Starting phenix.real_space_refine on Wed Nov 19 20:39:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.754 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.map" model { file = "/net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fhs_4264/11_2025/6fhs_4264.cif" } resolution = 3.754 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 123 5.16 5 C 17165 2.51 5 N 4859 2.21 5 O 5221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27383 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3383 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain: "E" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3396 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3376 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2127 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 21, 'TRANS': 245} Chain: "H" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "I" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 829 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 8, 'TRANS': 94} Chain breaks: 1 Chain: "J" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3521 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 412} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" 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: 6.97, per 1000 atoms: 0.25 Number of scatterers: 27383 At special positions: 0 Unit cell: (139.92, 163.24, 181.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 15 15.00 O 5221 8.00 N 4859 7.00 C 17165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 38 sheets defined 40.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.827A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.503A pdb=" N ALA A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.520A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 290 removed outlier: 3.806A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.879A pdb=" N TYR A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 removed outlier: 3.692A pdb=" N GLN A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 370 through 384 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.982A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.711A pdb=" N ILE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.730A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.920A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 removed outlier: 3.659A pdb=" N GLY B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.719A pdb=" N TYR B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.621A pdb=" N ILE B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 273 through 290 removed outlier: 3.602A pdb=" N ARG B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.536A pdb=" N THR B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.932A pdb=" N GLN B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.758A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.786A pdb=" N CYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.658A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 438 removed outlier: 3.819A pdb=" N ILE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.594A pdb=" N SER B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.538A pdb=" N GLY C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.639A pdb=" N GLU C 101 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.510A pdb=" N LYS C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 273 through 290 removed outlier: 3.747A pdb=" N ARG C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.671A pdb=" N PHE C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 371 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.837A pdb=" N CYS C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.641A pdb=" N ILE C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.588A pdb=" N SER C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.792A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.905A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.689A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.516A pdb=" N LYS D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.760A pdb=" N ARG D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.654A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.593A pdb=" N MET D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.059A pdb=" N TYR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 4.165A pdb=" N GLN D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 397 removed outlier: 3.851A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.541A pdb=" N ALA D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 445 removed outlier: 4.006A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.538A pdb=" N ALA E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 185 removed outlier: 4.346A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.309A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR E 214 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.880A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 3.521A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 378 removed outlier: 3.718A pdb=" N GLU E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 415 removed outlier: 3.803A pdb=" N GLU E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N ARG E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR E 400 " --> pdb=" O ALA E 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 401 " --> pdb=" O GLY E 397 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG E 415 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 removed outlier: 4.354A pdb=" N ARG E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 444 Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.785A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY F 66 " --> pdb=" O MET F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.996A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 removed outlier: 4.183A pdb=" N ASP F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.736A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 315 removed outlier: 4.400A pdb=" N TYR F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 removed outlier: 3.902A pdb=" N GLN F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 402 removed outlier: 3.521A pdb=" N ALA