.6882 (t0) REVERT: F 1 MET cc_start: -0.0923 (ptm) cc_final: -0.2166 (ptm) REVERT: F 38 MET cc_start: 0.1802 (OUTLIER) cc_final: 0.1120 (ptt) REVERT: F 106 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7626 (mp) REVERT: F 108 LYS cc_start: 0.7412 (ttpt) cc_final: 0.6192 (mmmt) REVERT: F 142 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7155 (mm-30) REVERT: F 145 ARG cc_start: 0.7230 (tmm-80) cc_final: 0.6700 (tmm-80) REVERT: F 195 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5709 (ttpt) outliers start: 127 outliers final: 63 residues processed: 333 average time/residue: 0.5280 time to fit residues: 200.4090 Evaluate side-chains 310 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 231 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 195 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 162 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.196693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.156229 restraints weight = 17680.950| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.89 r_work: 0.4097 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19816 Z= 0.242 Angle : 0.734 11.669 27284 Z= 0.395 Chirality : 0.047 0.186 3065 Planarity : 0.006 0.061 3098 Dihedral : 20.229 172.364 3781 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 7.39 % Allowed : 20.99 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2044 helix: -0.14 (0.17), residues: 859 sheet: -1.43 (0.29), residues: 315 loop : -1.10 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 27 TYR 0.023 0.003 TYR F 172 PHE 0.028 0.003 PHE D 150 TRP 0.022 0.002 TRP E 333 HIS 0.006 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (19814) covalent geometry : angle 0.73334 / 0.39 (27280) SS BOND : bond 0.00996 / 0.48 ( 2) SS BOND : angle 3.10525 / 1.75 ( 4) hydrogen bonds : bond 0.05918 / 3.78 ( 809) hydrogen bonds : angle 5.16393 / 3.63 ( 2207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 240 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7163 (pmt170) cc_final: 0.6653 (ppt90) REVERT: A 141 LYS cc_start: 0.6011 (mppt) cc_final: 0.5482 (mptt) REVERT: A 297 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: B 7 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5420 (mtp180) REVERT: B 238 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6611 (mmm160) REVERT: B 248 TYR cc_start: 0.6161 (m-10) cc_final: 0.5951 (m-10) REVERT: B 342 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6665 (pp) REVERT: B 408 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: C 125 GLN cc_start: 0.7494 (mp-120) cc_final: 0.7080 (mt0) REVERT: C 315 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.5870 (tttp) REVERT: C 399 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4477 (tt) REVERT: D 45 ASP cc_start: 0.4593 (OUTLIER) cc_final: 0.4330 (t0) REVERT: D 143 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: D 221 ARG cc_start: 0.7108 (mtt-85) cc_final: 0.6709 (tmt170) REVERT: E 68 ARG cc_start: 0.7773 (ttm170) cc_final: 0.7536 (ttt180) REVERT: E 72 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.6508 (tmmt) REVERT: E 119 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6433 (ptpt) REVERT: E 129 GLU cc_start: 0.7811 (pt0) cc_final: 0.7405 (pt0) REVERT: E 132 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: E 140 ARG cc_start: 0.7216 (mmm160) cc_final: 0.6685 (mmm160) REVERT: E 170 GLU cc_start: 0.7981 (mp0) cc_final: 0.7087 (tm-30) REVERT: E 175 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6034 (tm-30) REVERT: E 320 LYS cc_start: 0.7276 (mmmt) cc_final: 0.7011 (mmtm) REVERT: E 358 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.6990 (t) REVERT: E 442 GLU cc_start: 0.7953 (pt0) cc_final: 0.7689 (pm20) REVERT: E 497 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6496 (mp) REVERT: F 1 MET cc_start: -0.0640 (ptm) cc_final: -0.2032 (ptm) REVERT: F 38 MET cc_start: 0.1852 (OUTLIER) cc_final: 0.0878 (ppp) REVERT: F 106 LEU cc_start: 0.7910 (tp) cc_final: 0.7664 (mp) REVERT: F 108 LYS cc_start: 0.7365 (ttpt) cc_final: 0.6174 (mmmt) REVERT: F 142 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: F 164 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7690 (mp-120) outliers start: 137 outliers final: 80 residues processed: 334 average time/residue: 0.5390 time to fit residues: 205.1766 Evaluate side-chains 317 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 491 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 202 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 49 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN D 356 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.197479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.147495 restraints weight = 17634.523| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 1.87 r_work: 0.4197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19816 Z= 0.202 Angle : 0.695 10.950 27284 Z= 0.376 Chirality : 0.045 0.300 3065 Planarity : 0.005 0.061 3098 Dihedral : 20.207 173.588 3779 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer: Outliers : 7.23 % Allowed : 21.96 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2044 helix: -0.04 (0.17), residues: 858 sheet: -1.40 (0.28), residues: 328 loop : -1.06 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 140 TYR 0.024 0.002 TYR B 65 PHE 0.024 0.002 PHE D 150 TRP 0.030 0.002 TRP E 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (19814) covalent geometry : angle 0.69416 / 0.38 (27280) SS BOND : bond 0.00968 / 0.47 ( 2) SS BOND : angle 2.85145 / 1.63 ( 4) hydrogen bonds : bond 0.05142 / 3.36 ( 809) hydrogen bonds : angle 5.07522 / 3.58 ( 2207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 231 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.7484 (mt) cc_final: 0.6849 (mm) REVERT: A 141 LYS cc_start: 0.6019 (mppt) cc_final: 0.5521 (mptt) REVERT: A 297 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: B 238 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6530 (mmm160) REVERT: B 248 TYR cc_start: 0.6166 (m-10) cc_final: 0.5921 (m-10) REVERT: B 408 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5487 (pp20) REVERT: C 125 GLN cc_start: 0.7472 (mp-120) cc_final: 0.7072 (mt0) REVERT: C 315 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.5741 (tttp) REVERT: C 399 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4324 (tt) REVERT: D 45 ASP cc_start: 0.4510 (OUTLIER) cc_final: 0.4156 (t0) REVERT: D 143 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: D 336 MET cc_start: 0.6639 (pmm) cc_final: 0.5448 (mtm) REVERT: D 356 GLN cc_start: 0.6090 (OUTLIER) cc_final: 0.4992 (mt0) REVERT: E 72 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6478 (tmmt) REVERT: E 119 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6417 (ptpt) REVERT: E 129 GLU cc_start: 0.7870 (pt0) cc_final: 0.7440 (pt0) REVERT: E 132 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.6047 (t0) REVERT: E 140 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6714 (mmm160) REVERT: E 161 LEU cc_start: 0.7602 (tp) cc_final: 0.7133 (mp) REVERT: E 175 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6063 (tm-30) REVERT: E 320 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6979 (mmtm) REVERT: E 328 SER cc_start: 0.5846 (OUTLIER) cc_final: 0.5550 (m) REVERT: E 336 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5407 (tpp) REVERT: E 358 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.6890 (t) REVERT: E 442 GLU cc_start: 0.8022 (pt0) cc_final: 0.7645 (pm20) REVERT: E 497 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6433 (mp) REVERT: F 1 MET cc_start: -0.0499 (ptm) cc_final: -0.1945 (ptm) REVERT: F 38 MET cc_start: 0.1834 (OUTLIER) cc_final: 0.1139 (ppp) REVERT: F 106 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7650 (mp) REVERT: F 108 LYS cc_start: 0.7341 (ttpt) cc_final: 0.6140 (mmmt) outliers start: 134 outliers final: 79 residues processed: 326 average time/residue: 0.5429 time to fit residues: 202.8019 Evaluate side-chains 313 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 217 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.197508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.152800 restraints weight = 17739.106| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.66 r_work: 0.4208 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19816 