Starting phenix.real_space_refine on Thu Feb 5 18:33:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhe_65064/02_2026/9vhe_65064.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhe_65064/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vhe_65064/02_2026/9vhe_65064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhe_65064/02_2026/9vhe_65064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vhe_65064/02_2026/9vhe_65064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhe_65064/02_2026/9vhe_65064.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.56, per 1000 atoms: 0.24 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: 1.75 Conformation dependent library (CDL) restraints added in 758.0 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: 2.58 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: 3.59 Time building geometry restraints manager: 2.26 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: 27093 3.43 - 6.86: 150 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: 2669 0.062 - 0.124: 362 0.124 - 0.186: 26 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 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= 0.501 Angle : 0.751 17.151 27284 Z= 0.482 Chirality : 0.044 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 covalent geometry : bond 0.00664 (19814) covalent geometry : angle 0.75002 (27280) SS BOND : bond 0.01153 ( 2) SS BOND : angle 2.89918 ( 4) hydrogen bonds : bond 0.14064 ( 809) hydrogen bonds : angle 6.62709 ( 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 : 0.720 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: 0.7318 (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: 0.6063 time to fit residues: 195.5105 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 : 0.667 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 218 ASN C 314 GLN D 241 HIS ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.203460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.158780 restraints weight = 17688.520| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 1.80 r_work: 0.4265 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19816 Z= 0.164 Angle : 0.649 11.059 27284 Z= 0.344 Chirality : 0.043 0.233 3065 Planarity : 0.005 0.055 3098 Dihedral : 20.109 169.103 3798 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 5.07 % Allowed : 20.13 % Favored : 74.80 % 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: -0.94 (0.19), residues: 2044 helix: 0.32 (0.18), residues: 843 sheet: -1.65 (0.28), residues: 336 loop : -1.01 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 59 TYR 0.024 0.002 TYR F 93 PHE 0.019 0.002 PHE A 136 TRP 0.021 0.002 TRP E 333 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00366 (19814) covalent geometry : angle 0.64793 (27280) SS BOND : bond 0.00789 ( 2) SS BOND : angle 2.46677 ( 4) hydrogen bonds : bond 0.04495 ( 809) hydrogen bonds : angle 5.09022 ( 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 361 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 267 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.7410 (mt) cc_final: 0.6811 (mm) REVERT: A 141 LYS cc_start: 0.5899 (mppt) cc_final: 0.5352 (mptt) REVERT: B 1 MET cc_start: 0.6847 (pmm) cc_final: 0.6600 (pmm) REVERT: B 396 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6220 (mt-10) REVERT: B 408 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5286 (pp20) REVERT: C 125 GLN cc_start: 0.7545 (mp-120) cc_final: 0.7060 (mt0) REVERT: C 223 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5976 (tp30) REVERT: C 315 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6081 (tttp) REVERT: C 398 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.5986 (pm20) REVERT: D 184 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5653 (t0) REVERT: D 227 ASP cc_start: 0.6780 (m-30) cc_final: 0.6297 (t70) REVERT: D 244 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5931 (tp30) REVERT: E 68 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7079 (ttm-80) REVERT: E 72 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6490 (tmmt) REVERT: E 129 GLU cc_start: 0.7789 (pt0) cc_final: 0.7459 (pt0) REVERT: E 140 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6532 (mmm160) REVERT: E 170 GLU cc_start: 0.8047 (mp0) cc_final: 0.7031 (tm-30) REVERT: E 175 GLU cc_start: 0.6705 (tm-30) cc_final: 0.5790 (tm-30) REVERT: E 246 TYR cc_start: 0.4189 (m-10) cc_final: 0.3975 (m-80) REVERT: E 329 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6926 (tt) REVERT: E 356 GLN cc_start: 0.5366 (OUTLIER) cc_final: 0.4099 (mm-40) REVERT: E 442 GLU cc_start: 0.7952 (pt0) cc_final: 0.7686 (pm20) REVERT: E 472 GLN cc_start: 0.6594 (mm-40) cc_final: 0.5969 (mt0) REVERT: E 497 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6468 (mp) REVERT: E 542 ASN cc_start: 0.7577 (t0) cc_final: 0.6964 (t0) REVERT: F 38 MET cc_start: 0.2018 (OUTLIER) cc_final: 0.1497 (ptt) REVERT: F 106 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7755 (mt) REVERT: F 108 LYS cc_start: 0.7358 (ttpt) cc_final: 0.6234 (mmmt) REVERT: F 142 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7107 (mm-30) REVERT: F 169 ASN cc_start: 0.5577 (t0) cc_final: 0.5315 (t0) outliers start: 94 outliers final: 36 residues processed: 329 average time/residue: 0.5871 time to fit residues: 218.7827 Evaluate side-chains 279 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain A residue 270 ASP 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 366 SER Chi-restraints excluded: chain B residue 375 MET 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 223 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 184 ASP 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 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 329 ILE Chi-restraints excluded: chain E residue 356 GLN Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 420 ILE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 74 optimal weight: 0.0470 chunk 177 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 119 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 194 ASN A 242 ASN A 262 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 421 GLN C 450 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.203929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.159582 restraints weight = 17554.175| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 1.89 r_work: 0.4259 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19816 Z= 0.154 Angle : 0.623 12.980 27284 Z= 0.330 Chirality : 0.042 0.250 3065 Planarity : 0.004 0.055 3098 Dihedral : 19.830 169.924 3782 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 5.34 % Allowed : 20.83 % Favored : 73.83 % 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: -0.71 (0.19), residues: 2044 helix: 0.40 (0.18), residues: 862 sheet: -1.39 (0.29), residues: 325 loop : -0.88 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 221 TYR 0.018 0.002 TYR C 141 PHE 0.019 0.002 PHE A 136 TRP 0.021 0.002 TRP E 333 HIS 0.004 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00343 (19814) covalent geometry : angle 0.62219 (27280) SS BOND : bond 0.00843 ( 2) SS BOND : angle 2.48293 ( 4) hydrogen bonds : bond 0.04259 ( 809) hydrogen bonds : angle 4.83642 ( 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 376 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 277 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.7478 (mt) cc_final: 0.6893 (mm) REVERT: A 141 LYS cc_start: 0.5977 (mppt) cc_final: 0.5548 (mptt) REVERT: B 1 MET cc_start: 0.6813 (pmm) cc_final: 0.6110 (mmp) REVERT: B 336 MET cc_start: 0.6392 (mtm) cc_final: 0.6162 (mtm) REVERT: B 381 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6756 (mt) REVERT: B 396 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6271 (mt-10) REVERT: B 408 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5241 (pp20) REVERT: C 125 GLN cc_start: 0.7581 (mp-120) cc_final: 0.7095 (mt0) REVERT: C 223 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.6075 (tp30) REVERT: C 315 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.5863 (tttt) REVERT: C 398 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: C 399 LEU cc_start: 0.4555 (OUTLIER) cc_final: 0.3905 (tt) REVERT: D 221 ARG cc_start: 0.6692 (mtt-85) cc_final: 0.6189 (ttm110) REVERT: D 227 ASP cc_start: 0.6698 (m-30) cc_final: 0.6168 (t70) REVERT: E 68 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7122 (ttm-80) REVERT: E 72 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6446 (tmmt) REVERT: E 119 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6411 (ptpt) REVERT: E 129 GLU cc_start: 0.7880 (pt0) cc_final: 0.7473 (pt0) REVERT: E 140 ARG cc_start: 0.7316 (mmm160) cc_final: 0.6768 (mmp80) REVERT: E 161 LEU cc_start: 0.7547 (tp) cc_final: 0.7145 (mp) REVERT: E 170 GLU cc_start: 0.8015 (mp0) cc_final: 0.7031 (tm-30) REVERT: E 175 GLU cc_start: 0.6793 (tm-30) cc_final: 0.5847 (tm-30) REVERT: E 226 PHE cc_start: 0.6906 (m-80) cc_final: 0.6680 (m-80) REVERT: E 320 LYS cc_start: 0.7132 (mmmt) cc_final: 0.6865 (mmtm) REVERT: E 329 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6954 (tt) REVERT: E 442 GLU cc_start: 0.7932 (pt0) cc_final: 0.7700 (pm20) REVERT: E 472 GLN cc_start: 0.6623 (mm-40) cc_final: 0.6005 (mt0) REVERT: E 542 ASN cc_start: 0.7506 (t0) cc_final: 0.6861 (t0) REVERT: F 38 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.1089 (ppp) REVERT: F 94 LYS cc_start: 0.6923 (tttp) cc_final: 0.6692 (tmtm) REVERT: F 106 LEU cc_start: 0.7961 (tp) cc_final: 0.7686 (mp) REVERT: F 108 LYS cc_start: 0.7333 (ttpt) cc_final: 0.6163 (mmmt) REVERT: F 142 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6965 (mm-30) REVERT: F 145 ARG cc_start: 0.7399 (tmm-80) cc_final: 0.6846 (tmm-80) outliers start: 99 outliers final: 52 residues processed: 341 average time/residue: 0.6323 time to fit residues: 243.2540 Evaluate side-chains 303 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL 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 240 ASP 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 375 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 381 LEU 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 89 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 376 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 70 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 145 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 486 SER 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 103 LEU 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 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 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 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 159 ARG 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: 3.9990 chunk 29 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 