F 401 " --> pdb=" O GLY F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 415 Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.839A pdb=" N VAL F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 1334 through 1345 removed outlier: 4.508A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G1340 " --> pdb=" O ALA G1336 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1357 removed outlier: 3.674A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.569A pdb=" N LEU G1368 " --> pdb=" O PHE G1365 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1382 Processing helix chain 'G' and resid 1386 through 1394 Processing helix chain 'G' and resid 1399 through 1407 removed outlier: 4.097A pdb=" N GLN G1404 " --> pdb=" O LEU G1400 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1417 through 1421 removed outlier: 3.530A pdb=" N LEU G1421 " --> pdb=" O VAL G1418 " (cutoff:3.500A) Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 3.815A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) Processing helix chain 'G' and resid 1447 through 1456 removed outlier: 3.687A pdb=" N VAL G1451 " --> pdb=" O ASN G1447 " (cutoff:3.500A) Processing helix chain 'G' and resid 1480 through 1491 removed outlier: 3.705A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 removed outlier: 3.619A pdb=" N ARG G1497 " --> pdb=" O HIS G1493 " (cutoff:3.500A) Processing helix chain 'G' and resid 1504 through 1513 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.510A pdb=" N LEU H 465 " --> pdb=" O PRO H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 475 removed outlier: 4.567A pdb=" N PHE H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 204 through 213 removed outlier: 4.051A pdb=" N LEU I 209 " --> pdb=" O GLY I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 20 removed outlier: 3.548A pdb=" N TRP J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS J 20 " --> pdb=" O GLU J 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 16 through 20' Processing helix chain 'J' and resid 45 through 50 Processing helix chain 'J' and resid 101 through 105 removed outlier: 3.510A pdb=" N ASP J 104 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS J 105 " --> pdb=" O GLY J 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 105' Processing helix chain 'J' and resid 128 through 144 removed outlier: 3.984A pdb=" N HIS J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 234 through 250 removed outlier: 3.580A pdb=" N TYR J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.737A pdb=" N THR J 263 " --> pdb=" O ASN J 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP J 269 " --> pdb=" O HIS J 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS J 271 " --> pdb=" O VAL J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.059A pdb=" N ALA J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 removed outlier: 3.834A pdb=" N ARG J 293 " --> pdb=" O GLY J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 607 through 614 removed outlier: 4.142A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 623 through 628 removed outlier: 3.866A pdb=" N THR J 627 " --> pdb=" O SER J 623 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS J 628 " --> pdb=" O GLN J 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 623 through 628' Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.794A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 645 through 650 removed outlier: 3.598A pdb=" N ILE J 649 " --> pdb=" O GLN J 645 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA J 650 " --> pdb=" O PRO J 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 645 through 650' Processing helix chain 'J' and resid 656 through 668 removed outlier: 3.716A pdb=" N ARG J 668 " --> pdb=" O ILE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 678 through 683 removed outlier: 3.871A pdb=" N PHE J 682 " --> pdb=" O ALA J 678 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 683 " --> pdb=" O PRO J 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 678 through 683' Processing helix chain 'J' and resid 698 through 710 Processing helix chain 'J' and resid 726 through 736 removed outlier: 3.969A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.583A pdb=" N GLY J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 6.516A pdb=" N LEU A 300 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA A 331 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 302 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 240 Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 135 removed outlier: 3.940A pdb=" N GLY A 205 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98 removed outlier: 5.928A pdb=" N VAL B 67 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.629A pdb=" N LEU B 173 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.552A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 205 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 337 through 338 Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 303 removed outlier: 6.622A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.464A pdb=" N LEU C 159 " --> pdb=" O MET C 139 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET C 139 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY C 161 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.700A pdb=" N TYR C 193 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 191 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 155 removed outlier: 6.566A pdb=" N THR D 161 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE D 145 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS D 159 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE D 147 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN D 157 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.580A pdb=" N GLY D 140 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 191 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 202 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.108A pdb=" N THR D 101 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP D 298 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU D 103 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU D 295 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA D 326 