Z= 0.203 Angle : 0.697 10.707 27284 Z= 0.376 Chirality : 0.045 0.173 3065 Planarity : 0.005 0.059 3098 Dihedral : 20.190 174.599 3779 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 7.29 % Allowed : 22.18 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2044 helix: -0.02 (0.17), residues: 858 sheet: -1.37 (0.29), residues: 320 loop : -1.06 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 59 TYR 0.025 0.002 TYR F 172 PHE 0.023 0.002 PHE D 150 TRP 0.028 0.002 TRP E 245 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (19814) covalent geometry : angle 0.69620 / 0.38 (27280) SS BOND : bond 0.00958 / 0.46 ( 2) SS BOND : angle 2.81190 / 1.62 ( 4) hydrogen bonds : bond 0.05123 / 3.34 ( 809) hydrogen bonds : angle 5.03674 / 3.54 ( 2207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 232 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.6645 (ppp) cc_final: 0.6405 (ppp) REVERT: A 131 ILE cc_start: 0.7437 (mt) cc_final: 0.6790 (mm) REVERT: A 141 LYS cc_start: 0.6062 (mppt) cc_final: 0.5614 (mptt) REVERT: A 297 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: A 304 MET cc_start: 0.6519 (mpt) cc_final: 0.5007 (mmt) REVERT: B 238 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6538 (mmm160) REVERT: B 248 TYR cc_start: 0.6165 (m-10) cc_final: 0.5936 (m-10) REVERT: B 408 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5395 (pp20) REVERT: C 125 GLN cc_start: 0.7465 (mp-120) cc_final: 0.7021 (mt0) REVERT: C 315 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.5748 (tttp) REVERT: C 399 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4426 (tt) REVERT: D 45 ASP cc_start: 0.4516 (OUTLIER) cc_final: 0.4195 (t0) REVERT: D 86 GLU cc_start: 0.7880 (tt0) cc_final: 0.7059 (tp30) REVERT: D 143 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: E 72 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6498 (tmmt) REVERT: E 119 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6444 (ptpt) REVERT: E 129 GLU cc_start: 0.7852 (pt0) cc_final: 0.7402 (pt0) REVERT: E 132 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: E 140 ARG cc_start: 0.7267 (mmm160) cc_final: 0.6739 (mmm160) REVERT: E 161 LEU cc_start: 0.7540 (tp) cc_final: 0.7137 (mp) REVERT: E 175 GLU cc_start: 0.6914 (tm-30) cc_final: 0.5991 (tm-30) REVERT: E 320 LYS cc_start: 0.7336 (mmmt) cc_final: 0.7046 (mmtm) REVERT: E 328 SER cc_start: 0.5846 (OUTLIER) cc_final: 0.5605 (m) REVERT: E 358 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.6914 (t) REVERT: E 442 GLU cc_start: 0.7999 (pt0) cc_final: 0.7713 (pm20) REVERT: E 491 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: E 497 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6404 (mp) REVERT: F 1 MET cc_start: -0.0432 (ptm) cc_final: -0.1800 (ptm) REVERT: F 38 MET cc_start: 0.1888 (OUTLIER) cc_final: 0.1212 (ppp) REVERT: F 94 LYS cc_start: 0.7214 (tttp) cc_final: 0.6840 (tmtm) REVERT: F 106 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7681 (mp) REVERT: F 108 LYS cc_start: 0.7451 (ttpt) cc_final: 0.6242 (mmmt) outliers start: 135 outliers final: 82 residues processed: 330 average time/residue: 0.5342 time to fit residues: 201.2851 Evaluate side-chains 318 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 220 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 491 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 14 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.197318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.156953 restraints weight = 17686.576| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 2.88 r_work: 0.4109 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19816 Z= 0.205 Angle : 0.706 11.845 27284 Z= 0.379 Chirality : 0.045 0.330 3065 Planarity : 0.005 0.062 3098 Dihedral : 20.193 175.498 3779 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.16 % Favored : 93.74 % Rotamer: Outliers : 7.12 % Allowed : 22.50 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2044 helix: -0.01 (0.17), residues: 858 sheet: -1.32 (0.29), residues: 316 loop : -1.09 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.022 0.002 TYR B 65 PHE 0.025 0.002 PHE D 150 TRP 0.029 0.002 TRP E 