Starting phenix.real_space_refine on Wed Mar 20 12:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_4264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_4264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_4264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_4264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fhs_4264/03_2024/6fhs_4264_updated.pdb" } resolution = 3.754 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 221": "NH1" <-> "NH2" Residue "J ARG 279": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 295": "NH1" <-> "NH2" Residue "J ARG 703": "NH1" <-> "NH2" Residue "J ARG 717": "NH1" <-> "NH2" Residue "J ARG 719": "NH1" <-> "NH2" Residue "J ARG 720": "NH1" <-> "NH2" Residue "J ARG 730": "NH1" <-> "NH2" Residue "J ARG 748": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 14.19, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.14 Conformation dependent library (CDL) restraints added in 4.9 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... running ksdssp... Secondary structure from input PDB file: 140 helices and 38 sheets defined 35.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.827A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.828A pdb=" N GLU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 258 through 261 No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.806A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 310 through 320 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 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.683A pdb=" N LEU A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 410' Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.711A pdb=" N ILE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 4.146A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 78 through 88 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.779A pdb=" N LYS B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 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) removed outlier: 4.741A pdb=" N GLU B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 353 through 356 No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 389 through 401 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 404 through 409 removed outlier: 3.535A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 411 through 419 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) Processing helix chain 'B' and resid 428 through 437 removed outlier: 4.075A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'C' and resid 44 through 58 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 109 through 120 removed outlier: 4.293A pdb=" N LEU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 184 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 249 Processing helix chain 'C' and resid 259 through 262 No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 274 through 290 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 310 through 320 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 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 389 through 401 Processing helix chain 'C' and resid 404 through 407 No H-bonds generated for 'chain 'C' and resid 404 through 407' Processing helix chain 'C' and resid 412 through 421 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.689A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 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 251 Processing helix chain 'D' and resid 269 through 284 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 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 305 through 314 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) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 363 through 376 removed outlier: 4.165A pdb=" N GLN D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 414 removed outlier: 3.851A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ARG D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) 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 422 through 431 Processing helix chain 'D' and resid 435 through 444 removed outlier: 4.006A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 63 Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.538A pdb=" N ALA E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 184 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 213 removed outlier: 5.309A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.794A pdb=" N SER E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 269 through 284 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 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 305 through 314 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 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 363 through 377 removed outlier: 3.718A pdb=" N GLU E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 414 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) Processing helix chain 'E' and resid 422 through 431 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 435 through 443 Processing helix chain 'F' and resid 50 through 65 removed outlier: 3.785A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.619A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 115 through 125 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) Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 255 through 261 removed outlier: 3.750A pdb=" N LEU F 259 " --> pdb=" O PHE F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 305 through 314 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 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 363 through 376 removed outlier: 3.902A pdb=" N GLN F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 396 Processing helix chain 'F' and resid 398 through 401 No H-bonds generated for 'chain 'F' and resid 398 through 401' Processing helix chain 'F' and