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 297 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL D 73 " --> pdb=" O MET D 325 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 233 through 242 Processing sheet with id=AC1, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.075A pdb=" N SER E 43 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 46 " --> pdb=" O SER E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.688A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU E 295 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA E 326 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 297 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 233 through 242 Processing sheet with id=AC5, first strand: chain 'E' and resid 141 through 147 removed outlier: 5.206A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.673A pdb=" N GLY E 205 " --> pdb=" O ILE E 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.612A pdb=" N SER F 43 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.071A pdb=" N LEU F 295 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA F 326 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE F 297 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL F 73 " --> pdb=" O MET F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 168 through 173 removed outlier: 7.812A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 191 through 195 Processing sheet with id=AD3, first strand: chain 'F' and resid 206 through 207 removed outlier: 6.205A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AD5, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.735A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 1313 through 1314 removed outlier: 6.438A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 80 through 82 removed outlier: 3.646A pdb=" N LEU J 185 " --> pdb=" O ILE J 746 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 746 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 85 through 86 removed outlier: 3.771A pdb=" N MET J 86 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG J 116 " --> pdb=" O MET J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 203 through 208 Processing sheet with id=AE1, first strand: chain 'J' and resid 295 through 297 Processing sheet with id=AE2, first strand: chain 'J' and resid 686 through 688 removed outlier: 6.144A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 1010 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9256 1.34 - 1.46: 5013 1.46 - 1.58: 13339 1.58 - 1.70: 23 1.70 - 1.81: 211 Bond restraints: 27842 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.27e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.19e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.344 0.043 1.00e-02 1.00e+04 1.81e+01 ... (remaining 27837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 37430 3.81 - 7.62: 198 7.62 - 11.43: 14 11.43 - 15.24: 4 15.24 - 19.05: 2 Bond angle restraints: 37648 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 120.82 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 119.14 7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.34e+01 angle pdb=" N GLY E 140 " pdb=" CA GLY E 140 " pdb=" C GLY E 140 " ideal model delta sigma weight residual 111.72 118.44 -6.72 1.31e+00 5.83e-01 2.63e+01 ... (remaining 37643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 16908 29.86 - 59.71: 128 59.71 - 89.57: 17 89.57 - 119.42: 6 119.42 - 149.28: 6 Dihedral angle restraints: 17065 sinusoidal: 7021 harmonic: 10044 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 150.72 149.28 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 159.87 140.13 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 163.19 136.80 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 17062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3615 0.073 - 0.147: 619 0.147 - 0.220: 42 0.220 - 0.293: 0 0.293 - 0.366: 3 Chirality restraints: 4279 Sorted by residual: chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB ILE A 324 " pdb=" CA ILE A 324 " pdb=" CG1 ILE A 324 " pdb=" CG2 ILE A 324 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4276 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 177 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 178 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 178 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 178 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 83 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO J 84 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO J 84 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 84 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 193 " 0.029 2.00e-02 2.50e+03 1.78e-02 6.34e+00 pdb=" CG TYR A 193 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 193 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 193 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 193 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 193 " 0.008 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5661 2.78 - 3.31: 23644 3.31 - 3.84: 42742 3.84 - 4.37: 50039 4.37 - 4.90: 87553 Nonbonded interactions: 209639 Sorted by model distance: nonbonded pdb=" OD2 ASP B 256 " pdb=" OG SER B 259 " model vdw 2.249 3.040 nonbonded pdb=" O SER C 100 " pdb=" OG1 THR F 116 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OG1 THR G1279 " model vdw 2.293 3.040 nonbonded pdb=" O LYS I 42 " pdb=" OG SER J 127 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.307 3.040 ... (remaining 209634 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 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.050 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.600 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.005 0.082 27842 Z= 0.245 Angle : 0.854 19.052 37648 Z= 0.473 Chirality : 0.053 0.366 4279 Planarity : 0.007 0.077 4878 Dihedral : 9.829 149.279 10599 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.29 (0.11), residues: 3474 helix: -3.17 (0.09), residues: 1349 sheet: -2.14 (0.21), residues: 509 loop : -2.70 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 268 TYR 0.041 0.002 TYR A 193 PHE 0.033 0.003 PHE B 117 TRP 0.024 0.003 TRP J 236 HIS 0.010 0.002 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00544 (27842) covalent