333 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (19814) covalent geometry : angle 0.70477 / 0.38 (27280) SS BOND : bond 0.00938 / 0.45 ( 2) SS BOND : angle 2.81081 / 1.62 ( 4) hydrogen bonds : bond 0.05150 / 3.35 ( 809) hydrogen bonds : angle 5.03313 / 3.54 ( 2207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 235 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7090 (pmt170) cc_final: 0.6659 (ppt90) REVERT: A 74 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6723 (ppp) REVERT: A 115 MET cc_start: 0.6719 (ppp) cc_final: 0.6376 (ppp) REVERT: A 131 ILE cc_start: 0.7436 (mt) cc_final: 0.6835 (mm) REVERT: A 141 LYS cc_start: 0.6028 (mppt) cc_final: 0.5644 (mptt) REVERT: A 297 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: A 304 MET cc_start: 0.6673 (mpt) cc_final: 0.5174 (mmt) REVERT: B 238 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6545 (mmm160) REVERT: B 248 TYR cc_start: 0.6132 (m-10) cc_final: 0.5922 (m-10) REVERT: B 396 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: B 408 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5469 (pp20) REVERT: C 125 GLN cc_start: 0.7474 (mp-120) cc_final: 0.7045 (mt0) REVERT: C 315 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5744 (tttp) REVERT: D 45 ASP cc_start: 0.4435 (OUTLIER) cc_final: 0.4123 (t0) REVERT: D 143 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: D 336 MET cc_start: 0.6579 (pmm) cc_final: 0.5413 (mtm) REVERT: E 72 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6498 (tmmt) REVERT: E 119 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6464 (ptpt) REVERT: E 129 GLU cc_start: 0.7827 (pt0) cc_final: 0.7378 (pt0) REVERT: E 132 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: E 140 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6779 (mmp-170) REVERT: E 161 LEU cc_start: 0.7591 (tp) cc_final: 0.7149 (mp) REVERT: E 175 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6035 (tm-30) REVERT: E 311 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6235 (mt-10) REVERT: E 320 LYS cc_start: 0.7277 (mmmt) cc_final: 0.7003 (mmtm) REVERT: E 328 SER cc_start: 0.5846 (OUTLIER) cc_final: 0.5633 (m) REVERT: E 358 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.6918 (t) REVERT: E 442 GLU cc_start: 0.7964 (pt0) cc_final: 0.7709 (pm20) REVERT: E 491 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: E 497 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6359 (mp) REVERT: F 94 LYS cc_start: 0.7144 (tttp) cc_final: 0.6754 (tmtm) REVERT: F 108 LYS cc_start: 0.7464 (ttpt) cc_final: 0.6301 (mmmt) REVERT: F 159 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6426 (mtp180) outliers start: 132 outliers final: 87 residues processed: 330 average time/residue: 0.5249 time to fit residues: 198.4903 Evaluate side-chains 330 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 226 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 376 VAL 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 C residue 71 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP 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 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 491 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 159 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 99 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN D 48 GLN E 241 HIS ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.197040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.152259 restraints weight = 17624.406| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.72 r_work: 0.4191 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19816 Z= 0.202 Angle : 0.711 12.985 27284 Z= 0.381 Chirality : 0.045 0.174 3065 Planarity : 0.005 0.059 3098 Dihedral : 20.176 176.183 3779 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 7.07 % Allowed : 23.15 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2044 helix: 0.00 (0.17), residues: 858 sheet: -1.30 (0.29), residues: 317 loop : -1.08 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.024 0.002 TYR F 172 PHE 0.022 0.002 PHE A 136 TRP 0.032 0.002 TRP E 333 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (19814) covalent