Starting phenix.real_space_refine on Wed Mar 20 19:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooc_17010/03_2024/8ooc_17010_updated.pdb" } resolution = 2.93 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 17787 2.51 5 N 5035 2.21 5 O 5400 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 "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28371 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: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3582 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain breaks: 3 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.82, per 1000 atoms: 0.52 Number of scatterers: 28371 At special positions: 0 Unit cell: (133.164, 161.934, 176.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 15 15.00 Mg 1 11.99 O 5400 8.00 N 5035 7.00 C 17787 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: 11.08 Conformation dependent library (CDL) restraints added in 5.0 seconds 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 30 sheets defined 39.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 58 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.603A pdb=" N ILE A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.679A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 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: 3.995A 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 353 through 358 removed outlier: 3.642A pdb=" N GLN A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.610A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.598A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 175 through 183 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 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.768A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.236A 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 358 removed outlier: 4.478A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 382 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.904A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 428 through 437 removed outlier: 3.863A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 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 102 Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.602A pdb=" N GLN C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 274 through 290 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 310 through 320 removed outlier: 3.817A 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 353 through 358 removed outlier: 4.526A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 389 through 401 Processing helix chain 'C' and resid 404 through 420 removed outlier: 3.724A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.528A pdb=" N GLU C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 451 Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.506A pdb=" N ILE D 108 " --> pdb=" O ALA D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.660A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.348A pdb=" N SER D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 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: 4.836A 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 347 through 352 removed outlier: 4.248A pdb=" N ARG D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 Processing helix chain 'D' and resid 383 through 395 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.616A pdb=" N ILE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 435 through 445 Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 83 through 97 removed outlier: 6.825A pdb=" N GLN E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 removed outlier: 3.773A pdb=" N ILE E 108 " --> pdb=" O ALA E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.619A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 208 through 213 removed outlier: 5.013A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.507A pdb=" N PHE E 260 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER E 261 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 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 316 removed outlier: 3.936A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU E 316 " --> pdb=" O ASN E 312 " (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 352 removed outlier: 4.093A pdb=" N ARG E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 376 Processing helix chain 'E' and resid 383 through 396 Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.972A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 105 through 108 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.601A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 183 Processing helix chain 'F' and resid 208 through 212 removed outlier: 4.178A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 255 through 261 removed outlier: 3.741A pdb=" N SER F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 285 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 316 removed outlier: 3.950A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU F 316 " --> pdb=" O ASN F 312 " (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 352 removed outlier: 4.259A pdb=" N ARG F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 376 Processing helix chain 'F' and resid 383 through 396 Processing helix chain 'F' and resid 398 through 414 removed outlier: 4.081A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 435 through 444 Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'G' and resid 1224 through 1239 removed outlier: 4.046A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE G1239 " --> pdb=" O ASN G1235 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1269 Processing helix chain 'G' and resid 1271 through 1274 No H-bonds generated for 'chain 'G' and resid 1271 through 1274' Processing helix chain 'G' and resid 1317 through 1320 No H-bonds generated for 'chain 'G' and resid 1317 through 1320' Processing helix chain 'G' and resid 1334 through 1344 removed outlier: 4.187A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1358 