geometry : angle 0.85438 (37648) hydrogen bonds : bond 0.16056 ( 998) hydrogen bonds : angle 7.04635 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8963 (tttt) cc_final: 0.8726 (ttmm) REVERT: A 179 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6920 (mt-10) REVERT: A 245 ASP cc_start: 0.8241 (m-30) cc_final: 0.7872 (t0) REVERT: A 385 VAL cc_start: 0.8772 (t) cc_final: 0.8551 (p) REVERT: A 401 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6679 (mtt-85) REVERT: B 264 LEU cc_start: 0.9040 (tp) cc_final: 0.8646 (mt) REVERT: B 303 ASP cc_start: 0.7467 (t0) cc_final: 0.7034 (t0) REVERT: B 402 ILE cc_start: 0.8936 (mt) cc_final: 0.8735 (mm) REVERT: C 146 ASN cc_start: 0.9027 (m-40) cc_final: 0.8811 (m-40) REVERT: C 260 MET cc_start: 0.8532 (mtt) cc_final: 0.8274 (mtp) REVERT: D 113 MET cc_start: 0.8781 (ptt) cc_final: 0.8440 (ptt) REVERT: D 257 LEU cc_start: 0.6767 (tt) cc_final: 0.6476 (mm) REVERT: D 271 ILE cc_start: 0.8940 (mt) cc_final: 0.8571 (mm) REVERT: D 416 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7885 (tpp80) REVERT: E 136 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6409 (mt-10) REVERT: F 25 SER cc_start: 0.8739 (m) cc_final: 0.8387 (p) REVERT: F 36 THR cc_start: 0.9189 (p) cc_final: 0.8798 (t) REVERT: F 88 MET cc_start: 0.7896 (mmt) cc_final: 0.7604 (mmt) REVERT: F 201 ILE cc_start: 0.9219 (mt) cc_final: 0.8819 (mt) REVERT: F 247 ASP cc_start: 0.6682 (m-30) cc_final: 0.6360 (m-30) REVERT: F 316 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7699 (mm-30) REVERT: F 331 VAL cc_start: 0.9241 (t) cc_final: 0.8953 (p) REVERT: G 1278 ASP cc_start: 0.7806 (t0) cc_final: 0.7536 (t0) REVERT: G 1305 TYR cc_start: 0.8555 (t80) cc_final: 0.8323 (t80) REVERT: G 1326 LEU cc_start: 0.8448 (mt) cc_final: 0.8175 (mp) REVERT: G 1453 TYR cc_start: 0.8627 (t80) cc_final: 0.8420 (t80) REVERT: G 1534 LYS cc_start: 0.8393 (mttt) cc_final: 0.8059 (mptt) REVERT: I 31 ASN cc_start: 0.8688 (t0) cc_final: 0.8382 (t0) REVERT: I 48 LEU cc_start: 0.8881 (tt) cc_final: 0.8405 (mm) REVERT: I 166 MET cc_start: 0.7316 (ptp) cc_final: 0.7099 (ptt) REVERT: I 173 THR cc_start: 0.9066 (p) cc_final: 0.8775 (t) REVERT: J 128 ASN cc_start: 0.8264 (t0) cc_final: 0.7745 (t0) REVERT: J 145 MET cc_start: 0.7409 (mmm) cc_final: 0.7197 (mmm) REVERT: J 610 HIS cc_start: 0.7963 (t70) cc_final: 0.7749 (t70) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 0.2139 time to fit residues: 233.8846 Evaluate side-chains 358 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0060 chunk 298 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 19 HIS A 146 ASN A 237 GLN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS C 242 HIS C 421 ASN C 458 HIS D 274 GLN D 394 GLN E 24 HIS E 394 GLN E 409 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 HIS G1402 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN J 262 GLN J 633 ASN J 762 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095401 restraints weight = 48186.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097493 restraints weight = 30156.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098905 restraints weight = 21535.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099909 restraints weight = 16900.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100505 restraints weight = 14141.867| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27842 Z= 0.121 Angle : 0.624 10.429 37648 Z= 0.309 Chirality : 0.044 0.156 4279 Planarity : 0.005 0.064 4878 Dihedral : 8.483 135.173 3920 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.58 % Allowed : 8.04 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.86 (0.13), residues: 3474 helix: -1.46 (0.12), residues: 1364 sheet: -1.83 (0.22), residues: 530 loop : -2.24 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 358 TYR 0.023 0.002 TYR A 193 PHE 0.016 0.001 PHE D 223 TRP 0.028 0.002 TRP I 34 HIS 0.011 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00273 (27842) covalent geometry : angle 0.62400 (37648) hydrogen bonds : bond 0.03728 ( 998) hydrogen bonds : angle 5.04250 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6886 (mt-10) REVERT: B 303 ASP cc_start: 0.7142 (t0) cc_final: 0.6866 (t0) REVERT: B 351 ILE cc_start: 0.8761 (mm) cc_final: 0.8306 (mt) REVERT: C 393 ASP cc_start: 0.7744 (m-30) cc_final: 0.7511 (m-30) REVERT: C 448 LEU cc_start: 0.8873 (tp) cc_final: 0.8577 (tt) REVERT: D 187 MET cc_start: 0.8796 (tpp) cc_final: 0.8497 (mmm) REVERT: D 191 ILE cc_start: 0.9110 (mp) cc_final: 0.8657 (mt) REVERT: D 250 ASN cc_start: 0.8442 (m-40) cc_final: 0.8204 (m-40) REVERT: D 256 PHE cc_start: 0.6480 (m-80) cc_final: 0.6239 (m-80) REVERT: D 334 ILE cc_start: 0.8537 (mt) cc_final: 0.8262 (mt) REVERT: E 147 ILE cc_start: 0.8520 (mm) cc_final: 0.8262 (mm) REVERT: E 149 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6746 (ptp-110) REVERT: E 313 ARG cc_start: 0.7798 (mpt180) cc_final: 0.7192 (mmt-90) REVERT: F 25 SER cc_start: 0.8611 (m) cc_final: 0.8306 (p) REVERT: F 88 MET cc_start: 0.7916 (mmt) cc_final: 0.7555 (tpp) REVERT: F 245 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7947 (mm-30) REVERT: F 331 VAL cc_start: 0.9062 (t) cc_final: 0.8818 (p) REVERT: F 369 ILE cc_start: 0.8358 (mt) cc_final: 0.8095 (mt) REVERT: G 1453 TYR cc_start: 0.8532 (t80) cc_final: 0.8300 (t80) REVERT: I 31 ASN cc_start: 0.8639 (t0) cc_final: 0.8354 (t0) REVERT: I 166 MET cc_start: 0.7357 (ptp) cc_final: 0.7132 (ptt) REVERT: I 173 THR cc_start: 0.9086 (p) cc_final: 0.8865 (t) REVERT: J 128 ASN cc_start: 0.8330 (t0) cc_final: 0.7787 (t0) REVERT: J 132 MET cc_start: 0.9188 (tpp) cc_final: 0.8907 (tpp) outliers start: 46 outliers final: 23 residues processed: 461 average time/residue: 0.1848 time to fit residues: 134.4334 Evaluate side-chains 350 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 327 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS D 244 HIS ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** J 762 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 = 0.3380 r_free = 0.3380 target = 0.108281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091517 restraints weight = 49115.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093270 restraints weight = 31838.