geometry : angle 0.71076 / 0.38 (27280) SS BOND : bond 0.00920 / 0.44 ( 2) SS BOND : angle 2.75665 / 1.60 ( 4) hydrogen bonds : bond 0.05091 / 3.32 ( 809) hydrogen bonds : angle 5.02310 / 3.53 ( 2207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 236 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6993 (ppp) cc_final: 0.6512 (ppp) REVERT: A 94 LYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5322 (pttp) REVERT: A 115 MET cc_start: 0.6758 (ppp) cc_final: 0.6398 (ppp) REVERT: A 141 LYS cc_start: 0.6080 (mppt) cc_final: 0.5702 (mptt) REVERT: A 164 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6510 (pmm) REVERT: A 168 ASP cc_start: 0.6997 (m-30) cc_final: 0.6779 (m-30) REVERT: A 297 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: A 304 MET cc_start: 0.6643 (mpt) cc_final: 0.5271 (mmt) REVERT: B 206 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: B 238 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6564 (mmm160) REVERT: B 248 TYR cc_start: 0.6187 (m-10) cc_final: 0.5944 (m-10) REVERT: B 396 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 408 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5491 (pp20) REVERT: C 72 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5978 (tmmm) REVERT: C 125 GLN cc_start: 0.7489 (mp-120) cc_final: 0.7041 (mt0) REVERT: C 315 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.5707 (tttp) REVERT: D 45 ASP cc_start: 0.4377 (OUTLIER) cc_final: 0.4030 (t0) REVERT: D 64 PHE cc_start: 0.6864 (m-10) cc_final: 0.6608 (m-10) REVERT: D 143 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: D 336 MET cc_start: 0.6602 (pmm) cc_final: 0.5417 (mtm) REVERT: E 72 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6489 (tmmt) REVERT: E 119 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6477 (ptpt) REVERT: E 129 GLU cc_start: 0.7897 (pt0) cc_final: 0.7427 (pt0) REVERT: E 132 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: E 140 ARG cc_start: 0.7280 (mmm160) cc_final: 0.6780 (mmp-170) REVERT: E 161 LEU cc_start: 0.7627 (tp) cc_final: 0.7164 (mp) REVERT: E 175 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6005 (tm-30) REVERT: E 311 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6244 (mt-10) REVERT: E 320 LYS cc_start: 0.7331 (mmmt) cc_final: 0.7042 (mmtm) REVERT: E 328 SER cc_start: 0.5817 (OUTLIER) cc_final: 0.5616 (m) REVERT: E 336 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5351 (tpp) REVERT: E 358 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.6908 (t) REVERT: E 442 GLU cc_start: 0.8055 (pt0) cc_final: 0.7736 (pm20) REVERT: E 497 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6373 (mp) REVERT: F 94 LYS cc_start: 0.7199 (tttp) cc_final: 0.6796 (tmtm) REVERT: F 108 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6375 (mmmt) REVERT: F 159 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6486 (mtp180) outliers start: 131 outliers final: 81 residues processed: 327 average time/residue: 0.4875 time to fit residues: 183.0040 Evaluate side-chains 324 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 223 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 376 VAL 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 C residue 71 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP 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 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 159 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 163 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN E 241 HIS E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.200627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.156333 restraints weight = 17652.675| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.66 r_work: 0.4243 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19816 Z= 0.147 Angle : 0.665 11.335 27284 Z= 0.359 Chirality : 0.043 0.317 3065 Planarity : 0.005 0.062 3098 Dihedral : 20.068 179.184 3779 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 4.26 % Allowed : 25.90 % 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: -0.88 (0.18), residues: 2044 helix: 0.19 (0.18), residues: 861 sheet: -1.19 (0.29), residues: 321 