removed outlier: 3.553A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER G1358 " --> pdb=" O ASN G1354 " (cutoff:3.500A) Processing helix chain 'G' and resid 1366 through 1369 removed outlier: 3.749A 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 1383 Processing helix chain 'G' and resid 1386 through 1395 removed outlier: 3.924A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1399 through 1406 removed outlier: 3.723A 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 1424 through 1427 No H-bonds generated for 'chain 'G' and resid 1424 through 1427' Processing helix chain 'G' and resid 1430 through 1434 Processing helix chain 'G' and resid 1441 through 1445 Processing helix chain 'G' and resid 1448 through 1455 Processing helix chain 'G' and resid 1481 through 1491 Processing helix chain 'G' and resid 1494 through 1501 Processing helix chain 'G' and resid 1505 through 1513 Processing helix chain 'G' and resid 1545 through 1551 Processing helix chain 'G' and resid 1553 through 1567 removed outlier: 3.791A pdb=" N GLU G1560 " --> pdb=" O ALA G1556 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1592 removed outlier: 3.896A pdb=" N ASP G1583 " --> pdb=" O THR G1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 removed outlier: 4.293A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 191 through 199 removed outlier: 3.707A pdb=" N ASN I 199 " --> pdb=" O ALA I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 212 removed outlier: 4.005A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 20 No H-bonds generated for 'chain 'J' and resid 17 through 20' Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 129 through 142 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 225 through 227 No H-bonds generated for 'chain 'J' and resid 225 through 227' Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 removed outlier: 3.873A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 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 604 through 606 No H-bonds generated for 'chain 'J' and resid 604 through 606' Processing helix chain 'J' and resid 608 through 614 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 633 through 638 removed outlier: 3.904A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing helix chain 'J' and resid 646 through 650 Processing helix chain 'J' and resid 657 through 667 Processing helix chain 'J' and resid 669 through 671 No H-bonds generated for 'chain 'J' and resid 669 through 671' Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.419A pdb=" N ASP J 685 " --> pdb=" O ALA J 681 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 693 No H-bonds generated for 'chain 'J' and resid 691 through 693' Processing helix chain 'J' and resid 698 through 709 removed outlier: 3.636A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 735 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 363 removed outlier: 6.971A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 330 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 297 Processing sheet with id= C, first strand: chain 'A' and resid 167 through 174 removed outlier: 3.614A pdb=" N GLU A 138 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 163 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 136 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 190 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 336 through 339 removed outlier: 5.666A pdb=" N LEU A 345 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 359 through 363 removed outlier: 6.904A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 293 through 297 Processing sheet with id= G, first strand: chain 'B' and resid 167 through 173 removed outlier: 6.623A pdb=" N LYS B 163 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 136 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.869A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 359 through 364 removed outlier: 6.927A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 328 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 69 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 330 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY C 71 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER C 332 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 293 through 297 Processing sheet with id= K, first strand: chain 'C' and resid 167 through 173 removed outlier: 3.589A pdb=" N GLY C 167 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU C 195 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N CYS C 201 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 336 through 339 removed outlier: 6.016A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 353 through 357 removed outlier: 6.747A pdb=" N ALA D 72 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 356 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 74 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N MET D 325 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 288 through 292 Processing sheet with id= O, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.729A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP D 195 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE D 201 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 331 through 333 Processing sheet with id= Q, first strand: chain 'E' and resid 353 through 358 removed outlier: 6.853A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR E 358 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA E 76 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY E 77 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER E 327 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 288 through 292 Processing sheet with id= S, first strand: chain 'E' and resid 168 through 172 removed outlier: 3.623A pdb=" N GLU E 144 " --> pdb=" O THR E 161 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP E 190 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER E 193 " --> pdb=" O LYS E 203 