250 HIS D 250 HIS D 427 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 F 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.197764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.152852 restraints weight = 17632.681| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.73 r_work: 0.4194 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4070 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19816 Z= 0.234 Angle : 0.711 13.237 27284 Z= 0.375 Chirality : 0.045 0.264 3065 Planarity : 0.005 0.059 3098 Dihedral : 20.082 169.805 3782 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 7.34 % Allowed : 20.18 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2044 helix: 0.05 (0.17), residues: 862 sheet: -1.39 (0.29), residues: 314 loop : -1.00 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 75 TYR 0.029 0.002 TYR F 93 PHE 0.024 0.002 PHE D 150 TRP 0.022 0.002 TRP E 333 HIS 0.006 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00528 (19814) covalent geometry : angle 0.70968 (27280) SS BOND : bond 0.01003 ( 2) SS BOND : angle 3.06519 ( 4) hydrogen bonds : bond 0.05386 ( 809) hydrogen bonds : angle 5.00352 ( 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 384 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 248 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.5567 (pttp) cc_final: 0.5216 (pttp) REVERT: A 131 ILE cc_start: 0.7457 (mt) cc_final: 0.6905 (mm) REVERT: A 141 LYS cc_start: 0.5998 (mppt) cc_final: 0.5564 (mptt) REVERT: A 237 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7452 (p) REVERT: A 297 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: A 303 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6926 (tp) REVERT: A 304 MET cc_start: 0.6718 (mpt) cc_final: 0.5407 (mmt) REVERT: B 1 MET cc_start: 0.7249 (pmm) cc_final: 0.6938 (pmm) REVERT: B 238 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6749 (mmm160) REVERT: B 248 TYR cc_start: 0.6214 (m-10) cc_final: 0.5945 (m-10) REVERT: B 408 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5290 (pp20) REVERT: C 125 GLN cc_start: 0.7379 (mp-120) cc_final: 0.7046 (mt0) REVERT: C 399 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4426 (tt) REVERT: D 45 ASP cc_start: 0.4460 (OUTLIER) cc_final: 0.3982 (t0) REVERT: D 336 MET cc_start: 0.6587 (pmm) cc_final: 0.5444 (mtm) REVERT: E 68 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7375 (ttp-110) REVERT: E 72 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6504 (tmmt) REVERT: E 119 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6523 (ptpt) REVERT: E 129 GLU cc_start: 0.7864 (pt0) cc_final: 0.7436 (pt0) REVERT: E 140 ARG cc_start: 0.7376 (mmm160) cc_final: 0.6787 (mmm160) REVERT: E 175 GLU cc_start: 0.6898 (tm-30) cc_final: 0.5997 (tm-30) REVERT: E 246 TYR cc_start: 0.4665 (m-80) cc_final: 0.3597 (m-80) REVERT: E 311 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: E 320 LYS cc_start: 0.7278 (mmmt) cc_final: 0.6897 (ptmm) REVERT: E 358 SER cc_start: 0.7714 (OUTLIER) cc_final: 0.6888 (t) REVERT: E 408 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: E 442 GLU cc_start: 0.7996 (pt0) cc_final: 0.7728 (pm20) REVERT: F 94 LYS cc_start: 0.6931 (tttp) cc_final: 0.6643 (tmtm) REVERT: F 106 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7648 (mp) REVERT: F 108 LYS cc_start: 0.7424 (ttpt) cc_final: 0.6247 (mmmt) REVERT: F 142 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7337 (mm-30) REVERT: F 164 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7700 (mp-120) outliers start: 136 outliers final: 73 residues processed: 344 average time/residue: 0.6281 time to fit residues: 243.6344 Evaluate side-chains 309 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 221 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 THR 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 42 THR Chi-restraints excluded: chain B residue 67 ARG 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 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 89 THR 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 345 VAL Chi-restraints excluded: chain C residue 376 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 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 68 ARG Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 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 195 ILE 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 321 SER Chi-restraints excluded: chain E residue 326 VAL 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 408 GLU 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 46 CYS Chi-restraints excluded: chain F residue 87 TRP Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 162 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 250 HIS E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.201437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.151528 restraints weight = 17524.182| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 1.88 r_work: 0.4235 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19816 Z= 0.156 Angle : 0.635 12.811 27284 Z= 0.336 Chirality : 0.041 0.170 3065 Planarity : 0.005 0.060 3098 Dihedral : 19.872 171.018 3782 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 6.15 % Allowed : 22.29 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 2044 helix: 0.36 (0.18), residues: 858 sheet: -1.30 (0.29), residues: 330 loop : -0.86 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.019 0.002 TYR B 65 PHE 0.020 0.002 PHE D 150 TRP 0.023 0.001 TRP E 333 HIS 0.004 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00348 (19814) covalent geometry : angle 0.63419 (27280) SS BOND : bond 0.00838 ( 2) SS BOND : angle 2.45819 ( 4) hydrogen bonds : bond 0.04161 ( 809) hydrogen bonds : angle 4.78996 ( 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 366 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 252 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8202 (t70) cc_final: 0.7946 (t70) REVERT: A 131 ILE cc_start: 0.7406 (mt) cc_final: 0.6736 (mm) REVERT: A 141 LYS cc_start: 0.5988 (mppt) cc_final: 0.5680 (mptt) REVERT: A 168 ASP cc_start: 0.6893 (m-30) cc_final: 0.6687 (m-30) REVERT: A 297 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: A 304 MET cc_start: 0.6637 (mpt) cc_final: 0.5157 (mmt) REVERT: B 1 MET cc_start: 0.6971 (pmm) cc_final: 0.6598 (pmm) REVERT: B 396 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 408 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5221 (pp20) REVERT: C 125 GLN cc_start: 0.7497 (mp-120) cc_final: 0.7050 (mt0) REVERT: C 399 LEU cc_start: 0.4731 (OUTLIER) cc_final: 0.4049 (tt) REVERT: D 45 ASP cc_start: 0.4456 (OUTLIER) cc_final: 0.4098 (t0) REVERT: D 227 ASP cc_start: 0.6402 (m-30) cc_final: 0.6014 (t70) REVERT: E 68 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7214 (ttp-110) REVERT: E 72 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6499 (tmmt) REVERT: E 119 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6450 (ptpt) REVERT: E 129 GLU cc_start: 0.7885 (pt0) cc_final: 0.7454 (pt0) REVERT: E 132 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: E 140 ARG cc_start: 0.7393 (mmm160) cc_final: 0.7053 (mmp-170) REVERT: E 161 LEU cc_start: 0.7556 (tp) cc_final: 0.7194 (mp) REVERT: E 175 GLU cc_start: 0.6830 (tm-30) cc_final: 0.5927 (tm-30) REVERT: E 245 TRP cc_start: 0.5873 (OUTLIER) cc_final: 0.5630 (m-90) REVERT: E 246 TYR cc_start: 0.4405 (m-80) cc_final: 0.3545 (m-80) REVERT: E 311 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6269 (mt-10) REVERT: E 335 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6059 (tt0) REVERT: E 358 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.6793 (t) REVERT: E 442 GLU cc_start: 0.7964 (pt0) cc_final: 0.7686 (pm20) REVERT: F 38 MET cc_start: 0.1880 (OUTLIER) cc_final: 0.1198 (ppp) REVERT: F 108 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6161 (mmmt) REVERT: F 130 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6528 (pt) REVERT: F 142 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7201 (mm-30) outliers start: 114 outliers final: 53 residues processed: 326 average time/residue: 0.5195 time to fit residues: 193.3045 Evaluate side-chains 302 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 136 ASP 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 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 205 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 376 VAL 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 145 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 184 ASP 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 510 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 103 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 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 329 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 336 MET 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 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 130 ILE Chi-restraints excluded: chain F residue 159 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 49 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 250 HIS D 250 HIS ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN F 54 HIS F 164 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.195243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.145502 restraints weight = 17839.380| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 1.88 r_work: 0.4176 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19816 Z= 0.247 Angle : 0.722 12.931 27284 Z= 0.381 Chirality : 0.045 0.291 3065 Planarity : 0.005 0.061 3098 Dihedral : 20.003 170.530 3772 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 7.18 % Allowed : 22.29 % 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: -0.98 (0.18), residues: 2044 helix: 0.06 (0.17), residues: 864 sheet: -1.32 (0.29), residues: 319 loop : -0.98 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.026 0.003 TYR F 172 PHE 0.027 0.003 PHE D 150 TRP 0.025 0.002 TRP E 333 HIS 0.012 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00557 (19814) covalent geometry : angle 0.72160 (27280) SS BOND : bond 0.01005 ( 2) SS BOND : angle 3.03036 ( 4) hydrogen bonds : bond 0.05367 ( 809) hydrogen bonds : angle 4.97984 ( 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 371 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 238 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8084 (tp) cc_final: 0.7795 (pt) REVERT: A 115 MET cc_start: 0.6583 (ppp) cc_final: 0.5564 (tmm) REVERT: A 141 LYS cc_start: 0.6034 (mppt) cc_final: 0.5710 (mptt) REVERT: A 237 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7673 (p) REVERT: A 297 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: A 304 MET cc_start: 0.6545 (mpt) cc_final: 0.5402 (mmt) REVERT: B 206 