resid 405 through 414 Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 435 through 444 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 1335 through 1344 removed outlier: 3.636A pdb=" N SER G1340 " --> pdb=" O ALA G1336 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1356 Processing helix chain 'G' and resid 1366 through 1369 removed outlier: 3.812A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1366 through 1369' Processing helix chain 'G' and resid 1375 through 1381 Processing helix chain 'G' and resid 1387 through 1395 removed outlier: 3.791A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1400 through 1406 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 1418 through 1420 No H-bonds generated for 'chain 'G' and resid 1418 through 1420' Processing helix chain 'G' and resid 1430 through 1434 Processing helix chain 'G' and resid 1448 through 1455 Processing helix chain 'G' and resid 1481 through 1490 Processing helix chain 'G' and resid 1494 through 1501 Processing helix chain 'G' and resid 1505 through 1512 Processing helix chain 'H' and resid 463 through 465 No H-bonds generated for 'chain 'H' and resid 463 through 465' Processing helix chain 'H' and resid 469 through 471 No H-bonds generated for 'chain 'H' and resid 469 through 471' Processing helix chain 'I' and resid 11 through 19 Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 205 through 212 removed outlier: 4.051A pdb=" N LEU I 209 " --> pdb=" O GLY I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 46 through 49 No H-bonds generated for 'chain 'J' and resid 46 through 49' Processing helix chain 'J' and resid 102 through 104 No H-bonds generated for 'chain 'J' and resid 102 through 104' Processing helix chain 'J' and resid 129 through 143 removed outlier: 3.984A pdb=" N HIS J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 removed outlier: 3.641A pdb=" N ASP J 269 " --> pdb=" O HIS J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 removed outlier: 4.059A pdb=" N ALA J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 293 No H-bonds generated for 'chain 'J' and resid 290 through 293' Processing helix chain 'J' and resid 608 through 613 Processing helix chain 'J' and resid 624 through 627 No H-bonds generated for 'chain 'J' and resid 624 through 627' Processing helix chain 'J' and resid 634 through 641 removed outlier: 4.093A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL J 639 " --> pdb=" O ARG J 636 " (cutoff:3.500A) Proline residue: J 640 - end of helix Processing helix chain 'J' and resid 646 through 649 No H-bonds generated for 'chain 'J' and resid 646 through 649' Processing helix chain 'J' and resid 657 through 667 Processing helix chain 'J' and resid 679 through 682 No H-bonds generated for 'chain 'J' and resid 679 through 682' Processing helix chain 'J' and resid 699 through 709 Processing helix chain 'J' and resid 727 through 735 removed outlier: 3.969A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 744 Processing helix chain 'J' and resid 748 through 754 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 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) removed outlier: 6.529A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 330 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 294 through 297 Processing sheet with id= C, 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= D, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= E, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= F, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= G, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.593A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 230 through 240 Processing sheet with id= I, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.764A pdb=" N GLY B 205 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 139 through 141 Processing sheet with id= K, first strand: chain 'B' and resid 336 through 338 Processing sheet with id= L, first strand: chain 'C' and resid 67 through 69 removed outlier: 6.177A pdb=" N LEU C 360 " --> pdb=" O LEU C 68 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 230 through 240 Processing sheet with id= N, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.828A pdb=" N GLY C 205 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 158 through 163 Processing sheet with id= P, first strand: chain 'C' and resid 299 through 302 removed outlier: 6.824A pdb=" N ILE C 327 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE C 302 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 329 " --> pdb=" O ILE C 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 336 through 338 Processing sheet with id= R, first strand: chain 'D' and resid 354 through 358 removed outlier: 6.686A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET D 325 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY D 77 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 295 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 288 through 292 Processing sheet with id= T, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.946A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 331 through 333 Processing sheet with id= V, first strand: chain 'D' and resid 190 through 194 removed outlier: 3.838A pdb=" N GLY D 205 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 354 through 357 removed outlier: 6.621A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 326 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 290 through 292 Processing sheet with id= Y, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.423A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 331 through 333 Processing sheet with id= AA, first strand: chain 'F' and resid 323 through 326 removed outlier: 6.136A pdb=" N VAL F 354 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 100 through 104 removed