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094283 restraints weight = 24862.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.095396 restraints weight = 18616.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095508 restraints weight = 16167.013| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27842 Z= 0.197 Angle : 0.654 10.222 37648 Z= 0.324 Chirality : 0.045 0.173 4279 Planarity : 0.004 0.058 4878 Dihedral : 8.085 120.069 3920 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.20 % Allowed : 9.79 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.27 (0.13), residues: 3474 helix: -0.85 (0.14), residues: 1384 sheet: -1.74 (0.22), residues: 527 loop : -1.94 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 234 TYR 0.022 0.002 TYR A 193 PHE 0.014 0.002 PHE C 214 TRP 0.025 0.002 TRP I 34 HIS 0.011 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00470 (27842) covalent geometry : angle 0.65384 (37648) hydrogen bonds : bond 0.03760 ( 998) hydrogen bonds : angle 4.77478 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6594 (mt-10) REVERT: A 190 ASP cc_start: 0.8314 (m-30) cc_final: 0.7823 (m-30) REVERT: B 264 LEU cc_start: 0.9149 (tp) cc_final: 0.8663 (mt) REVERT: B 351 ILE cc_start: 0.8807 (mm) cc_final: 0.8339 (mt) REVERT: C 448 LEU cc_start: 0.8883 (tp) cc_final: 0.8466 (tt) REVERT: D 263 ASP cc_start: 0.8014 (t0) cc_final: 0.7581 (t0) REVERT: E 310 TYR cc_start: 0.8775 (t80) cc_final: 0.8479 (t80) REVERT: E 312 ASN cc_start: 0.8759 (t0) cc_final: 0.8554 (t0) REVERT: F 25 SER cc_start: 0.8727 (m) cc_final: 0.8349 (p) REVERT: F 88 MET cc_start: 0.7878 (mmt) cc_final: 0.7594 (tpp) REVERT: F 139 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6909 (mt-10) REVERT: F 245 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7991 (mm-30) REVERT: F 273 ASP cc_start: 0.7016 (t0) cc_final: 0.6785 (t0) REVERT: F 331 VAL cc_start: 0.9106 (t) cc_final: 0.8880 (p) REVERT: F 369 ILE cc_start: 0.8446 (mt) cc_final: 0.8186 (mt) REVERT: G 1346 MET cc_start: 0.8613 (mmm) cc_final: 0.8242 (mtt) REVERT: I 31 ASN cc_start: 0.8691 (t0) cc_final: 0.8428 (t0) REVERT: I 166 MET cc_start: 0.7541 (ptp) cc_final: 0.7246 (ptm) REVERT: I 173 THR cc_start: 0.9221 (p) cc_final: 0.8945 (t) REVERT: J 128 ASN cc_start: 0.8435 (t0) cc_final: 0.7834 (t0) outliers start: 64 outliers final: 42 residues processed: 398 average time/residue: 0.1780 time to fit residues: 113.8076 Evaluate side-chains 347 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 271 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 291 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 368 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 HIS G1419 HIS G1423 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093173 restraints weight = 48620.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095139 restraints weight = 31787.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095911 restraints weight = 23377.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097456 restraints weight = 18219.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097451 restraints weight = 15151.720| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27842 Z= 0.133 Angle : 0.592 9.019 37648 Z= 0.289 Chirality : 0.043 0.158 4279 Planarity : 0.004 0.050 4878 Dihedral : 7.708 116.752 3920 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.09 % Allowed : 10.65 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.85 (0.14), residues: 3474 helix: -0.42 (0.14), residues: 1384 sheet: -1.60 (0.22), residues: 519 loop : -1.77 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 234 TYR 0.024 0.002 TYR G1453 PHE 0.018 0.001 PHE D 223 TRP 0.030 0.001 TRP I 34 HIS 0.008 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00314 (27842) covalent geometry : angle 0.59219 (37648) hydrogen bonds : bond 0.03210 ( 998) hydrogen bonds : angle 4.55669 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8260 (tpp) cc_final: 0.7940 (mmm) REVERT: A 179 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 190 ASP cc_start: 0.8283 (m-30) cc_final: 0.7816 (m-30) REVERT: B 303 ASP cc_start: 0.7519 (t0) cc_final: 0.6664 (t0) REVERT: C 448 LEU cc_start: 0.8858 (tp) cc_final: 0.8455 (tt) REVERT: D 187 MET cc_start: 0.8830 (tpp) cc_final: 0.8530 (mmm) REVERT: D 191 ILE cc_start: 0.9206 (mp) cc_final: 0.8630 (mt) REVERT: D 263 ASP cc_start: 0.7934 (t0) cc_final: 0.7536 (t0) REVERT: E 115 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8847 (ptmt) REVERT: E 250 ASN cc_start: 0.7396 (t0) cc_final: 0.7141 (t0) REVERT: E 310 TYR cc_start: 0.8773 (t80) cc_final: 0.8556 (t80) REVERT: E 313 ARG cc_start: 0.8014 (mpt180) cc_final: 0.7779 (mpt180) REVERT: F 25 SER cc_start: 0.8683 (m) cc_final: 0.8316 (p) REVERT: F 88 MET cc_start: 0.7835 (mmt) cc_final: 0.7571 (tpp) REVERT: F 138 MET cc_start: 0.8581 (ppp) cc_final: 0.8289 (tmm) REVERT: F 245 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7939 (mm-30) REVERT: G 1305 TYR cc_start: 0.8385 (t80) cc_final: 0.8124 (t80) REVERT: G 1346 MET cc_start: 0.8589 (mmm) cc_final: 0.8101 (ttm) REVERT: I 31 ASN cc_start: 0.8721 (t0) cc_final: 0.8461 (t0) REVERT: I 166 MET cc_start: 0.7424 (ptp) cc_final: 0.7152 (ptm) REVERT: I 173 THR cc_start: 0.9241 (p) cc_final: 0.8952 (t) REVERT: J 128 ASN cc_start: 0.8411 (t0) cc_final: 0.7780 (t0) outliers start: 61 outliers final: 42 residues processed: 384 average time/residue: 0.1893 time to fit residues: 115.2906 Evaluate side-chains 341 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1423 GLN Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 253 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN I 38 GLN I 168 HIS ** J 762 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 = 0.3355 r_free = 0.3355 target = 0.106599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089827 restraints weight = 49091.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.091514 restraints weight = 32056.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092572 restraints weight = 25012.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093571 restraints weight = 18726.