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 238 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6652 (mmm160) REVERT: B 248 TYR cc_start: 0.6235 (m-10) cc_final: 0.5954 (m-10) REVERT: B 408 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5498 (pp20) REVERT: C 125 GLN cc_start: 0.7407 (mp-120) cc_final: 0.7071 (mt0) REVERT: C 399 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4604 (tt) REVERT: D 45 ASP cc_start: 0.4216 (OUTLIER) cc_final: 0.3868 (t0) REVERT: D 336 MET cc_start: 0.6516 (pmm) cc_final: 0.5303 (mtm) REVERT: D 356 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.4915 (mt0) REVERT: E 68 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7395 (ttp-110) REVERT: E 72 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6495 (tmmt) REVERT: E 119 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6497 (ptpt) REVERT: E 129 GLU cc_start: 0.7927 (pt0) cc_final: 0.7472 (pt0) REVERT: E 132 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: E 140 ARG cc_start: 0.7414 (mmm160) cc_final: 0.7095 (mmp-170) REVERT: E 161 LEU cc_start: 0.7580 (tp) cc_final: 0.7183 (mp) REVERT: E 175 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6117 (tm-30) REVERT: E 246 TYR cc_start: 0.4656 (m-80) cc_final: 0.3813 (m-80) REVERT: E 311 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: E 358 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.6925 (t) REVERT: E 442 GLU cc_start: 0.7979 (pt0) cc_final: 0.7720 (pm20) REVERT: F 108 LYS cc_start: 0.7456 (ttpt) cc_final: 0.6302 (mmmt) outliers start: 133 outliers final: 77 residues processed: 328 average time/residue: 0.5301 time to fit residues: 197.8163 Evaluate side-chains 316 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 225 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 195 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 237 THR 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 42 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 154 LEU 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 366 SER 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 72 LYS 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 173 ASP Chi-restraints excluded: chain C residue 205 VAL 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 376 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 72 LYS 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 355 ASP Chi-restraints excluded: chain D residue 356 GLN 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 510 LEU Chi-restraints excluded: chain D residue 541 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 103 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 195 ILE 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 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 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 469 ILE 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 105 ASP Chi-restraints excluded: chain F residue 159 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 132 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 250 HIS D 250 HIS ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.195294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.152853 restraints weight = 17789.123| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.83 r_work: 0.4102 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19816 Z= 0.255 Angle : 0.745 12.875 27284 Z= 0.393 Chirality : 0.046 0.286 3065 Planarity : 0.006 0.062 3098 Dihedral : 20.122 170.688 3770 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Rotamer: Outliers : 7.29 % Allowed : 22.56 % Favored : 70.16 % 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: -1.19 (0.18), residues: 2044 helix: -0.10 (0.17), residues: 863 sheet: -1.33 (0.29), residues: 327 loop : -1.14 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 59 TYR 0.034 0.003 TYR F 93 PHE 0.024 0.003 PHE B 242 TRP 0.028 0.002 TRP C 333 HIS 0.009 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00577 (19814) covalent geometry : angle 0.74400 (27280) SS BOND : bond 0.01035 ( 2) SS BOND : angle 3.09421 ( 4) hydrogen bonds : bond 0.05537 ( 809) hydrogen bonds : angle 5.06441 ( 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 381 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 246 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8233 (tp) cc_final: 0.7962 (pt) REVERT: A 51 LEU cc_start: 0.7077 (pt) cc_final: 0.6659 (pp) REVERT: A 115 MET cc_start: 0.6772 (ppp) cc_final: 0.6446 (ppp) REVERT: A 141 LYS cc_start: 0.6297 (mppt) cc_final: 0.6003 (mptt) REVERT: A 304 MET cc_start: 0.6596 (mpt) cc_final: 0.5496 (mmt) REVERT: B 1 MET cc_start: 0.7123 (pmm) cc_final: 0.6818 (pmm) REVERT: B 238 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6567 (mmm160) REVERT: B 248 TYR cc_start: 0.6417 (m-10) cc_final: 0.6122 (m-10) REVERT: B 335 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 396 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: B 408 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5554 (pp20) REVERT: C 125 GLN cc_start: 0.7507 (mp-120) cc_final: 0.7153 (mt0) REVERT: C 399 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4523 (tt) REVERT: D 45 ASP cc_start: 0.4225 (OUTLIER) cc_final: 0.3913 (t0) REVERT: D 86 GLU cc_start: 0.7993 (tt0) cc_final: 0.7069 (tp30) REVERT: D 336 MET cc_start: 0.6363 (pmm) cc_final: 0.5083 (mtp) REVERT: E 68 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7480 (ttp-110) REVERT: E 72 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.6523 (tmmt) REVERT: E 119 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6528 (ptpt) REVERT: E 129 GLU cc_start: 0.8023 (pt0) cc_final: 0.7562 (pt0) REVERT: E 132 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: E 140 ARG cc_start: 0.7469 (mmm160) cc_final: 0.7113 (mmp-170) REVERT: E 161 LEU cc_start: 0.7649 (tp) cc_final: 0.7230 (mp) REVERT: E 175 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6281 (tm-30) REVERT: E 311 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: E 328 SER cc_start: 0.6119 (OUTLIER) cc_final: 0.5770 (m) REVERT: E 333 TRP cc_start: 0.4500 (m-90) cc_final: 0.4223 (m-90) REVERT: E 358 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7016 (t) REVERT: E 442 GLU cc_start: 0.8115 (pt0) cc_final: 0.7791 (pm20) REVERT: F 108 LYS cc_start: 0.7291 (ttpt) cc_final: 0.6314 (mmtm) REVERT: F 130 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6583 (pp) REVERT: F 164 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8130 (mm110) outliers start: 135 outliers final: 78 residues processed: 340 average time/residue: 0.5160 time to fit residues: 199.0488 Evaluate side-chains 323 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 232 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 136 ASP 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 326 VAL 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 128 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 410 ILE 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 72 LYS 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 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 510 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 103 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 194 THR Chi-restraints excluded: chain E residue 195 ILE 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 469 ILE 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 105 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 159 ARG Chi-restraints excluded: chain F residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 14 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN D 250 HIS ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.196979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.153744 restraints weight = 17692.604| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 1.66 r_work: 0.4208 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2813 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= 0.190 Angle : 0.695 12.557 27284 Z= 0.366 Chirality : 0.043 0.167 3065 Planarity : 0.005 0.062 3098 Dihedral : 19.965 171.676 3770 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 6.31 % Allowed : 24.07 % Favored : 69.62 % 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: -0.97 (0.18), residues: 2044 helix: 0.10 (0.17), residues: 862 sheet: -1.22 (0.29), residues: 326 loop : -1.04 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 59 TYR 0.029 0.002 TYR F 172 PHE 0.025 0.002 PHE A 136 TRP 0.027 0.002 TRP C 333 HIS 0.007 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00429 (19814) covalent geometry : angle 0.69387 (27280) SS BOND : bond 0.00858 ( 2) SS BOND : angle 2.98835 ( 4) hydrogen bonds : bond 0.04711 ( 809) hydrogen bonds : angle 4.89905 ( 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 360 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 243 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8117 (tp) cc_final: 0.7877 (pt) REVERT: A 115 MET cc_start: 0.6871 (ppp) cc_final: 0.6531 (ppp) REVERT: A 164 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6250 (pmm) REVERT: A 297 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: A 304 MET cc_start: 0.6533 (mpt) cc_final: 0.5543 (mmt) REVERT: B 134 LYS cc_start: 0.7145 (ttmp) cc_final: 0.6923 (ttmp) REVERT: B 206 GLU cc_start: 0.7803 (mp0) cc_final: 0.7559 (mm-30) REVERT: B 238 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6721 (mmm160) REVERT: B 248 TYR cc_start: 0.6137 (m-10) cc_final: 0.5820 (m-10) REVERT: B 396 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: C 125 GLN cc_start: 0.7402 (mp-120) cc_final: 0.6994 (mt0) REVERT: C 399 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4095 (tt) REVERT: D 86 GLU cc_start: 0.7812 (tt0) cc_final: 0.6952 (tp30) REVERT: D 336 MET cc_start: 0.6384 (pmm) cc_final: 0.5175 (mtp) REVERT: E 68 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7360 (ttp-110) REVERT: E 72 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6404 (tmmt) REVERT: E 119 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6458 (ptpt) REVERT: E 129 GLU cc_start: 0.7928 (pt0) cc_final: 0.7461 (pt0) REVERT: E 132 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7097 (m-30) REVERT: E 140 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6933 (mmp-170) REVERT: E 161 LEU cc_start: 0.7557 (tp) cc_final: 0.7182 (mp) REVERT: E 175 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6046 (tm-30) REVERT: E 246 TYR cc_start: 0.4549 (m-10) cc_final: 0.3872 (m-80) REVERT: E 358 SER cc_start: 0.7673 (OUTLIER) cc_final: 0.6884 (t) REVERT: E 442 GLU cc_start: 0.7980 (pt0) cc_final: 0.7659 (pm20) REVERT: F 38 MET cc_start: 0.1422 (OUTLIER) cc_final: 0.0681 (ppp) REVERT: F 108 LYS cc_start: 0.7404 (ttpt) cc_final: 0.6480 (mmtm) outliers start: 117 outliers final: 73 residues