outlier: 7.389A pdb=" N VAL F 294 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU F 103 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE F 296 " --> pdb=" O LEU F 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 289 through 292 removed outlier: 3.557A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 201 through 203 removed outlier: 7.106A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= AF, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.720A pdb=" N GLU G1475 " --> pdb=" O TYR G1313 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 449 through 452 Processing sheet with id= AH, first strand: chain 'J' and resid 80 through 82 removed outlier: 7.502A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 85 through 87 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= AI Processing sheet with id= AJ, first strand: chain 'J' and resid 203 through 208 Processing sheet with id= AK, first strand: chain 'J' and resid 295 through 298 Processing sheet with id= AL, first strand: chain 'J' and resid 686 through 688 840 hydrogen bonds defined for protein. 2424 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: 9.35 Time building geometry restraints manager: 9.94 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: 97.85 - 105.55: 667 105.55 - 113.25: 15500 113.25 - 120.95: 13263 120.95 - 128.65: 8062 128.65 - 136.35: 156 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: 5673 2.78 - 3.31: 23748 3.31 - 3.84: 42905 3.84 - 4.37: 50330 4.37 - 4.90: 87615 Nonbonded interactions: 210271 Sorted by model distance: nonbonded pdb=" OD2 ASP B 256 " pdb=" OG SER B 259 " model vdw 2.249 2.440 nonbonded pdb=" O SER C 100 " pdb=" OG1 THR F 116 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR A 193 " pdb=" OG1 THR G1279 " model vdw 2.293 2.440 nonbonded pdb=" O LYS I 42 " pdb=" OG SER J 127 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.307 2.440 ... (remaining 210266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 462 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 462 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'F' and (resid 20 through 458 or resid 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.240 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 67.960 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.160 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.280 ------------------------------------------------------------------------------- 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= 0.358 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP J 236 HIS 0.010 0.002 HIS C 242 PHE 0.033 0.003 PHE B 117 TYR 0.041 0.002 TYR A 193 ARG 0.007 0.001 ARG E 268 *********************** 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 fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 3.424 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: 0.4507 time to fit residues: 492.1671 Evaluate side-chains 358 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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 28 ASN C 285 GLN C 289 ASN C 421 ASN C 458 HIS D 274 GLN D 394 GLN D 403 ASN E 24 HIS ** E 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** F 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1402 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 633 ASN J 762 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27842 Z= 0.261 Angle : 0.633 9.936 37648 Z= 0.312 Chirality : 0.044 0.165 4279 Planarity : 0.005 0.067 4878 Dihedral : 8.313 123.350 3920 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.89 % Allowed : 8.07 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3474 helix: -1.66 (0.12), residues: 1357 sheet: -1.90 (0.21), residues: 527 loop : -2.26 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 34 HIS 0.010 0.001 HIS J 762 PHE 0.016 0.002 PHE D 223 TYR 0.029 0.002 TYR A 193 ARG 0.008 0.001 ARG A 358 *********************** 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 444 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 389 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.8935 (tttt) cc_final: 0.8705 (ttmm) REVERT: A 179 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 215 ASP cc_start: 0.7171 (t0) cc_final: 0.6860 (t0) REVERT: B 351 ILE cc_start: 0.8872 (mm) cc_final: 0.8443 (mt) REVERT: C 101 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7234 (tm-30) REVERT: C 393 ASP cc_start: 0.7998 (m-30) cc_final: 0.7784 (m-30) REVERT: C 448 LEU cc_start: 0.8969 (tp) cc_final: 0.8659 (tt) REVERT: D 191 ILE cc_start: 0.8999 (mp) cc_final: 0.8551 (mt) REVERT: D 214 TYR cc_start: 0.7339 (m-80) cc_final: 0.7014 (m-80) REVERT: D 250 ASN cc_start: 0.8486 (m-40) cc_final: 0.8283 (m-40) REVERT: D 271 ILE cc_start: 0.8907 (mt) cc_final: 0.8698 (mm) REVERT: D 283 LYS cc_start: 0.9078 (tttt) cc_final: 0.8852 (ttpp) REVERT: D 334 ILE cc_start: 0.8425 (mt) cc_final: 0.8108 (mt) REVERT: D 416 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7928 (tpp80) REVERT: E 147 ILE cc_start: 0.8533 (mm) cc_final: 0.8254 (mm) REVERT: E 149 ARG cc_start: 0.7024 (ttm110) cc_final: 0.6690 (ptp-110) REVERT: E 310 TYR cc_start: 0.8759 (t80) cc_final: 0.8473 (t80) REVERT: F 25 SER cc_start: 0.8676 (m) cc_final: 0.8355 (p) REVERT: F 245 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8042 (mm-30) REVERT: F 273 ASP cc_start: 0.7179 (t0) cc_final: 0.6907 (t0) REVERT: F 328 ASN cc_start: 0.8223 (m-40) cc_final: 0.7894 (m-40) REVERT: F 331 VAL cc_start: 0.9229 (t) cc_final: 0.8991 (p) REVERT: G 1346 MET cc_start: 0.8525 (tpp) cc_final: 0.7767 (ttm) REVERT: G 1450 ARG cc_start: 0.7709 (mpt180) cc_final: 0.7223 (mtm180) REVERT: G 1453 TYR cc_start: 0.8529 (t80) cc_final: 0.8271 (t80) REVERT: H 464 GLU cc_start: 0.8230 (mp0) cc_final: 0.7926 (mp0) REVERT: I 31 ASN cc_start: 0.8685 (t0) cc_final: 0.8274 (t0) REVERT: I 38 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8109 (tm-30) REVERT: I 166 MET cc_start: 0.7477 (ptp) cc_final: 0.7045 (ptm) REVERT: I 173 THR cc_start: 0.9129 (p) cc_final: 0.8911 (t) REVERT: J 128 ASN cc_start: 0.8279 (t0) cc_final: 0.7755 (t0) outliers start: 55 outliers final: 31 residues processed: 429 average time/residue: 0.3851 time to fit residues: 262.3147 Evaluate side-chains 353 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 105 THR 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 207 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 90 MET 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 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 J residue 27 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 168 SER Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 707 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 313 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 251 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS C 28 ASN D 368 GLN D 403 ASN E 368 GLN E 394 GLN ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27842 Z= 0.165 Angle : 0.573 9.454 37648 Z= 0.277 Chirality : 0.043 0.172 4279 Planarity : 0.004 0.055 4878 Dihedral : 7.709 118.377 3920 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.65 % Allowed : 10.13 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 3474 helix: -0.91 (0.14), residues: 1367 sheet: -1.66 (0.22), residues: 508 loop : -1.96 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 34 HIS 0.012 0.001 HIS J 762 PHE 0.013 0.001 PHE C 214 TYR 0.018 0.001 TYR A 193 ARG 0.005 0.000 ARG G1399 *********************** 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 420 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 372 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8549 (mmm) cc_final: 0.8338 (tpp) REVERT: A 158 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6445 (mp) REVERT: A 170 LYS cc_start: 0.8945 (tttt) cc_final: 0.8727 (ttmm) REVERT: A 179 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7070 (mt-10) REVERT: A 260 MET cc_start: 0.8436 (tpp) cc_final: 0.8218 (tpp) REVERT: B 179 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7747 (mp0) REVERT: B 285 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 351 ILE cc_start: 0.8828 (mm) cc_final: 0.8406 (mt) REVERT: C 101 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7232 (tm-30) REVERT: C 393 ASP cc_start: 0.7943 (m-30) cc_final: 0.7723 (m-30) REVERT: C 448 LEU cc_start: 0.8917 (tp) cc_final: 0.8623 (tt) REVERT: D 191 ILE cc_start: 0.9036 (mp) cc_final: 0.8572 (mt) REVERT: D 250 ASN cc_start: 0.8504 (m-40) cc_final: 0.8302 (m-40) REVERT: D 263 ASP cc_start: 0.7962 (t0) cc_final: 0.7507 (t0) REVERT: D 271 ILE cc_start: 0.8858 (mt) cc_final: 0.8318 (mm) REVERT: D 275 ILE cc_start: 0.9032 (mt) cc_final: 0.8819 (mp) REVERT: D 283 LYS cc_start: 0.9053 (tttt) cc_final: 0.8832 (ttpp) REVERT: D 334 ILE cc_start: 0.8415 (mt) cc_final: 0.8084 (mt) REVERT: D 416 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7942 (tpp80) REVERT: E 310 TYR cc_start: 0.8782 (t80) cc_final: 0.8500 (t80) REVERT: E 313 ARG cc_start: 0.7450 (mpt180) cc_final: 0.7100 (mmm160) REVERT: F 25 SER cc_start: 0.8629 (m) cc_final: 0.8268 (p) REVERT: F 88 MET cc_start: 0.7837 (mmt) cc_final: 0.7356 (tpp) REVERT: F 138 MET cc_start: 0.8323 (ttp) cc_final: 0.8029 (ppp) REVERT: F 245 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7896 (mm-30) REVERT: F 331 VAL cc_start: 0.9219 (t) cc_final: 0.8999 (p) REVERT: I 31 ASN cc_start: 0.8712 (t0) cc_final: 0.8380 (t0) REVERT: I 166 MET cc_start: 0.7388 (ptp) cc_final: 0.7069 (ptm) REVERT: I 173 THR cc_start: 0.9184 (p) cc_final: 0.8926 (t) REVERT: J 86 MET cc_start: 0.7276 (ptm) cc_final: 0.7053 (ptm) REVERT: J 128 ASN cc_start: 0.8301 (t0) cc_final: 0.7770 (t0) outliers start: 48 outliers final: 24 residues processed: 408 average time/residue: 0.3687 time to fit residues: 241.9008 Evaluate side-chains 346 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 343 ASP 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 407 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 325 MET 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 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 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 168 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 162 optimal weight: 0.0050 chunk 34 optimal weight: 3.9990 chunk 149 optimal weight: 0.0270 chunk 210 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 298 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 overall best weight: 0.4252 ------------------------------------------------------------------------------- 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 28 ASN D 146 GLN F 368 GLN G1423 GLN G1535 GLN G1539 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27842 Z= 0.138 Angle : 0.548 8.851 37648 Z= 0.263 Chirality : 0.042 0.145 4279 Planarity : 0.004 0.049 4878 Dihedral : 7.189 112.285 3920 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.82 % Allowed : 10.51 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3474 helix: -0.35 (0.14), residues: 1356 sheet: -1.40 (0.23), residues: 517 loop : -1.74 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 34 HIS 0.014 0.001 HIS J 762 PHE 0.017 0.001 PHE D 223 TYR 0.026 0.001 TYR G1453 ARG 0.005 0.000 ARG J 34 *********************** 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 420 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 367 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8625 (mmm) cc_final: 0.8214 (tpp) REVERT: A 170 LYS cc_start: 0.8896 (tttt) cc_final: 0.8690 (ttmm) REVERT: A 179 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 285 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 351 ILE cc_start: 0.8811 (mm) cc_final: 0.8374 (mt) REVERT: C 101 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7230 (tm-30) REVERT: C 393 ASP cc_start: 0.7904 (m-30) cc_final: 0.7678 (m-30) REVERT: C 448 LEU cc_start: 0.8872 (tp) cc_final: 0.8591 (tt) REVERT: D 191 ILE cc_start: 0.9010 (mp) cc_final: 0.8612 (mt) REVERT: D 250 ASN cc_start: 0.8497 (m-40) cc_final: 0.8274 (m-40) REVERT: D 263 ASP cc_start: 0.7985 (t0) cc_final: 0.7472 (t0) REVERT: D 283 LYS cc_start: 0.9067 (tttt) cc_final: 0.8859 (ttpp) REVERT: D 334 ILE cc_start: 0.8467 (mt) cc_final: 0.8135 (mt) REVERT: E 310 TYR cc_start: 0.8749 (t80) cc_final: 0.8430 (t80) REVERT: F 25 SER cc_start: 0.8633 (m) cc_final: 0.8282 (p) REVERT: F 245 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7868 (mm-30) REVERT: F 331 VAL cc_start: 0.9202 (t) cc_final: 0.8981 (p) REVERT: G 1423 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: H 454 LYS cc_start: 0.8790 (tttm) cc_final: 0.8586 (tttm) REVERT: I 31 ASN cc_start: 0.8672 (t0) cc_final: 0.8358 (t0) REVERT: I 166 MET cc_start: 0.7395 (ptp) cc_final: 0.7090 (ptm) REVERT: I 173 THR cc_start: 0.9181 (p) cc_final: 0.8913 (t) REVERT: J 86 MET cc_start: 0.7259 (ptm) cc_final: 0.6950 (ptm) REVERT: J 128 ASN cc_start: 0.8260 (t0) cc_final: 0.7692 (t0) outliers start: 53 outliers final: 30 residues processed: 402 average time/residue: 0.3864 time to fit residues: 247.3522 Evaluate side-chains 349 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 318 time to evaluate : 3.289 ------------------------------------------------------------------------------- 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 296 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 407 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 224 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 1411 GLU Chi-restraints excluded: chain G residue 1423 GLN Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain I residue 19 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.0570 chunk 189 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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** C 285 GLN C 289 ASN D 49 GLN F 368 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27842 Z= 0.231 Angle : 0.577 8.461 37648 Z= 0.278 Chirality : 0.044 0.155 4279 Planarity : 0.004 0.046 4878 Dihedral : 7.014 111.108 3920 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.20 % Allowed : 11.09 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3474 helix: -0.13 (0.15), residues: 1354 sheet: -1.40 (0.23), residues: 518 loop : -1.65 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 34 HIS 0.012 0.001 HIS J 762 PHE 0.013 0.001 PHE C 214 TYR 0.021 0.001 TYR A 193 ARG 0.005 0.000 ARG A 401 *********************** 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 405 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 341 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8607 (mmm) cc_final: 0.8202 (tpp) REVERT: A 170 LYS cc_start: 0.8948 (tttt) cc_final: 0.8743 (ttmm) REVERT: A 179 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6765 (mt-10) REVERT: B 179 GLU cc_start: 0.7749 (mp0) cc_final: 0.7449 (mp0) REVERT: B 351 ILE cc_start: 0.8855 (mm) cc_final: 0.8420 (mt) REVERT: C 101 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7206 (tm-30) REVERT: C 393 ASP cc_start: 0.7955 (m-30) cc_final: 0.7746 (m-30) REVERT: C 448 LEU cc_start: 0.8915 (tp) cc_final: 0.8631 (tt) REVERT: D 191 ILE cc_start: 0.9043 (mp) cc_final: 0.8626 (mt) REVERT: D 250 ASN cc_start: 0.8592 (m-40) cc_final: 0.8335 (m-40) REVERT: D 263 ASP cc_start: 0.7993 (t0) cc_final: 0.7459 (t0) REVERT: D 334 ILE cc_start: 0.8516 (mt) cc_final: 0.8190 (mt) REVERT: E 310 TYR cc_start: 0.8797 (t80) cc_final: 0.8485 (t80) REVERT: F 25 SER cc_start: 0.8698 (m) cc_final: 0.8332 (p) REVERT: F 88 MET cc_start: 0.7908 (mmt) cc_final: 0.7497 (tpp) REVERT: F 245 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7940 (mm-30) REVERT: F 273 ASP cc_start: 0.7227 (t0) cc_final: 0.6940 (t0) REVERT: F 331 VAL cc_start: 0.9205 (t) cc_final: 0.8990 (p) REVERT: G 1450 ARG cc_start: 0.7750 (mpt180) cc_final: 0.7489 (mmp-170) REVERT: I 31 ASN cc_start: 0.8699 (t0) cc_final: 0.8372 (t0) REVERT: I 166 MET cc_start: 0.7468 (ptp) cc_final: 0.7144 (ptm) REVERT: I 173 THR cc_start: 0.9211 (p) cc_final: 0.8908 (t) REVERT: J 86 MET cc_start: 0.7384 (ptm) cc_final: 0.6952 (ptm) REVERT: J 128 ASN cc_start: 0.8375 (t0) cc_final: 0.7830 (t0) REVERT: J 291 GLU cc_start: 0.8694 (pm20) cc_final: 0.8402 (pm20) outliers start: 64 outliers final: 48 residues processed: 384 average time/residue: 0.3840 time to fit residues: 235.1738 Evaluate side-chains 358 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 310 time to evaluate : 3.516 ------------------------------------------------------------------------------- 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 105 THR Chi-restraints excluded: chain A residue 158 LEU 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 324 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL 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 242 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP 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 182 THR Chi-restraints excluded: chain F residue 224 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 1327 ASP 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 I residue 19 GLN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 197 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 0.1980 chunk 300 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 110 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.2482 ------------------------------------------------------------------------------- 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 ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27842 Z= 0.235 Angle : 0.589 10.762 37648 Z= 0.283 Chirality : 0.044 0.178 4279 Planarity : 0.004 0.043 4878 Dihedral : 6.831 107.098 