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093722 restraints weight = 16581.102| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27842 Z= 0.208 Angle : 0.642 8.150 37648 Z= 0.316 Chirality : 0.045 0.172 4279 Planarity : 0.004 0.046 4878 Dihedral : 7.610 121.236 3920 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.75 % Allowed : 10.75 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.75 (0.14), residues: 3474 helix: -0.30 (0.14), residues: 1391 sheet: -1.68 (0.22), residues: 548 loop : -1.69 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 335 TYR 0.021 0.002 TYR A 193 PHE 0.015 0.001 PHE C 214 TRP 0.037 0.002 TRP I 34 HIS 0.006 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00499 (27842) covalent geometry : angle 0.64202 (37648) hydrogen bonds : bond 0.03578 ( 998) hydrogen bonds : angle 4.56869 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6738 (mt-10) REVERT: B 109 LYS cc_start: 0.8732 (ptpt) cc_final: 0.8528 (ptpt) REVERT: B 264 LEU cc_start: 0.9167 (tp) cc_final: 0.8645 (mt) REVERT: B 303 ASP cc_start: 0.7647 (t0) cc_final: 0.7092 (t0) REVERT: C 91 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7608 (ptmm) REVERT: D 187 MET cc_start: 0.8821 (tpp) cc_final: 0.8517 (mmm) REVERT: D 191 ILE cc_start: 0.9233 (mp) cc_final: 0.8702 (mt) REVERT: D 263 ASP cc_start: 0.8017 (t0) cc_final: 0.7533 (t0) REVERT: F 25 SER cc_start: 0.8776 (m) cc_final: 0.8410 (p) REVERT: F 88 MET cc_start: 0.7873 (mmt) cc_final: 0.7620 (tpp) REVERT: F 138 MET cc_start: 0.8571 (ppp) cc_final: 0.8250 (tmm) REVERT: F 208 TYR cc_start: 0.7908 (m-80) cc_final: 0.7546 (m-80) REVERT: F 245 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7989 (mm-30) REVERT: F 273 ASP cc_start: 0.7123 (t0) cc_final: 0.6873 (t0) REVERT: G 1305 TYR cc_start: 0.8438 (t80) cc_final: 0.8203 (t80) REVERT: G 1346 MET cc_start: 0.8609 (mmm) cc_final: 0.8144 (ttm) REVERT: I 31 ASN cc_start: 0.8686 (t0) cc_final: 0.8385 (t0) REVERT: I 34 TRP cc_start: 0.7303 (t60) cc_final: 0.7050 (t60) REVERT: I 37 ASN cc_start: 0.8303 (t0) cc_final: 0.7986 (t0) REVERT: I 166 MET cc_start: 0.7480 (ptp) cc_final: 0.7185 (ptm) REVERT: J 128 ASN cc_start: 0.8445 (t0) cc_final: 0.7839 (t0) REVERT: J 624 GLN cc_start: 0.7429 (mt0) cc_final: 0.6106 (tm-30) outliers start: 80 outliers final: 59 residues processed: 389 average time/residue: 0.1902 time to fit residues: 117.1025 Evaluate side-chains 357 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1359 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 240 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 6 optimal weight: 0.7980 chunk 289 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 368 GLN I 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.091374 restraints weight = 49072.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092943 restraints weight = 31516.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094350 restraints weight = 24586.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095044 restraints weight = 18219.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095232 restraints weight = 16316.481| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27842 Z= 0.146 Angle : 0.598 9.882 37648 Z= 0.293 Chirality : 0.044 0.146 4279 Planarity : 0.004 0.047 4878 Dihedral : 7.360 117.993 3920 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.30 % Allowed : 12.02 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.14), residues: 3474 helix: -0.07 (0.14), residues: 1386 sheet: -1.60 (0.22), residues: 557 loop : -1.58 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 440 TYR 0.027 0.001 TYR G1453 PHE 0.018 0.001 PHE D 223 TRP 0.022 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00347 (27842) covalent geometry : angle 0.59830 (37648) hydrogen bonds : bond 0.03178 ( 998) hydrogen bonds : angle 4.39287 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 272 ILE cc_start: 0.8950 (mt) cc_final: 0.8729 (mm) REVERT: C 448 LEU cc_start: 0.8909 (tp) cc_final: 0.8535 (tt) REVERT: D 187 MET cc_start: 0.8754 (tpp) cc_final: 0.8496 (mmm) REVERT: D 191 ILE cc_start: 0.9197 (mp) cc_final: 0.8671 (mt) REVERT: D 298 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: F 25 SER cc_start: 0.8725 (m) cc_final: 0.8373 (p) REVERT: F 88 MET cc_start: 0.7885 (mmt) cc_final: 0.7635 (tpp) REVERT: F 138 MET cc_start: 0.8523 (ppp) cc_final: 0.8221 (tmm) REVERT: F 208 TYR cc_start: 0.7882 (m-80) cc_final: 0.7529 (m-80) REVERT: F 245 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7941 (mm-30) REVERT: F 273 ASP cc_start: 0.7062 (t0) cc_final: 0.6796 (t0) REVERT: F 351 ASP cc_start: 0.7875 (m-30) cc_final: 0.7641 (t0) REVERT: G 1305 TYR cc_start: 0.8406 (t80) cc_final: 0.8092 (t80) REVERT: G 1346 MET cc_start: 0.8513 (mmm) cc_final: 0.8112 (ttm) REVERT: I 31 ASN cc_start: 0.8673 (t0) cc_final: 0.8390 (t0) REVERT: I 34 TRP cc_start: 0.7238 (t60) cc_final: 0.6923 (t60) REVERT: I 37 ASN cc_start: 0.8278 (t0) cc_final: 0.7966 (t0) REVERT: I 166 MET cc_start: 0.7424 (ptp) cc_final: 0.7180 (ptm) REVERT: J 128 ASN cc_start: 0.8394 (t0) cc_final: 0.7811 (t0) REVERT: J 238 MET cc_start: 0.8507 (mtt) cc_final: 0.8209 (mtm) REVERT: J 624 GLN cc_start: 0.7387 (mt0) cc_final: 0.6075 (tm-30) outliers start: 67 outliers final: 51 residues processed: 369 average time/residue: 0.1805 time to fit residues: 107.5001 Evaluate side-chains 347 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 21 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 334 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 251 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS G1333 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092709 restraints weight = 48553.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094380 restraints weight = 31009.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096013 restraints weight = 22912.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096510 restraints weight = 16555.