processed: 323 average time/residue: 0.5880 time to fit residues: 215.8680 Evaluate side-chains 310 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 227 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 131 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 195 ILE 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 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 100 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 326 VAL 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 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 317 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 64 PHE 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 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 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 510 LEU Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 103 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 99 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS D 250 HIS ** D 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.195489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.146935 restraints weight = 17625.546| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 1.84 r_work: 0.4184 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19816 Z= 0.219 Angle : 0.728 12.474 27284 Z= 0.384 Chirality : 0.044 0.324 3065 Planarity : 0.005 0.056 3098 Dihedral : 20.002 171.613 3770 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.92 % Favored : 93.98 % Rotamer: Outliers : 5.56 % Allowed : 24.61 % 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: -1.05 (0.18), residues: 2044 helix: 0.01 (0.17), residues: 863 sheet: -1.17 (0.29), residues: 327 loop : -1.11 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.040 0.003 TYR F 93 PHE 0.026 0.002 PHE A 136 TRP 0.029 0.002 TRP E 333 HIS 0.007 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00497 (19814) covalent geometry : angle 0.72725 (27280) SS BOND : bond 0.00886 ( 2) SS BOND : angle 3.08150 ( 4) hydrogen bonds : bond 0.05133 ( 809) hydrogen bonds : angle 4.94942 ( 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 339 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 236 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8205 (tp) cc_final: 0.7980 (pt) REVERT: A 115 MET cc_start: 0.6887 (ppp) cc_final: 0.6547 (ppp) REVERT: A 164 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6459 (pmm) REVERT: A 304 MET cc_start: 0.6517 (mpt) cc_final: 0.5577 (mmt) REVERT: B 206 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 238 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6546 (mmm160) REVERT: B 248 TYR cc_start: 0.6192 (m-10) cc_final: 0.5888 (m-10) REVERT: B 408 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5493 (pp20) REVERT: C 82 ILE cc_start: 0.7940 (tt) cc_final: 0.7366 (mt) REVERT: C 125 GLN cc_start: 0.7406 (mp-120) cc_final: 0.6990 (mt0) REVERT: C 399 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4399 (tt) REVERT: D 72 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7207 (pttt) REVERT: D 86 GLU cc_start: 0.7838 (tt0) cc_final: 0.6988 (tp30) REVERT: D 336 MET cc_start: 0.6316 (pmm) cc_final: 0.5165 (mtp) REVERT: E 68 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7407 (ttp-110) REVERT: E 72 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.6346 (tmmt) REVERT: E 119 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6488 (ptpt) REVERT: E 129 GLU cc_start: 0.7931 (pt0) cc_final: 0.7461 (pt0) REVERT: E 132 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: E 140 ARG cc_start: 0.7416 (mmm160) cc_final: 0.6925 (mmp-170) REVERT: E 161 LEU cc_start: 0.7567 (tp) cc_final: 0.7165 (mp) REVERT: E 175 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6077 (tm-30) REVERT: E 246 TYR cc_start: 0.4705 (m-10) cc_final: 0.3998 (m-80) REVERT: E 358 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.6902 (t) REVERT: E 375 MET cc_start: 0.7519 (ttm) cc_final: 0.7318 (mtp) REVERT: E 442 GLU cc_start: 0.7999 (pt0) cc_final: 0.7725 (pm20) REVERT: F 38 MET cc_start: 0.1474 (OUTLIER) cc_final: 0.1243 (pmt) REVERT: F 108 LYS cc_start: 0.7464 (ttpt) cc_final: 0.6457 (mmtm) outliers start: 103 outliers final: 75 residues processed: 300 average time/residue: 0.5499 time to fit residues: 188.6502 Evaluate side-chains 306 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 220 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 131 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 195 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 SER 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 100 THR Chi-restraints excluded: chain B residue 154 LEU 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 326 VAL 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 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 317 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 376 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 64 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LYS 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 164 SER 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 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 103 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS D 250 HIS D 427 HIS D 450 ASN E 427 HIS ** E 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.199703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.161211 restraints weight = 