loop : -1.02 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.025 0.002 TYR E 248 PHE 0.020 0.002 PHE D 242 TRP 0.034 0.002 TRP E 333 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (19814) covalent geometry : angle 0.66371 / 0.36 (27280) SS BOND : bond 0.01456 / 0.75 ( 2) SS BOND : angle 3.40726 / 2.16 ( 4) hydrogen bonds : bond 0.04304 / 2.86 ( 809) hydrogen bonds : angle 4.89090 / 3.43 ( 2207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 233 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.6956 (pmt170) cc_final: 0.6606 (ppt90) REVERT: A 74 MET cc_start: 0.6965 (ppp) cc_final: 0.6560 (ppp) REVERT: A 94 LYS cc_start: 0.5465 (OUTLIER) cc_final: 0.5060 (pttp) REVERT: A 115 MET cc_start: 0.6756 (ppp) cc_final: 0.6407 (ppp) REVERT: A 141 LYS cc_start: 0.6255 (mppt) cc_final: 0.5943 (mptt) REVERT: A 164 MET cc_start: 0.7022 (pmm) cc_final: 0.6557 (pmm) REVERT: A 297 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: A 304 MET cc_start: 0.6719 (mpt) cc_final: 0.5066 (mmt) REVERT: B 238 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7321 (mmm-85) REVERT: B 248 TYR cc_start: 0.6054 (m-10) cc_final: 0.5853 (m-10) REVERT: B 396 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: C 72 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5921 (tmmm) REVERT: C 125 GLN cc_start: 0.7492 (mp-120) cc_final: 0.7012 (mt0) REVERT: C 315 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5618 (tttp) REVERT: C 442 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7251 (pm20) REVERT: D 227 ASP cc_start: 0.6425 (m-30) cc_final: 0.6074 (t70) REVERT: D 336 MET cc_start: 0.6597 (pmm) cc_final: 0.5363 (mtm) REVERT: E 119 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6445 (ptpt) REVERT: E 129 GLU cc_start: 0.7878 (pt0) cc_final: 0.7412 (pt0) REVERT: E 132 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: E 140 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6601 (mmm160) REVERT: E 161 LEU cc_start: 0.7590 (tp) cc_final: 0.7162 (mp) REVERT: E 175 GLU cc_start: 0.6843 (tm-30) cc_final: 0.5909 (tm-30) REVERT: E 320 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6929 (mmtm) REVERT: E 442 GLU cc_start: 0.8001 (pt0) cc_final: 0.7678 (pm20) REVERT: E 491 ASP cc_start: 0.6818 (m-30) cc_final: 0.6414 (t0) REVERT: E 497 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6269 (mp) REVERT: F 94 LYS cc_start: 0.7238 (tttp) cc_final: 0.6818 (tmtm) REVERT: F 108 LYS cc_start: 0.7444 (ttpt) cc_final: 0.6332 (mmmt) outliers start: 79 outliers final: 53 residues processed: 286 average time/residue: 0.5018 time to fit residues: 164.4968 Evaluate side-chains 292 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 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 398 GLU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 537 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN D 427 HIS E 241 HIS ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS F 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.199360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.155404 restraints weight = 17490.402| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 1.84 r_work: 0.4215 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19816 Z= 0.174 Angle : 0.685 10.944 27284 Z= 0.368 Chirality : 0.043 0.173 3065 Planarity : 0.006 0.161 3098 Dihedral : 19.999 179.524 3774 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 4.37 % Allowed : 25.90 % Favored : 69.72 % 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: -0.91 (0.18), residues: 2044 helix: 0.17 (0.17), residues: 862 sheet: -1.23 (0.29), residues: 323 loop : -1.02 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.029 0.002 TYR A 185 PHE 0.019 0.002 PHE D 242 TRP 0.034 0.002 TRP E 333 HIS 0.005 0.001 HIS C 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19814) covalent geometry : angle 0.68424 / 0.37 (27280) SS BOND : bond 0.00794 / 0.38 ( 2) SS BOND : angle 3.15625 / 1.97 ( 4) hydrogen bonds : bond 0.04716 / 3.10 ( 809) hydrogen bonds : angle 4.89334 / 3.44 ( 2207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8503.87 seconds wall clock time: 145 minutes 8.95 seconds (8708.95 seconds total)