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096712 restraints weight = 16012.307| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27842 Z= 0.120 Angle : 0.582 9.109 37648 Z= 0.283 Chirality : 0.043 0.148 4279 Planarity : 0.004 0.044 4878 Dihedral : 7.132 115.267 3920 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.13 % Allowed : 12.43 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.32 (0.14), residues: 3474 helix: 0.16 (0.14), residues: 1378 sheet: -1.52 (0.22), residues: 564 loop : -1.53 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 440 TYR 0.025 0.001 TYR E 310 PHE 0.014 0.001 PHE C 214 TRP 0.018 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00286 (27842) covalent geometry : angle 0.58230 (37648) hydrogen bonds : bond 0.02949 ( 998) hydrogen bonds : angle 4.26197 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6682 (mt-10) REVERT: A 272 ILE cc_start: 0.8958 (mt) cc_final: 0.8729 (mm) REVERT: A 274 ASP cc_start: 0.7350 (t0) cc_final: 0.7145 (t0) REVERT: C 448 LEU cc_start: 0.8882 (tp) cc_final: 0.8516 (tt) REVERT: D 187 MET cc_start: 0.8780 (tpp) cc_final: 0.8520 (mmm) REVERT: D 191 ILE cc_start: 0.9182 (mp) cc_final: 0.8676 (mt) REVERT: D 263 ASP cc_start: 0.7845 (t0) cc_final: 0.7320 (t0) REVERT: D 298 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: F 25 SER cc_start: 0.8759 (m) cc_final: 0.8358 (p) REVERT: F 88 MET cc_start: 0.7919 (mmt) cc_final: 0.7651 (tpp) REVERT: F 138 MET cc_start: 0.8486 (ppp) cc_final: 0.8227 (tmm) REVERT: F 351 ASP cc_start: 0.7914 (m-30) cc_final: 0.7701 (t0) REVERT: G 1346 MET cc_start: 0.8482 (mmm) cc_final: 0.8102 (ttm) REVERT: G 1372 ASP cc_start: 0.7527 (t0) cc_final: 0.7321 (t0) REVERT: I 31 ASN cc_start: 0.8638 (t0) cc_final: 0.8380 (t0) REVERT: I 34 TRP cc_start: 0.7206 (t60) cc_final: 0.6995 (t60) REVERT: I 37 ASN cc_start: 0.8267 (t0) cc_final: 0.7955 (t0) REVERT: I 166 MET cc_start: 0.7456 (ptp) cc_final: 0.7246 (ptm) REVERT: J 22 LEU cc_start: 0.8266 (tp) cc_final: 0.7932 (pt) REVERT: J 128 ASN cc_start: 0.8371 (t0) cc_final: 0.7780 (t0) REVERT: J 238 MET cc_start: 0.8593 (mtt) cc_final: 0.8338 (mtm) outliers start: 62 outliers final: 44 residues processed: 367 average time/residue: 0.1835 time to fit residues: 109.2427 Evaluate side-chains 342 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1411 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 290 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 297 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 281 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.091241 restraints weight = 49001.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093266 restraints weight = 30913.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094664 restraints weight = 22152.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095639 restraints weight = 17471.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096306 restraints weight = 14686.283| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27842 Z= 0.153 Angle : 0.604 9.374 37648 Z= 0.294 Chirality : 0.044 0.148 4279 Planarity : 0.004 0.044 4878 Dihedral : 7.049 115.465 3920 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.99 % Allowed : 13.19 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3474 helix: 0.23 (0.14), residues: 1383 sheet: -1.47 (0.22), residues: 557 loop : -1.50 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 34 TYR 0.039 0.001 TYR E 310 PHE 0.019 0.001 PHE D 223 TRP 0.015 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00369 (27842) covalent geometry : angle 0.60413 (37648) hydrogen bonds : bond 0.03139 ( 998) hydrogen bonds : angle 4.27940 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6700 (mt-10) REVERT: B 264 LEU cc_start: 0.9144 (tp) cc_final: 0.8707 (mt) REVERT: B 351 ILE cc_start: 0.8816 (mm) cc_final: 0.8349 (mt) REVERT: C 91 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (ptmm) REVERT: D 187 MET cc_start: 0.8759 (tpp) cc_final: 0.8492 (mmm) REVERT: D 191 ILE cc_start: 0.9192 (mp) cc_final: 0.8635 (mt) REVERT: D 208 TYR cc_start: 0.7248 (m-10) cc_final: 0.6822 (m-10) REVERT: D 298 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: F 25 SER cc_start: 0.8788 (m) cc_final: 0.8399 (p) REVERT: F 88 MET cc_start: 0.7938 (mmt) cc_final: 0.7663 (tpp) REVERT: F 138 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8153 (tmm) REVERT: F 245 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7817 (mm-30) REVERT: F 273 ASP cc_start: 0.7119 (t0) cc_final: 0.6841 (t0) REVERT: F 351 ASP cc_start: 0.7906 (m-30) cc_final: 0.7682 (t0) REVERT: G 1305 TYR cc_start: 0.8414 (t80) cc_final: 0.8104 (t80) REVERT: G 1346 MET cc_start: 0.8452 (mmm) cc_final: 0.8128 (ttm) REVERT: G 1372 ASP cc_start: 0.7554 (t0) cc_final: 0.7338 (t0) REVERT: I 31 ASN cc_start: 0.8598 (t0) cc_final: 0.8366 (t0) REVERT: I 37 ASN cc_start: 0.8254 (t0) cc_final: 0.8014 (t0) REVERT: I 166 MET cc_start: 0.7498 (ptp) cc_final: 0.7282 (ptm) REVERT: J 128 ASN cc_start: 0.8368 (t0) cc_final: 0.7811 (t0) REVERT: J 172 MET cc_start: 0.9272 (tpt) cc_final: 0.9037 (mmm) REVERT: J 238 MET cc_start: 0.8646 (mtt) cc_final: 0.8392 (mtm) REVERT: J 687 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7486 (p90) outliers start: 58 outliers final: 47 residues processed: 343 average time/residue: 0.1833 time to fit residues: 101.3328 Evaluate side-chains 341 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 687 PHE Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 146 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 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 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092291 restraints weight = 48682.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094338 restraints weight = 30657.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095740 restraints weight = 21888.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096623 restraints weight = 17244.