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS E 203 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP E 195 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE E 201 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 331 through 333 Processing sheet with id= U, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.534A pdb=" N VAL F 323 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE F 75 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET F 325 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY F 77 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER F 327 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 289 through 292 removed outlier: 3.566A pdb=" N SER F 135 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 168 through 173 removed outlier: 3.600A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS F 163 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL F 142 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP F 190 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER F 193 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS F 203 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP F 195 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE F 201 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= Y, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.806A pdb=" N GLU G1475 " --> pdb=" O TYR G1313 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'H' and resid 449 through 453 Processing sheet with id= AA, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.735A pdb=" N ILE J 296 " --> pdb=" O TYR J 28 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 80 through 82 removed outlier: 7.507A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN J 63 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR J 159 " --> pdb=" O ASN J 63 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 115 through 117 Processing sheet with id= AD, first strand: chain 'J' and resid 718 through 720 removed outlier: 6.486A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU J 204 " --> pdb=" O PHE J 687 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR J 689 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL J 206 " --> pdb=" O THR J 689 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3090 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: 10.13 Time building geometry restraints manager: 12.03 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: 9565 1.34 - 1.46: 3166 1.46 - 1.57: 15863 1.57 - 1.69: 23 1.69 - 1.81: 230 Bond restraints: 28847 Sorted by residual: bond pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CB CYS A 407 " pdb=" SG CYS A 407 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CA PRO G1522 " pdb=" CB PRO G1522 " ideal model delta sigma weight residual 1.533 1.556 -0.023 1.80e-02 3.09e+03 1.59e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CG1 ILE B 102 " pdb=" CD1 ILE B 102 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 98.25 - 106.56: 897 106.56 - 114.86: 17433 114.86 - 123.16: 19058 123.16 - 131.46: 1570 131.46 - 139.77: 35 Bond angle restraints: 38993 Sorted by residual: angle pdb=" C1' ADP A 501 " pdb=" C2' ADP A 501 " pdb=" C3' ADP A 501 " ideal model delta sigma weight residual 111.00 100.95 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO G1522 " pdb=" C PRO G1522 " pdb=" N PRO G1523 " ideal model delta sigma weight residual 117.10 126.25 -9.15 2.80e+00 1.28e-01 1.07e+01 angle pdb=" C1' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C3' ADP F 501 " ideal model delta sigma weight residual 111.00 101.27 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C1' ADP D 501 " pdb=" C2' ADP D 501 " pdb=" C3' ADP D 501 " ideal model delta sigma weight residual 111.00 102.27 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " ideal model delta sigma weight residual 111.00 102.41 8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 38988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 17387 35.46 - 70.91: 263 70.91 - 106.36: 28 106.36 - 141.82: 3 141.82 - 177.27: 6 Dihedral angle restraints: 17687 sinusoidal: 7292 harmonic: 10395 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 122.72 177.27 1 2.00e+01 2.50e-03 4.80e+01 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 -60.00 97.98 -157.99 1 2.00e+01 2.50e-03 4.63e+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 300.00 148.52 151.49 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3278 0.048 - 0.096: 879 0.096 - 0.145: 242 0.145 - 0.193: 19 0.193 - 0.241: 1 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CA THR D 81 " pdb=" N THR D 81 " pdb=" C THR D 81 " pdb=" CB THR D 81 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" C3' ADP D 501 " pdb=" O2' ADP D 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 351 " pdb=" N ILE B 351 " pdb=" C ILE B 351 " pdb=" CB ILE B 351 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4416 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.380 9.50e-02 1.11e+02 1.71e-01 2.10e+01 pdb=" NE ARG D 252 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 313 " -0.359 9.50e-02 1.11e+02 1.62e-01 2.08e+01 pdb=" NE ARG E 313 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 313 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG E 313 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG E 313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.351 9.50e-02 1.11e+02 1.58e-01 1.86e+01 pdb=" NE ARG F 437 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.002 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 321 2.64 - 3.20: 26660 3.20 - 3.77: 43591 3.77 - 4.33: 65253 4.33 - 4.90: 104162 Nonbonded interactions: 239987 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 801 " model vdw 2.069 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1G ATP J 802 " model vdw 2.096 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1B ATP J 802 " model vdw 2.159 2.170 nonbonded pdb=" ND1 HIS J 197 " pdb=" OD2 ASP J 727 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.208 2.440 ... (remaining 239982 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 460 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 460 or resid 501)) selection = (chain 'F' and (resid 20 through 460 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 10.560 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 76.950 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.150 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.065 28847 Z= 0.191 Angle : 0.695 10.048 38993 Z= 0.390 Chirality : 0.047 0.241 4419 Planarity : 0.011 0.171 5049 Dihedral : 14.059 177.274 10997 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -1.01 (0.13), residues: 3590 helix: -1.47 (0.11), residues: 1523 sheet: 0.59 (0.21), residues: 544 loop : -0.02 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 450 HIS 0.007 0.001 HIS G1345 PHE 0.020 0.002 PHE G1501 TYR 0.032 0.005 TYR A 210 ARG 0.039 0.004 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7672 (ttp80) REVERT: B 181 ILE cc_start: 0.8499 (mm) cc_final: 0.8291 (mt) REVERT: B 265 MET cc_start: 0.8698 (mmt) cc_final: 0.8359 (mmt) REVERT: B 378 ILE cc_start: 0.8669 (mt) cc_final: 0.8307 (mp) REVERT: B 449 THR cc_start: 0.8041 (m) cc_final: 0.7763 (p) REVERT: C 6 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 103 TYR cc_start: 0.8282 (m-80) cc_final: 0.8002 (m-10) REVERT: C 106 GLU cc_start: 0.7902 (tt0) cc_final: 0.7596 (mt-10) REVERT: C 303 ASP cc_start: 0.7487 (t0) cc_final: 0.6616 (t0) REVERT: C 307 MET cc_start: 0.8592 (mmp) cc_final: 0.8201 (mmt) REVERT: C 368 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 134 GLU cc_start: 0.7432 (tt0) cc_final: 0.6774 (tt0) REVERT: D 167 MET cc_start: 0.8664 (mtp) cc_final: 0.8325 (ttm) REVERT: D 184 GLU cc_start: 0.8022 (tp30) cc_final: 0.7576 (tp30) REVERT: D 232 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7666 (mm-40) REVERT: D 441 PHE cc_start: 0.8709 (t80) cc_final: 0.8452 (t80) REVERT: F 167 MET cc_start: 0.7945 (mtp) cc_final: 0.7675 (ttm) REVERT: F 183 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8191 (tptp) REVERT: G 1479 ASP cc_start: 0.7077 (p0) cc_final: 0.6724 (p0) REVERT: G 1538 THR cc_start: 0.8402 (p) cc_final: 0.8188 (t) REVERT: G 1545 MET cc_start: 0.7764 (mmt) cc_final: 0.7407 (mmt) REVERT: I 166 MET cc_start: 0.8411 (ptp) cc_final: 0.8204 (ptp) REVERT: J 142 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mptp) REVERT: J 168 SER cc_start: 0.8875 (m) cc_final: 0.8494 (p) REVERT: J 751 TYR cc_start: 0.8618 (t80) cc_final: 0.8036 (t80) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 1.8948 time to fit residues: 1499.8718 Evaluate side-chains 361 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS B 421 ASN B 446 ASN C 237 GLN D 225 GLN D 328 ASN E 312 ASN E 419 GLN F 96 GLN F 394 GLN G1345 HIS G1423 GLN I 199 ASN J 697 ASN J 722 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28847 Z= 0.305 Angle : 0.671 10.307 38993 Z= 0.341 Chirality : 0.046 0.183 4419 Planarity : 0.005 0.065 5049 Dihedral : 9.874 170.086 4058 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.01 % Allowed : 10.96 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.13 (0.13), residues: 3590 helix: -0.02 (0.12), residues: 1523 sheet: 0.46 (0.21), residues: 554 loop : 0.29 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 19 HIS 0.010 0.002 HIS G1345 PHE 0.021 0.002 PHE D 223 TYR 0.020 0.002 TYR A 193 ARG 0.011 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 386 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: A 373 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7650 (ttp80) REVERT: B 62 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: B 265 MET cc_start: 0.8734 (mmt) cc_final: 0.8487 (mmt) REVERT: B 317 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8409 (m-40) REVERT: B 386 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: B 449 THR cc_start: 0.8073 (m) cc_final: 0.7783 (p) REVERT: C 106 GLU cc_start: 0.8120 (tt0) cc_final: 0.7808 (mt-10) REVERT: C 307 MET cc_start: 0.8704 (mmp) cc_final: 0.8286 (mmt) REVERT: D 184 GLU cc_start: 0.8039 (tp30) cc_final: 0.7421 (tp30) REVERT: D 232 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7602 (mm110) REVERT: E 159 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8287 (tttm) REVERT: E 308 PHE cc_start: 0.8568 (m-80) cc_final: 0.8339 (m-80) REVERT: E 312 ASN cc_start: 0.8751 (m-40) cc_final: 0.8533 (m110) REVERT: F 62 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: F 97 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7154 (p0) REVERT: F 133 GLU cc_start: 0.6293 (tt0) cc_final: 0.6034 (pp20) REVERT: F 148 ASP cc_start: 0.7273 (m-30) cc_final: 0.7054 (t0) REVERT: G 1223 SER cc_start: 0.7299 (t) cc_final: 0.7009 (m) REVERT: G 1265 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7500 (ttm110) REVERT: G 1397 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7612 (mm-40) REVERT: G 1479 ASP cc_start: 0.7024 (p0) cc_final: 0.6745 (p0) REVERT: G 1538 THR cc_start: 0.8613 (p) cc_final: 0.8328 (t) REVERT: G 1545 MET cc_start: 0.7912 (mmt) cc_final: 0.7704 (mmt) REVERT: I 167 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: J 86 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (ptt) REVERT: J 168 SER cc_start: 0.8880 (m) cc_final: 0.8501 (p) REVERT: J 222 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7591 (ttmm) outliers start: 91 outliers final: 31 residues processed: 444 average time/residue: 1.7332 time to fit residues: 870.9381 Evaluate side-chains 361 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 319 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 623 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 349 optimal weight: 0.2980 chunk 288 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 259 optimal weight: 0.0050 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN B 446 ASN D 328 ASN F 96 GLN J 73 ASN J 237 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28847 Z= 0.290 Angle : 0.626 9.902 38993 Z= 0.315 Chirality : 0.045 0.332 4419 Planarity : 0.005 0.065 