Starting phenix.real_space_refine on Wed Mar 20 19:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oor_17026/03_2024/8oor_17026_updated.pdb" } resolution = 2.87 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= 0.029 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 None 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: {'PTRANS': 22, '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: 14.36, per 1000 atoms: 0.51 Number of scatterers: 28371 At special positions: 0 Unit cell: (132.342, 161.934, 175.908, 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: 10.86 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: 162 helices and 30 sheets defined 41.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 58 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.550A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 257 through 263 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 321 removed outlier: 3.653A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 321 " --> pdb=" O ASN A 317 " (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: 4.383A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.103A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.705A 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: 3.718A 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 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.564A pdb=" N ILE B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' 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: 3.650A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 3.749A 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: 4.538A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.604A pdb=" N HIS B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.674A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.458A 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 Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.591A pdb=" N ILE C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for '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: 3.589A pdb=" N GLN C 182 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 184 " --> pdb=" O ILE C 181 " (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 264 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 321 removed outlier: 3.913A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 321 " --> pdb=" O ASN C 317 " (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: 4.574A 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 421 removed outlier: 4.128A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix removed outlier: 3.597A pdb=" N ASN C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.993A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.709A pdb=" N GLU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.538A 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 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 316 removed outlier: 4.190A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU D 316 " --> pdb=" O ASN D 312 " (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: 4.327A 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 396 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.851A 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: 6.394A pdb=" N GLN E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.708A 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: 5.626A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 Processing helix chain 'E' and resid 255 through 261 removed outlier: 4.230A pdb=" N SER E 261 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 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: 4.152A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 4.143A 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: 4.559A 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: 4.036A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 407 " --> pdb=" O ASN E 403 " (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: 3.931A 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 213 removed outlier: 4.406A 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: 3.583A pdb=" N SER F 261 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.778A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 3.879A 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: 4.338A 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 415 removed outlier: 4.098A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 435 through 445 Processing helix chain 'G' and resid 1224 through 1239 removed outlier: 3.725A pdb=" N GLN G1236 " --> pdb=" O SER G1232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G1237 " --> pdb=" O LEU G1233 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER G1238 " --> pdb=" O ARG G1234 " (cutoff:3.500A) removed outlier: 4.555A 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: 4.171A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1358 removed outlier: 3.914A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER G1358 " --> pdb=" O ASN G1354 " (cutoff:3.500A) Processing helix chain 'G' and resid 1366 through 1370 removed outlier: 3.709A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1375 through 1383 Processing helix chain 'G' and resid 1386 through 1395 removed outlier: 3.757A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1399 through 1406 removed outlier: 3.646A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1410 through 1412 No H-bonds generated for 'chain 'G' and resid 1410 through 1412' 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 1455 removed outlier: 5.676A pdb=" N ALA G1449 " --> pdb=" O LEU G1445 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG G1450 " --> pdb=" O MET G1446 " (cutoff:3.500A) 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: 3.714A pdb=" N GLU G1564 " --> pdb=" O GLU G1560 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLU G1567 " --> pdb=" O ARG G1563 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1591 removed outlier: 3.532A pdb=" N ASP G1583 " --> pdb=" O THR G1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 removed outlier: 4.101A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 20 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 191 through 199 Processing helix chain 'I' and resid 204 through 211 removed outlier: 3.624A pdb=" N ALA I 211 " --> pdb=" O GLN I 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 21 Processing helix chain 'J' and resid 43 through 51 Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 198 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: 3.538A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 280 No H-bonds generated for 'chain 'J' and resid 277 through 280' 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: 3.860A 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 666 Processing helix chain 'J' and resid 668 through 671 No H-bonds generated for 'chain 'J' and resid 668 through 671' Processing helix chain 'J' and resid 680 through 685 removed outlier: 4.340A 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: 3.871A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 727 through 736 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: 6.963A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.666A 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 168 through 174 removed outlier: 3.697A pdb=" N GLU A 138 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 163 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 136 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 190 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.865A 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 338 Processing sheet with id= E, first strand: chain 'B' and resid 359 through 364 removed outlier: 6.966A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 364 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 70 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLY B 71 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER B 332 " --> pdb=" O GLY B 71 " (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: 3.639A pdb=" N LEU B 158 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 138 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 163 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B 136 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP B 190 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 removed outlier: 5.748A 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: 6.960A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL C 328 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 69 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 330 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY C 71 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 5.921A 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: 3.749A pdb=" N