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097351 restraints weight = 14669.769| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27842 Z= 0.131 Angle : 0.604 10.523 37648 Z= 0.293 Chirality : 0.044 0.223 4279 Planarity : 0.004 0.044 4878 Dihedral : 6.940 113.676 3920 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.06 % Allowed : 13.15 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.15 (0.14), residues: 3474 helix: 0.29 (0.14), residues: 1388 sheet: -1.35 (0.22), residues: 580 loop : -1.46 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 34 TYR 0.035 0.001 TYR E 310 PHE 0.015 0.001 PHE C 214 TRP 0.045 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00315 (27842) covalent geometry : angle 0.60396 (37648) hydrogen bonds : bond 0.03000 ( 998) hydrogen bonds : angle 4.23782 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6688 (mt-10) REVERT: A 272 ILE cc_start: 0.9011 (mt) cc_final: 0.8710 (mm) REVERT: B 351 ILE cc_start: 0.8796 (mm) cc_final: 0.8342 (mt) REVERT: D 187 MET cc_start: 0.8762 (tpp) cc_final: 0.8547 (mmm) REVERT: D 191 ILE cc_start: 0.9165 (mp) cc_final: 0.8628 (mt) REVERT: D 263 ASP cc_start: 0.7815 (t0) cc_final: 0.7284 (t0) REVERT: D 298 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: F 25 SER cc_start: 0.8772 (m) cc_final: 0.8383 (p) REVERT: F 88 MET cc_start: 0.7886 (mmt) cc_final: 0.7637 (tpp) REVERT: F 138 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (tmm) REVERT: F 144 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6730 (mm-30) REVERT: F 245 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7826 (mm-30) REVERT: F 351 ASP cc_start: 0.7875 (m-30) cc_final: 0.7661 (t0) REVERT: G 1305 TYR cc_start: 0.8277 (t80) cc_final: 0.7898 (t80) REVERT: G 1346 MET cc_start: 0.8450 (mmm) cc_final: 0.8111 (ttm) REVERT: I 31 ASN cc_start: 0.8589 (t0) cc_final: 0.8259 (t0) REVERT: I 37 ASN cc_start: 0.8265 (t0) cc_final: 0.8009 (t0) REVERT: I 166 MET cc_start: 0.7424 (ptp) cc_final: 0.7221 (ptm) REVERT: J 128 ASN cc_start: 0.8351 (t0) cc_final: 0.7782 (t0) REVERT: J 238 MET cc_start: 0.8643 (mtt) cc_final: 0.8403 (mtm) outliers start: 60 outliers final: 50 residues processed: 352 average time/residue: 0.1824 time to fit residues: 103.7717 Evaluate side-chains 340 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 296 ILE Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 343 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 280 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 319 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102815 restraints weight = 47492.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105268 restraints weight = 28400.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106825 restraints weight = 19668.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108012 restraints weight = 15301.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108690 restraints weight = 12688.206| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27842 Z= 0.118 Angle : 0.596 10.671 37648 Z= 0.290 Chirality : 0.043 0.198 4279 Planarity : 0.004 0.044 4878 Dihedral : 6.792 112.276 3920 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.89 % Allowed : 13.39 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3474 helix: 0.38 (0.15), residues: 1392 sheet: -1.30 (0.22), residues: 580 loop : -1.44 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 34 TYR 0.034 0.001 TYR E 310 PHE 0.019 0.001 PHE D 223 TRP 0.048 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00282 (27842) covalent geometry : angle 0.59646 (37648) hydrogen bonds : bond 0.02881 ( 998) hydrogen bonds : angle 4.17853 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6948 Ramachandran restraints generated. 3474 Oldfield, 0 Emsley, 3474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8537 (tp) cc_final: 0.8314 (tt) REVERT: A 179 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 215 ASP cc_start: 0.7609 (t0) cc_final: 0.7332 (t0) REVERT: A 272 ILE cc_start: 0.8992 (mt) cc_final: 0.8754 (mm) REVERT: B 264 LEU cc_start: 0.9138 (tp) cc_final: 0.8711 (mt) REVERT: B 351 ILE cc_start: 0.8793 (mm) cc_final: 0.8307 (mt) REVERT: D 187 MET cc_start: 0.8765 (tpp) cc_final: 0.8528 (mmm) REVERT: D 191 ILE cc_start: 0.9152 (mp) cc_final: 0.8620 (mt) REVERT: D 298 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: F 25 SER cc_start: 0.8746 (m) cc_final: 0.8373 (p) REVERT: F 88 MET cc_start: 0.7881 (mmt) cc_final: 0.7630 (tpp) REVERT: F 138 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: F 144 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6729 (mm-30) REVERT: F 245 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 351 ASP cc_start: 0.7870 (m-30) cc_final: 0.7651 (t0) REVERT: G 1305 TYR cc_start: 0.8235 (t80) cc_final: 0.7897 (t80) REVERT: G 1346 MET cc_start: 0.8370 (mmm) cc_final: 0.8066 (ttm) REVERT: I 37 ASN cc_start: 0.8305 (t0) cc_final: 0.8081 (t0) REVERT: I 166 MET cc_start: 0.7416 (ptp) cc_final: 0.7118 (ptm) REVERT: J 22 LEU cc_start: 0.7932 (tp) cc_final: 0.7720 (pt) REVERT: J 128 ASN cc_start: 0.8336 (t0) cc_final: 0.7781 (t0) REVERT: J 238 MET cc_start: 0.8652 (mtt) cc_final: 0.8406 (mtm) outliers start: 55 outliers final: 47 residues processed: 337 average time/residue: 0.1787 time to fit residues: 97.7554 Evaluate side-chains 335 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 1303 LEU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1455 GLU Chi-restraints excluded: chain H residue 451 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 754 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 335 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 chunk 113 optimal weight: 0.0050 chunk 212 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 GLN ** G1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104464 restraints weight = 47107.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106717 restraints weight = 29232.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108259 restraints weight = 20705.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109286 restraints weight = 16172.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110023 restraints weight = 13588.544| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27842 Z= 0.109 Angle : 0.587 10.932 37648 Z= 0.285 Chirality : 0.043 0.151 4279 Planarity : 0.004 0.044 4878 Dihedral : 6.620 109.579 3920 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.89 % Allowed : 13.74 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.95 (0.14), residues: 3474 helix: 0.45 (0.15), residues: 1396 sheet: -1.13 (0.22), residues: 566 loop : -1.41 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 34 TYR 0.031 0.001 TYR E 310 PHE 0.014 0.001 PHE C 214 TRP 0.052 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 Details of bonding type rmsd covalent geometry : bond 0.00259 (27842) covalent geometry : angle 0.58689 (37648) hydrogen bonds : bond 0.02782 ( 998) hydrogen bonds : angle 4.11102 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.00 seconds wall clock time: 75 minutes 19.19 seconds (4519.19 seconds total)