5049 Dihedral : 9.363 163.723 4058 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.34 % Allowed : 12.75 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.39 (0.14), residues: 3590 helix: 0.37 (0.13), residues: 1511 sheet: 0.41 (0.21), residues: 573 loop : 0.30 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 19 HIS 0.006 0.001 HIS F 24 PHE 0.028 0.002 PHE D 441 TYR 0.025 0.002 TYR J 751 ARG 0.008 0.001 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 344 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8453 (t) cc_final: 0.8153 (m) REVERT: A 279 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8194 (mm-30) REVERT: A 373 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7709 (ttp80) REVERT: B 62 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7985 (mpp) REVERT: B 449 THR cc_start: 0.8097 (m) cc_final: 0.7837 (p) REVERT: C 106 GLU cc_start: 0.8149 (tt0) cc_final: 0.7843 (mt-10) REVERT: C 307 MET cc_start: 0.8659 (mmp) cc_final: 0.8197 (mmt) REVERT: D 139 GLU cc_start: 0.6934 (pm20) cc_final: 0.6548 (pm20) REVERT: D 196 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8591 (mtpp) REVERT: D 220 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: D 232 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7736 (mm-40) REVERT: E 159 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8282 (tttm) REVERT: E 263 ASP cc_start: 0.7488 (t0) cc_final: 0.6789 (t0) REVERT: E 312 ASN cc_start: 0.8839 (m-40) cc_final: 0.8637 (m110) REVERT: F 62 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8214 (mtp) REVERT: F 97 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7391 (p0) REVERT: F 136 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: F 232 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: G 1223 SER cc_start: 0.7357 (t) cc_final: 0.6983 (m) REVERT: G 1265 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7612 (ttm110) REVERT: G 1392 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: G 1397 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: G 1479 ASP cc_start: 0.7067 (p0) cc_final: 0.6784 (p0) REVERT: G 1585 MET cc_start: 0.8220 (mmm) cc_final: 0.8008 (mmm) REVERT: I 167 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8017 (mttm) REVERT: J 154 MET cc_start: 0.7662 (tpp) cc_final: 0.6896 (mtt) REVERT: J 168 SER cc_start: 0.8867 (m) cc_final: 0.8523 (p) REVERT: J 174 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: J 222 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7602 (ttmm) REVERT: J 295 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6401 (mtm-85) outliers start: 101 outliers final: 42 residues processed: 415 average time/residue: 1.6854 time to fit residues: 798.1075 Evaluate side-chains 366 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 310 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 232 GLN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 344 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 308 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN B 421 ASN B 446 ASN D 328 ASN F 96 GLN ** H 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28847 Z= 0.203 Angle : 0.566 9.870 38993 Z= 0.282 Chirality : 0.043 0.218 4419 Planarity : 0.004 0.055 5049 Dihedral : 8.719 164.330 4058 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.05 % Allowed : 13.84 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.57 (0.14), residues: 3590 helix: 0.66 (0.13), residues: 1512 sheet: 0.35 (0.21), residues: 586 loop : 0.30 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.005 0.001 HIS J 134 PHE 0.021 0.001 PHE D 441 TYR 0.028 0.001 TYR J 751 ARG 0.007 0.000 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 341 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 279 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 373 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7679 (ttp80) REVERT: B 62 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8015 (mpp) REVERT: B 449 THR cc_start: 0.8059 (m) cc_final: 0.7822 (p) REVERT: C 106 GLU cc_start: 0.8119 (tt0) cc_final: 0.7827 (mt-10) REVERT: C 307 MET cc_start: 0.8606 (mmp) cc_final: 0.8092 (mmt) REVERT: C 442 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7247 (mmp-170) REVERT: D 139 GLU cc_start: 0.7012 (pm20) cc_final: 0.6649 (pm20) REVERT: D 144 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: D 145 ILE cc_start: 0.9091 (mt) cc_final: 0.8887 (tt) REVERT: D 163 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8439 (ttpp) REVERT: D 220 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: E 112 GLU cc_start: 0.7754 (tt0) cc_final: 0.7501 (tt0) REVERT: E 159 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8283 (tttm) REVERT: E 263 ASP cc_start: 0.7482 (t0) cc_final: 0.6778 (t0) REVERT: F 62 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8203 (mtp) REVERT: F 222 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8201 (pttm) REVERT: G 1265 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7714 (ttm110) REVERT: G 1392 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: G 1479 ASP cc_start: 0.7058 (p0) cc_final: 0.6797 (p0) REVERT: J 154 MET cc_start: 0.7583 (tpp) cc_final: 0.6861 (mtt) REVERT: J 168 SER cc_start: 0.8867 (m) cc_final: 0.8521 (p) REVERT: J 174 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: J 222 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7564 (ttmm) outliers start: 92 outliers final: 41 residues processed: 402 average time/residue: 1.7131 time to fit residues: 783.2272 Evaluate side-chains 357 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 305 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1587 GLU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 308 optimal weight: 0.0470 chunk 86 optimal weight: 9.