17671.697| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.96 r_work: 0.4166 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19816 Z= 0.147 Angle : 0.660 11.843 27284 Z= 0.348 Chirality : 0.041 0.157 3065 Planarity : 0.004 0.057 3098 Dihedral : 19.730 173.608 3770 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 3.94 % Allowed : 26.66 % Favored : 69.40 % 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: -0.73 (0.19), residues: 2044 helix: 0.34 (0.18), residues: 852 sheet: -1.04 (0.30), residues: 308 loop : -1.00 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.025 0.002 TYR F 172 PHE 0.024 0.001 PHE A 136 TRP 0.031 0.002 TRP E 333 HIS 0.005 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00328 (19814) covalent geometry : angle 0.65967 (27280) SS BOND : bond 0.00638 ( 2) SS BOND : angle 2.48677 ( 4) hydrogen bonds : bond 0.04046 ( 809) hydrogen bonds : angle 4.72028 ( 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 316 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 243 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.6642 (pmt170) cc_final: 0.5998 (ppt90) REVERT: A 34 ILE cc_start: 0.8061 (tp) cc_final: 0.7848 (pt) REVERT: A 115 MET cc_start: 0.6884 (ppp) cc_final: 0.6381 (ppp) REVERT: A 164 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6101 (pmm) REVERT: A 214 PHE cc_start: 0.7778 (m-80) cc_final: 0.7325 (m-80) REVERT: A 217 GLU cc_start: 0.7114 (mp0) cc_final: 0.6632 (mp0) REVERT: A 301 LEU cc_start: 0.8304 (mm) cc_final: 0.8104 (mm) REVERT: A 304 MET cc_start: 0.6446 (mpt) cc_final: 0.5713 (mmt) REVERT: B 206 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: B 254 ILE cc_start: 0.7532 (mt) cc_final: 0.7152 (mm) REVERT: B 336 MET cc_start: 0.6002 (mtm) cc_final: 0.5644 (mtp) REVERT: B 396 GLU cc_start: 0.7034 (mp0) cc_final: 0.6408 (mt-10) REVERT: C 125 GLN cc_start: 0.7406 (mp-120) cc_final: 0.7004 (mt0) REVERT: C 399 LEU cc_start: 0.4507 (OUTLIER) cc_final: 0.3893 (tt) REVERT: D 72 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7066 (pttt) REVERT: D 86 GLU cc_start: 0.7765 (tt0) cc_final: 0.6973 (tp30) REVERT: D 140 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7442 (mmt90) REVERT: D 336 MET cc_start: 0.6150 (pmm) cc_final: 0.5121 (mtp) REVERT: E 68 ARG cc_start: 0.7515 (ttm170) cc_final: 0.7175 (ttp-110) REVERT: E 72 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6364 (tmmt) REVERT: E 119 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6573 (ptpt) REVERT: E 129 GLU cc_start: 0.7923 (pt0) cc_final: 0.7467 (pt0) REVERT: E 132 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: E 161 LEU cc_start: 0.7590 (tp) cc_final: 0.7208 (mp) REVERT: E 175 GLU cc_start: 0.6802 (tm-30) cc_final: 0.5865 (tm-30) REVERT: E 246 TYR cc_start: 0.4281 (m-10) cc_final: 0.3662 (m-80) REVERT: E 358 SER cc_start: 0.7546 (OUTLIER) cc_final: 0.6776 (t) REVERT: E 442 GLU cc_start: 0.7969 (pt0) cc_final: 0.7679 (pm20) REVERT: E 472 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6384 (mt0) REVERT: F 108 LYS cc_start: 0.7318 (ttpt) cc_final: 0.6358 (mmtp) outliers start: 73 outliers final: 49 residues processed: 285 average time/residue: 0.5168 time to fit residues: 168.6019 Evaluate side-chains 277 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 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 195 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 317 ILE 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 64 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LYS 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 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 510 LEU Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 103 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 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 321 SER Chi-restraints excluded: chain E residue 329 ILE 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 420 ILE Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 455 ASP 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 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: 4.9990 chunk 32 optimal weight: 1.9990 chunk 178 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS D 250 HIS D 450 ASN D 539 ASN E 241 HIS E 427 HIS E 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.198607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.159699 restraints weight = 17617.769| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.89 r_work: 0.4159 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19816 Z= 0.155 Angle : 0.667 11.848 27284 Z= 0.353 Chirality : 0.042 0.292 3065 Planarity : 0.004 0.057 3098 Dihedral : 19.588 173.941 3766 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 3.89 % Allowed : 27.25 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 2044 helix: 0.35 (0.18), residues: 858 sheet: -1.02 (0.30), residues: 311 loop : -0.94 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 213 TYR 0.025 0.002 TYR F 172 PHE 0.022 0.002 PHE A 100 TRP 0.034 0.002 TRP E 245 HIS 0.008 0.001 HIS D 427 Details of bonding type rmsd covalent geometry : bond 0.00348 (19814) covalent geometry : angle 0.66648 (27280) SS BOND : bond 0.00728 ( 2) SS BOND : angle 2.57155 ( 4) hydrogen bonds : bond 0.04210 ( 809) hydrogen bonds : angle 4.72694 ( 2207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9180.65 seconds wall clock time: 156 minutes 36.81 seconds (9396.81 seconds total)