3920 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.51 % Allowed : 11.68 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3474 helix: 0.04 (0.15), residues: 1344 sheet: -1.36 (0.23), residues: 520 loop : -1.60 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 34 HIS 0.007 0.001 HIS J 762 PHE 0.019 0.001 PHE D 223 TYR 0.021 0.001 TYR A 193 ARG 0.006 0.000 ARG J 34 *********************** 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 409 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 336 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8573 (mmm) cc_final: 0.8175 (tpp) REVERT: A 170 LYS cc_start: 0.8944 (tttt) cc_final: 0.8743 (ttmm) REVERT: A 179 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6791 (mt-10) REVERT: B 351 ILE cc_start: 0.8870 (mm) cc_final: 0.8451 (mt) REVERT: C 393 ASP cc_start: 0.7978 (m-30) cc_final: 0.7769 (m-30) REVERT: C 448 LEU cc_start: 0.8917 (tp) cc_final: 0.8455 (tt) REVERT: D 191 ILE cc_start: 0.9050 (mp) cc_final: 0.8636 (mt) REVERT: D 250 ASN cc_start: 0.8713 (m-40) cc_final: 0.8442 (m-40) REVERT: D 263 ASP cc_start: 0.7944 (t0) cc_final: 0.7433 (t0) REVERT: D 298 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: F 25 SER cc_start: 0.8706 (m) cc_final: 0.8351 (p) REVERT: F 88 MET cc_start: 0.7938 (mmt) cc_final: 0.7569 (tpp) REVERT: F 208 TYR cc_start: 0.7977 (m-80) cc_final: 0.7651 (m-80) REVERT: F 245 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7915 (mm-30) REVERT: F 273 ASP cc_start: 0.7277 (t0) cc_final: 0.6952 (t0) REVERT: F 331 VAL cc_start: 0.9187 (t) cc_final: 0.8982 (p) REVERT: I 31 ASN cc_start: 0.8727 (t0) cc_final: 0.8396 (t0) REVERT: I 34 TRP cc_start: 0.7210 (t60) cc_final: 0.6905 (t60) REVERT: I 37 ASN cc_start: 0.8128 (t0) cc_final: 0.7831 (t0) REVERT: I 166 MET cc_start: 0.7446 (ptp) cc_final: 0.7143 (ptm) REVERT: J 128 ASN cc_start: 0.8365 (t0) cc_final: 0.7840 (t0) REVERT: J 238 MET cc_start: 0.8384 (mtt) cc_final: 0.8064 (mtm) REVERT: J 659 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7453 (tm-30) outliers start: 73 outliers final: 51 residues processed: 391 average time/residue: 0.3797 time to fit residues: 237.5236 Evaluate side-chains 358 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 306 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 171 LEU 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 198 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 CYS 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 112 GLU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 257 LEU 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 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 407 THR 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 182 THR Chi-restraints excluded: chain F residue 318 ASP 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 1327 ASP Chi-restraints excluded: chain G residue 1439 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 332 optimal weight: 0.1980 chunk 208 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 357 ASN ** G1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1423 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27842 Z= 0.203 Angle : 0.578 10.587 37648 Z= 0.276 Chirality : 0.043 0.163 4279 Planarity : 0.004 0.043 4878 Dihedral : 6.654 105.870 3920 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.34 % Allowed : 12.02 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3474 helix: 0.15 (0.15), residues: 1350 sheet: -1.28 (0.23), residues: 526 loop : -1.52 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 34 HIS 0.003 0.001 HIS F 239 PHE 0.014 0.001 PHE C 214 TYR 0.021 0.001 TYR B 178 ARG 0.009 0.000 ARG G1450 *********************** 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 385 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 317 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8303 (tp30) cc_final: 0.8083 (mm-30) REVERT: A 190 ASP cc_start: 0.8532 (m-30) cc_final: 0.7921 (m-30) REVERT: B 351 ILE cc_start: 0.8860 (mm) cc_final: 0.8438 (mt) REVERT: C 448 LEU cc_start: 0.8904 (tp) cc_final: 0.8436 (tt) REVERT: D 191 ILE cc_start: 0.9040 (mp) cc_final: 0.8652 (mt) REVERT: D 247 ASP cc_start: 0.8230 (m-30) cc_final: 0.7726 (m-30) REVERT: D 250 ASN cc_start: 0.8696 (m-40) cc_final: 0.8456 (m-40) REVERT: D 263 ASP cc_start: 0.7895 (t0) cc_final: 0.7380 (t0) REVERT: D 298 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: F 25 SER cc_start: 0.8700 (m) cc_final: 0.8348 (p) REVERT: F 88 MET cc_start: 0.7951 (mmt) cc_final: 0.7587 (tpp) REVERT: F 208 TYR cc_start: 0.7992 (m-80) cc_final: 0.7674 (m-80) REVERT: F 245 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7917 (mm-30) REVERT: F 357 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8236 (m110) REVERT: I 31 ASN cc_start: 0.8687 (t0) cc_final: 0.8344 (t0) REVERT: I 34 TRP cc_start: 0.7255 (t60) cc_final: 0.6973 (t60) REVERT: I 37 ASN cc_start: 0.8098 (t0) cc_final: 0.7810 (t0) REVERT: I 166 MET cc_start: 0.7393 (ptp) cc_final: 0.7108 (ptm) REVERT: J 128 ASN cc_start: 0.8397 (t0) cc_final: 0.7891 (t0) REVERT: J 238 MET cc_start: 0.8499 (mtt) cc_final: 0.8236 (mtm) REVERT: J 291 GLU cc_start: 0.8733 (pm20) cc_final: 0.8416 (pm20) REVERT: J 659 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7539 (tm-30) outliers start: 68 outliers final: 53 residues processed: 369 average time/residue: 0.3712 time to fit residues: 221.8974 Evaluate side-chains 352 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 3.454 ------------------------------------------------------------------------------- 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 296 ILE 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 198 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 112 GLU 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 298 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP 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 318 ASP Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 357 ASN 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 1327 ASP Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1411 GLU Chi-restraints excluded: chain G residue 1423 GLN Chi-restraints excluded: chain G residue 1439 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 I residue 197 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 170 LYS Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 211 optimal weight: 0.0570 chunk 226 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN ** G1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3287 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= 0.167 Angle : 0.563 10.486 37648 Z= 0.268 Chirality : 0.043 0.179 4279 Planarity : 0.003 0.041 4878 Dihedral : 6.491 103.505 3920 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.09 % Allowed : 12.40 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3474 helix: 0.28 (0.15), residues: 1351 sheet: -1.21 (0.22), residues: 525 loop : -1.48 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 PHE 0.018 0.001 PHE D 223 TYR 0.026 0.001 TYR E 310 ARG 0.007 0.000 ARG J 34 *********************** 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 376 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 315 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8393 (tpp) cc_final: 0.7796 (tpp) REVERT: A 179 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6919 (mt-10) REVERT: A 184 GLU cc_start: 0.8271 (tp30) cc_final: 0.8062 (mm-30) REVERT: A 190 ASP cc_start: 0.8513 (m-30) cc_final: 0.7916 (m-30) REVERT: B 351 ILE cc_start: 0.8837 (mm) cc_final: 0.8421 (mt) REVERT: C 448 LEU cc_start: 0.8919 (tp) cc_final: 0.8617 (tt) REVERT: D 187 MET cc_start: 0.8869 (mmm) cc_final: 0.8605 (mmm) REVERT: D 191 ILE cc_start: 0.9029 (mp) cc_final: 0.8662 (mt) REVERT: D 247 ASP cc_start: 0.8221 (m-30) cc_final: 0.7670 (m-30) REVERT: D 250 ASN cc_start: 0.8748 (m-40) cc_final: 0.8412 (m-40) REVERT: D 263 ASP cc_start: 0.7854 (t0) cc_final: 0.7318 (t0) REVERT: D 271 ILE cc_start: 0.9028 (mm) cc_final: 0.8680 (mm) REVERT: F 25 SER cc_start: 0.8675 (m) cc_final: 0.8328 (p) REVERT: F 88 MET cc_start: 0.7932 (mmt) cc_final: 0.7571 (tpp) REVERT: F 182 THR cc_start: 0.8816 (m) cc_final: 0.8525 (p) REVERT: F 245 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7918 (mm-30) REVERT: I 31 ASN cc_start: 0.8682 (t0) cc_final: 0.8344 (t0) REVERT: I 37 ASN cc_start: 0.8055 (t0) cc_final: 0.7773 (t0) REVERT: I 166 MET cc_start: 0.7352 (ptp) cc_final: 0.7054 (ptm) REVERT: J 128 ASN cc_start: 0.8390 (t0) cc_final: 0.7853 (t0) REVERT: J 238 MET cc_start: 0.8472 (mtt) cc_final: 0.8197 (mtm) REVERT: J 659 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7586 (tm-30) outliers start: 61 outliers final: 50 residues processed: 361 average time/residue: 0.3653 time to fit residues: 211.6762 Evaluate side-chains 344 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 294 time to evaluate : 3.148 ------------------------------------------------------------------------------- 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 324 ILE 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 324 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 216 LEU 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 112 GLU 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 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP 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 318 ASP 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 1327 ASP Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1411 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1461 LEU 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 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.3980 chunk 318 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 280 optimal weight: 7.9990 chunk 293 optimal weight: 0.5980 chunk 308 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 ASN ** G1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27842 Z= 0.256 Angle : 0.603 10.408 37648 Z= 0.290 Chirality : 0.044 0.204 4279 Planarity : 0.004 0.040 4878 Dihedral : 6.525 103.844 3920 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.13 % Allowed : 12.81 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3474 helix: 0.28 (0.15), residues: 1348 sheet: -1.25 (0.22), residues: 520 loop : -1.43 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 34 HIS 0.006 0.001 HIS J 762 PHE 0.015 0.001 PHE C 214 TYR 0.027 0.002 TYR E 310 ARG 0.008 0.000 ARG J 34 *********************** 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 368 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 306 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8766 (tp) cc_final: 0.8475 (tt) REVERT: A 179 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 215 ASP cc_start: 0.7927 (t0) cc_final: 0.7610 (t0) REVERT: B 264 LEU cc_start: 0.9174 (tp) cc_final: 0.8634 (mt) REVERT: B 351 ILE cc_start: 0.8883 (mm) cc_final: 0.8444 (mt) REVERT: C 448 LEU cc_start: 0.8943 (tp) cc_final: 0.8591 (tt) REVERT: D 187 MET cc_start: 0.8798 (mmm) cc_final: 0.8513 (mmm) REVERT: D 250 ASN cc_start: 0.8760 (m-40) cc_final: 0.8512 (m-40) REVERT: D 263 ASP cc_start: 0.7891 (t0) cc_final: 0.7342 (t0) REVERT: D 275 ILE cc_start: 0.9146 (mt) cc_final: 0.8886 (mp) REVERT: D 298 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: F 25 SER cc_start: 0.8713 (m) cc_final: 0.8374 (p) REVERT: F 88 MET cc_start: 0.7808 (mmt) cc_final: 0.7440 (tpp) REVERT: F 182 THR cc_start: 0.8836 (m) cc_final: 0.8538 (p) REVERT: F 245 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7948 (mm-30) REVERT: F 273 ASP cc_start: 0.7314 (t0) cc_final: 0.6991 (t0) REVERT: I 31 ASN cc_start: 0.8711 (t0) cc_final: 0.8359 (t0) REVERT: I 37 ASN cc_start: 0.8102 (t0) cc_final: 0.7867 (t0) REVERT: I 166 MET cc_start: 0.7466 (ptp) cc_final: 0.7168 (ptm) REVERT: J 128 ASN cc_start: 0.8460 (t0) cc_final: 0.7947 (t0) REVERT: J 238 MET cc_start: 0.8597 (mtt) cc_final: 0.8374 (mtm) REVERT: J 659 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7670 (tm-30) outliers start: 62 outliers final: 54 residues processed: 353 average time/residue: 0.3608 time to fit residues: 206.5774 Evaluate side-chains 347 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.098 ------------------------------------------------------------------------------- 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 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 324 ILE 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 324 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 216 LEU 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 112 GLU Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 325 MET 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 318 ASP 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 1327 ASP Chi-restraints excluded: chain G residue 1385 ASP Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1461 LEU 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 I residue 197 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 0.0970 chunk 327 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 343 optimal weight: 0.0670 chunk 316 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN C 237 GLN ** G1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1423 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27842 Z= 0.155 Angle : 0.567 10.080 37648 Z= 0.270 Chirality : 0.043 0.168 4279 Planarity : 0.003 0.040 4878 Dihedral : 6.276 100.839 3920 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.75 % Allowed : 13.39 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3474 helix: 0.44 (0.15), residues: 1339 sheet: -1.14 (0.22), residues: 517 loop : -1.35 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 34 HIS 0.005 0.001 HIS J 762 PHE 0.019 0.001 PHE D 223 TYR 0.026 0.001 TYR E 310 ARG 0.008 0.000 ARG J 34 ********************** 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 357 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8717 (tp) cc_final: 0.8448 (tt) REVERT: A 179 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 190 ASP cc_start: 0.8426 (m-30) cc_final: 0.7838 (m-30) REVERT: A 215 ASP cc_start: 0.7907 (t0) cc_final: 0.7612 (t0) REVERT: B 260 MET cc_start: 0.8814 (ptt) cc_final: 0.8498 (ptp) REVERT: B 351 ILE cc_start: 0.8834 (mm) cc_final: 0.8402 (mt) REVERT: C 448 LEU cc_start: 0.8915 (tp) cc_final: 0.8589 (tt) REVERT: D 187 MET cc_start: 0.8772 (mmm) cc_final: 0.8521 (mmm) REVERT: D 191 ILE cc_start: 0.9035 (mp) cc_final: 0.8347 (mt) REVERT: D 250 ASN cc_start: 0.8744 (m-40) cc_final: 0.8448 (m-40) REVERT: D 275 ILE cc_start: 0.9110 (mt) cc_final: 0.8853 (mp) REVERT: D 298 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: F 25 SER cc_start: 0.8692 (m) cc_final: 0.8319 (p) REVERT: F 88 MET cc_start: 0.7824 (mmt) cc_final: 0.7435 (tpp) REVERT: F 245 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7904 (mm-30) REVERT: I 31 ASN cc_start: 0.8685 (t0) cc_final: 0.8340 (t0) REVERT: I 37 ASN cc_start: 0.8087 (t0) cc_final: 0.7854 (t0) REVERT: I 166 MET cc_start: 0.7277 (ptp) cc_final: 0.6990 (ptm) REVERT: J 22 LEU cc_start: 0.8163 (tp) cc_final: 0.7869 (pt) REVERT: J 128 ASN cc_start: 0.8409 (t0) cc_final: 0.7860 (t0) REVERT: J 238 MET cc_start: 0.8521 (mtt) cc_final: 0.8274 (mtm) REVERT: J 659 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7660 (tm-30) REVERT: J 723 ASP cc_start: 0.6379 (t0) cc_final: 0.6108 (m-30) outliers start: 51 outliers final: 46 residues processed: 344 average time/residue: 0.3651 time to fit residues: 205.1910 Evaluate side-chains 345 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 3.133 ------------------------------------------------------------------------------- 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 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 324 ILE 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 324 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 216 LEU 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 144 GLU 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 325 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 325 MET 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 257 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 353 VAL 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 1423 GLN Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1461 LEU 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 30 VAL Chi-restraints excluded: chain J residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 2.9990 chunk 291 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 274 GLN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1423 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102210 restraints weight = 47368.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104383 restraints weight = 29594.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105895 restraints weight = 21210.029| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27842 Z= 0.223 Angle : 0.591 9.889 37648 Z= 0.283 Chirality : 0.044 0.182 4279 Planarity : 0.004 0.040 4878 Dihedral : 6.276 101.240 3920 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.89 % Allowed : 13.43 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3474 helix: 0.44 (0.15), residues: 1347 sheet: -1.13 (0.22), residues: 519 loop : -1.31 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 34 HIS 0.006 0.001 HIS J 762 PHE 0.015 0.001 PHE C 214 TYR 0.041 0.001 TYR E 310 ARG 0.008 0.000 ARG J 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.75 seconds wall clock time: 99 minutes 14.30 seconds (5954.30 seconds total)