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 421 ASN B 446 ASN D 24 HIS D 328 ASN E 24 HIS E 394 GLN F 24 HIS ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28847 Z= 0.348 Angle : 0.640 9.959 38993 Z= 0.320 Chirality : 0.046 0.320 4419 Planarity : 0.005 0.065 5049 Dihedral : 8.905 171.575 4058 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.61 % Allowed : 14.07 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.39 (0.14), residues: 3590 helix: 0.51 (0.13), residues: 1501 sheet: 0.32 (0.21), residues: 591 loop : 0.18 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1367 HIS 0.006 0.001 HIS B 21 PHE 0.019 0.002 PHE G1501 TYR 0.030 0.002 TYR J 751 ARG 0.007 0.001 ARG G1296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 318 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 373 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7723 (ttp80) REVERT: B 62 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7993 (mpp) REVERT: B 449 THR cc_start: 0.8061 (m) cc_final: 0.7823 (p) REVERT: C 106 GLU cc_start: 0.8098 (tt0) cc_final: 0.7870 (mt-10) REVERT: C 307 MET cc_start: 0.8609 (mmp) cc_final: 0.8083 (mmt) REVERT: C 442 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7281 (mmp-170) REVERT: D 139 GLU cc_start: 0.7058 (pm20) cc_final: 0.6650 (pm20) REVERT: D 163 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: D 175 SER cc_start: 0.8218 (p) cc_final: 0.7925 (t) REVERT: D 184 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7793 (tp30) REVERT: D 220 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: D 263 ASP cc_start: 0.7415 (m-30) cc_final: 0.7205 (m-30) REVERT: E 112 GLU cc_start: 0.7708 (tt0) cc_final: 0.7466 (tt0) REVERT: E 159 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8300 (tttm) REVERT: F 97 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7407 (p0) REVERT: G 1240 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.3054 (pmt) REVERT: G 1265 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7711 (ttm110) REVERT: G 1392 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: G 1479 ASP cc_start: 0.6895 (p0) cc_final: 0.6671 (p0) REVERT: I 167 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8046 (mttm) REVERT: J 82 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (mp) REVERT: J 128 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8068 (m-40) REVERT: J 154 MET cc_start: 0.7659 (tpp) cc_final: 0.6976 (mtt) REVERT: J 168 SER cc_start: 0.8889 (m) cc_final: 0.8564 (p) REVERT: J 174 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: J 222 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7610 (ttmm) REVERT: J 295 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6314 (mtm-85) outliers start: 109 outliers final: 58 residues processed: 396 average time/residue: 1.6835 time to fit residues: 763.6384 Evaluate side-chains 377 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 305 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1240 MET Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 MET Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN B 446 ASN D 328 ASN J 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28847 Z= 0.181 Angle : 0.550 9.049 38993 Z= 0.272 Chirality : 0.042 0.274 4419 Planarity : 0.004 0.056 5049 Dihedral : 8.394 170.614 4058 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.95 % Allowed : 15.33 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.62 (0.14), residues: 3590 helix: 0.81 (0.14), residues: 1506 sheet: 0.30 (0.21), residues: 585 loop : 0.24 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.004 0.001 HIS J 610 PHE 0.023 0.001 PHE G1274 TYR 0.025 0.001 TYR J 751 ARG 0.006 0.000 ARG G1296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 328 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8086 (tppp) REVERT: A 133 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7759 (pt0) REVERT: A 279 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 373 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7704 (ttp80) REVERT: B 62 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7970 (mpp) REVERT: B 421 ASN cc_start: 0.8276 (m-40) cc_final: 0.8043 (m110) REVERT: B 449 THR cc_start: 0.8066 (m) cc_final: 0.7861 (p) REVERT: C 106 GLU cc_start: 0.8084 (tt0) cc_final: 0.7816 (mt-10) REVERT: C 307 MET cc_start: 0.8527 (mmp) cc_final: 0.7901 (mmt) REVERT: C 442 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7297 (mmp-170) REVERT: D 139 GLU cc_start: 0.7096 (pm20) cc_final: 0.6681 (pm20) REVERT: D 163 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8622 (ttpp) REVERT: D 175 SER cc_start: 0.8175 (p) cc_final: 0.7897 (t) REVERT: D 220 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: E 112 GLU cc_start: 0.7707 (tt0) cc_final: 0.7438 (tt0) REVERT: E 159 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8287 (tttm) REVERT: E 263 ASP cc_start: 0.7591 (t0) cc_final: 0.7062 (t0) REVERT: F 62 MET cc_start: 0.8551 (ptt) cc_final: 0.8210 (mtp) REVERT: G 1240 MET cc_start: 0.3286 (mmt) cc_final: 0.2737 (pmt) REVERT: G 1265 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7757 (ttm110) REVERT: G 1392 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: I 23 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7004 (m170) REVERT: I 167 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7975 (mttm) REVERT: J 154 MET cc_start: 0.7651 (tpp) cc_final: 0.7013 (mtt) REVERT: J 168 SER cc_start: 0.8871 (m) cc_final: 0.8549 (p) REVERT: J 222 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7562 (ttmm) outliers start: 89 outliers final: 38 residues processed: 391 average time/residue: 1.6644 time to fit residues: 742.7401 Evaluate side-chains 348 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 301 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 194 optimal weight: 0.3980 chunk 289 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 446 ASN J 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28847 Z= 0.221 Angle : 0.571 9.149 38993 Z= 0.282 Chirality : 0.043 0.314 4419 Planarity : 0.004 0.059 5049 Dihedral : 8.363 172.330 4058 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.55 % Allowed : 16.06 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.64 (0.14), residues: 3590 helix: 0.82 (0.14), residues: 1509 sheet: 0.33 (0.21), residues: 585 loop : 0.25 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.004 0.001 HIS J 610 PHE 0.018 0.001 PHE J 35 TYR 0.019 0.001 TYR E 339 ARG 0.007 0.000 ARG G1296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 316 time to evaluate : 3.349 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8121 (tppt) REVERT: A 373 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7707 (ttp80) REVERT: B 62 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: B 449 THR cc_start: 0.8066 (m) cc_final: 0.7846 (p) REVERT: C 106 GLU cc_start: 0.8064 (tt0) cc_final: 0.7827 (mt-10) REVERT: C 307 MET cc_start: 0.8499 (mmp) cc_final: 0.7786 (mmt) REVERT: D 139 GLU cc_start: 0.7168 (pm20) cc_final: 0.6776 (pm20) REVERT: D 163 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8659 (ttpp) REVERT: D 175 SER cc_start: 0.8185 (p) cc_final: 0.7922 (t) REVERT: D 220 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: D 263 ASP cc_start: 0.7405 (m-30) cc_final: 0.7156 (m-30) REVERT: E 112 GLU cc_start: 0.7713 (tt0) cc_final: 0.7457 (tt0) REVERT: E 156 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7547 (mptp) REVERT: E 159 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8518 (tppt) REVERT: E 252 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7963 (ptt180) REVERT: E 263 ASP cc_start: 0.7655 (t0) cc_final: 0.7243 (t0) REVERT: F 62 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: F 333 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7863 (ttp80) REVERT: G 1392 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: I 167 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7967 (mttm) REVERT: J 154 MET cc_start: 0.7679 (tpp) cc_final: 0.7028 (mtt) REVERT: J 168 SER cc_start: 0.8869 (m) cc_final: 0.8553 (p) REVERT: J 174 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: J 222 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7545 (ttmm) REVERT: J 751 TYR cc_start: 0.7520 (t80) cc_final: 0.7261 (t80) outliers start: 77 outliers final: 45 residues processed: 372 average time/residue: 1.6857 time to fit residues: 717.4230 Evaluate side-chains 362 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 305 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS B 446 ASN C 230 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28847 Z= 0.327 Angle : 0.631 9.979 38993 Z= 0.313 Chirality : 0.045 0.327 4419 Planarity : 0.005 0.070 5049 Dihedral : 8.657 177.676 4058 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.85 % Allowed : 16.19 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.46 (0.14), residues: 3590 helix: 0.64 (0.13), residues: 1507 sheet: 0.28 (0.21), residues: 590 loop : 0.16 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G1367 HIS 0.005 0.001 HIS B 21 PHE 0.023 0.002 PHE G1274 TYR 0.021 0.002 TYR E 339 ARG 0.008 0.001 ARG G1265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 305 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7691 (ttp80) REVERT: B 62 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7952 (mpp) REVERT: B 449 THR cc_start: 0.8068 (m) cc_final: 0.7830 (p) REVERT: C 106 GLU cc_start: 0.8075 (tt0) cc_final: 0.7868 (mt-10) REVERT: C 307 MET cc_start: 0.8510 (mmp) cc_final: 0.7758 (mmt) REVERT: C 442 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7298 (mmp-170) REVERT: D 139 GLU cc_start: 0.7227 (pm20) cc_final: 0.6813 (pm20) REVERT: D 163 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (ttpp) REVERT: D 175 SER cc_start: 0.8246 (p) cc_final: 0.7972 (t) REVERT: D 184 GLU cc_start: 0.7952 (tp30) cc_final: 0.7565 (tm-30) REVERT: D 220 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: D 234 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7193 (mmm160) REVERT: D 263 ASP cc_start: 0.7433 (m-30) cc_final: 0.7217 (m-30) REVERT: E 112 GLU cc_start: 0.7724 (tt0) cc_final: 0.7484 (tt0) REVERT: E 159 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: E 252 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8014 (ptt180) REVERT: E 263 ASP cc_start: 0.7842 (t0) cc_final: 0.7424 (t0) REVERT: F 62 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: F 333 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: G 1265 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7544 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: I 16 LEU cc_start: 0.7843 (mm) cc_final: 0.7576 (tt) REVERT: I 23 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.6916 (m170) REVERT: I 167 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8009 (mttm) REVERT: J 128 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (m-40) REVERT: J 154 MET cc_start: 0.7662 (tpp) cc_final: 0.7019 (mtt) REVERT: J 168 SER cc_start: 0.8892 (m) cc_final: 0.8610 (p) REVERT: J 174 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: J 222 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7598 (ttmm) REVERT: J 751 TYR cc_start: 0.7596 (t80) cc_final: 0.7381 (t80) outliers start: 86 outliers final: 53 residues processed: 366 average time/residue: 1.7098 time to fit residues: 715.2613 Evaluate side-chains 362 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.9980 chunk 328 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 302 optimal weight: 0.2980 chunk 318 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28847 Z= 0.199 Angle : 0.575 12.857 38993 Z= 0.282 Chirality : 0.043 0.364 4419 Planarity : 0.004 0.064 5049 Dihedral : 8.328 176.099 4058 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.62 % Allowed : 16.79 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.63 (0.14), residues: 3590 helix: 0.83 (0.14), residues: 1508 sheet: 0.30 (0.21), residues: 581 loop : 0.23 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.004 0.001 HIS J 610 PHE 0.013 0.001 PHE G1501 TYR 0.021 0.001 TYR E 339 ARG 0.008 0.000 ARG G1296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 316 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8060 (tppp) REVERT: A 373 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7695 (ttp80) REVERT: A 401 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6899 (mtm180) REVERT: B 62 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7969 (mpp) REVERT: B 449 THR cc_start: 0.8050 (m) cc_final: 0.7837 (p) REVERT: C 106 GLU cc_start: 0.8041 (tt0) cc_final: 0.7833 (mt-10) REVERT: C 442 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7299 (mmp-170) REVERT: D 139 GLU cc_start: 0.7249 (pm20) cc_final: 0.6837 (pm20) REVERT: D 175 SER cc_start: 0.8191 (p) cc_final: 0.7953 (t) REVERT: D 184 GLU cc_start: 0.7917 (tp30) cc_final: 0.7630 (tm-30) REVERT: D 220 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: D 230 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8175 (tp30) REVERT: D 263 ASP cc_start: 0.7408 (m-30) cc_final: 0.7170 (m-30) REVERT: E 112 GLU cc_start: 0.7711 (tt0) cc_final: 0.7405 (tt0) REVERT: E 159 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (tppt) REVERT: E 252 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7992 (ptt180) REVERT: E 263 ASP cc_start: 0.7719 (t0) cc_final: 0.7324 (t0) REVERT: E 264 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.6855 (t) REVERT: F 62 MET cc_start: 0.8562 (ptt) cc_final: 0.8224 (mtp) REVERT: F 333 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: G 1265 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7584 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: I 16 LEU cc_start: 0.7868 (mm) cc_final: 0.7625 (tt) REVERT: I 167 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7951 (mttm) REVERT: J 128 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: J 154 MET cc_start: 0.7654 (tpp) cc_final: 0.7027 (mtt) REVERT: J 168 SER cc_start: 0.8896 (m) cc_final: 0.8629 (p) REVERT: J 222 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7541 (ttmm) outliers start: 79 outliers final: 49 residues processed: 374 average time/residue: 1.7102 time to fit residues: 728.7176 Evaluate side-chains 354 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 293 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 206 optimal weight: 0.0070 chunk 160 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28847 Z= 0.213 Angle : 0.585 13.142 38993 Z= 0.286 Chirality : 0.043 0.388 4419 Planarity : 0.004 0.067 5049 Dihedral : 8.270 176.855 4058 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.32 % Allowed : 17.48 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.63 (0.14), residues: 3590 helix: 0.83 (0.14), residues: 1514 sheet: 0.31 (0.21), residues: 571 loop : 0.22 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.004 0.001 HIS J 610 PHE 0.025 0.002 PHE D 223 TYR 0.025 0.001 TYR J 751 ARG 0.008 0.000 ARG G1296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 3.512 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8065 (tppp) REVERT: A 373 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7693 (ttp80) REVERT: B 62 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7984 (mpp) REVERT: B 449 THR cc_start: 0.8093 (m) cc_final: 0.7849 (p) REVERT: C 106 GLU cc_start: 0.8022 (tt0) cc_final: 0.7818 (mt-10) REVERT: C 442 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7268 (mmp-170) REVERT: D 139 GLU cc_start: 0.7266 (pm20) cc_final: 0.6858 (pm20) REVERT: D 175 SER cc_start: 0.8192 (p) cc_final: 0.7930 (t) REVERT: D 184 GLU cc_start: 0.7896 (tp30) cc_final: 0.7617 (tm-30) REVERT: D 220 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: D 263 ASP cc_start: 0.7419 (m-30) cc_final: 0.7180 (m-30) REVERT: E 112 GLU cc_start: 0.7709 (tt0) cc_final: 0.7404 (tt0) REVERT: E 159 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8500 (ttmt) REVERT: E 252 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8004 (ptt180) REVERT: E 263 ASP cc_start: 0.7715 (t0) cc_final: 0.7305 (t0) REVERT: E 264 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.6877 (t) REVERT: F 62 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: F 333 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7865 (ttp80) REVERT: G 1240 MET cc_start: 0.4458 (mpp) cc_final: 0.3973 (mpm) REVERT: G 1265 ARG cc_start: 0.7959 (ttm110) cc_final: 0.7695 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: H 442 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7580 (ttm-80) REVERT: I 16 LEU cc_start: 0.7893 (mm) cc_final: 0.7680 (tt) REVERT: I 23 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6800 (m170) REVERT: I 167 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7974 (mttm) REVERT: J 128 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: J 154 MET cc_start: 0.7689 (tpp) cc_final: 0.7051 (mtt) REVERT: J 168 SER cc_start: 0.8876 (m) cc_final: 0.8599 (p) REVERT: J 174 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: J 222 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7536 (ttmm) outliers start: 70 outliers final: 49 residues processed: 351 average time/residue: 1.7243 time to fit residues: 693.4111 Evaluate side-chains 354 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 291 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 ARG Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 252 ARG Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1233 LEU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 760 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.066621 restraints weight = 53434.563| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.93 r_work: 0.2830 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28847 Z= 0.322 Angle : 0.643 12.245 38993 Z= 0.317 Chirality : 0.046 0.390 4419 Planarity : 0.005 0.076 5049 Dihedral : 8.562 178.271 4058 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.78 % Allowed : 17.25 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.46 (0.14), residues: 3590 helix: 0.67 (0.13), residues: 1504 sheet: 0.32 (0.21), residues: 562 loop : 0.09 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 129 HIS 0.005 0.001 HIS B 21 PHE 0.018 0.002 PHE G1501 TYR 0.024 0.002 TYR J 751 ARG 0.006 0.001 ARG G1296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12573.15 seconds wall clock time: 221 minutes 57.76 seconds (13317.76 seconds total)