THR C 157 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP C 190 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU C 195 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.242A 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 338 Processing sheet with id= M, first strand: chain 'D' and resid 353 through 357 removed outlier: 6.785A pdb=" N ALA D 72 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE D 356 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU D 74 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.253A 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: 6.469A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP D 190 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 205 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP D 195 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.182A 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: 6.874A pdb=" N ALA E 72 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE E 356 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU E 74 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR E 358 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA E 76 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLY E 77 " --> pdb=" O MET E 325 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER E 327 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 289 through 292 Processing sheet with id= S, first strand: chain 'E' and resid 200 through 202 removed outlier: 4.064A pdb=" N LYS E 200 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR E 161 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE E 145 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS E 159 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE E 147 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN E 157 " --> pdb=" O ILE E 147 " (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 353 through 357 removed outlier: 6.797A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 323 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE F 75 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET F 325 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 289 through 292 Processing sheet with id= W, first strand: chain 'F' and resid 168 through 173 removed outlier: 3.662A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN F 157 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS F 163 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL F 142 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP F 190 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER F 193 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS F 203 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP F 195 " --> pdb=" O ILE F 201 " (cutoff:3.500A) removed outlier: 6.318A 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: 6.353A 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: 6.481A 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: 7.699A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN J 63 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 6.695A 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 removed outlier: 3.560A pdb=" N LYS J 96 " --> pdb=" O ASP J 91 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 718 through 720 removed outlier: 6.690A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU J 204 " --> pdb=" O PHE J 687 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR J 689 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL J 206 " --> pdb=" O THR J 689 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3126 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: 10.00 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8406 1.33 - 1.45: 4236 1.45 - 1.57: 15956 1.57 - 1.70: 19 1.70 - 1.82: 230 Bond restraints: 28847 Sorted by residual: bond pdb=" CB CYS B 407 " pdb=" SG CYS B 407 " ideal model delta sigma weight residual 1.808 1.702 0.106 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB THR D 337 " pdb=" CG2 THR D 337 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 bond pdb=" CB ARG G1339 " pdb=" CG ARG G1339 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.01e+00 bond pdb=" CB ARG A 379 " pdb=" CG ARG A 379 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.97e+00 bond pdb=" CG ARG A 118 " pdb=" CD ARG A 118 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.41e+00 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 96.68 - 105.33: 645 105.33 - 113.98: 16947 113.98 - 122.64: 18209 122.64 - 131.29: 3145 131.29 - 139.95: 47 Bond angle restraints: 38993 Sorted by residual: angle pdb=" CA LEU B 88 " pdb=" CB LEU B 88 " pdb=" CG LEU B 88 " ideal model delta sigma weight residual 116.30 132.09 -15.79 3.50e+00 8.16e-02 2.04e+01 angle pdb=" CB ARG C 118 " pdb=" CG ARG C 118 " pdb=" CD ARG C 118 " ideal model delta sigma weight residual 111.30 121.09 -9.79 2.30e+00 1.89e-01 1.81e+01 angle pdb=" CA ARG A 334 " pdb=" CB ARG A 334 " pdb=" CG ARG A 334 " ideal model delta sigma weight residual 114.10 106.60 7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU B 158 " pdb=" CB LEU B 158 " pdb=" CG LEU B 158 " ideal model delta sigma weight residual 116.30 129.25 -12.95 3.50e+00 8.16e-02 1.37e+01 angle pdb=" C GLU B 87 " pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta sigma weight residual 121.18 128.14 -6.96 1.98e+00 2.55e-01 1.23e+01 ... (remaining 38988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 17375 35.57 - 71.15: 267 71.15 - 106.72: 38 106.72 - 142.29: 4 142.29 - 177.86: 3 Dihedral angle restraints: 17687 sinusoidal: 7292 harmonic: 10395 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 122.13 177.86 1 2.00e+01 2.50e-03 4.80e+01 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 300.00 129.07 170.92 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 151.14 148.86 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2508 0.051 - 0.101: 1439 0.101 - 0.152: 405 0.152 - 0.202: 61 0.202 - 0.253: 6 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CA GLU I 158 " pdb=" N GLU I 158 " pdb=" C GLU I 158 " pdb=" CB GLU I 158 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C4' ADP F 501 " pdb=" O3' ADP F 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4416 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.418 9.50e-02 1.11e+02 1.88e-01 2.57e+01 pdb=" NE ARG F 437 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 8 " 0.348 9.50e-02 1.11e+02 1.57e-01 1.75e+01 pdb=" NE ARG C 8 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 8 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 8 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 8 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 118 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.59e+01 pdb=" NE ARG B 118 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 118 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 118 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 118 " -0.000 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 107 2.51 - 3.11: 21876 3.11 - 3.71: 43312 3.71 - 4.30: 67189 4.30 - 4.90: 109194 Nonbonded interactions: 241678 Sorted by model distance: nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.914 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.088 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.098 2.170 nonbonded pdb=" OD1 ASP J 137 " pdb=" OH TYR J 180 " model vdw 2.139 2.440 nonbonded pdb=" O GLU E 168 " pdb=" OH TYR I 188 " model vdw 2.141 2.440 ... (remaining 241673 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: 3.390 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: 0.030 Extract box with map and model: 10.790 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 72.550 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.140 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.011 0.106 28847 Z= 0.719 Angle : 0.960 15.794 38993 Z= 0.516 Chirality : 0.063 0.253 4419 Planarity : 0.012 0.188 5049 Dihedral : 14.051 177.863 10997 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -0.86 (0.13), residues: 3590 helix: -1.23 (0.11), residues: 1510 sheet: 0.36 (0.21), residues: 547 loop : 0.04 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G1367 HIS 0.020 0.003 HIS B 19 PHE 0.041 0.004 PHE G1501 TYR 0.033 0.005 TYR I 179 ARG 0.036 0.003 ARG F 437 *********************** 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 592 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7733 (mm-30) REVERT: A 216 LEU cc_start: 0.8283 (mt) cc_final: 0.8042 (mt) REVERT: A 419 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7675 (ttm170) REVERT: D 208 TYR cc_start: 0.8374 (p90) cc_final: 0.8165 (p90) REVERT: D 235 LYS cc_start: 0.8540 (tttt) cc_final: 0.8287 (ptmt) REVERT: D 237 VAL cc_start: 0.9089 (t) cc_final: 0.8879 (p) REVERT: D 299 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8388 (mt-10) REVERT: F 193 SER cc_start: 0.9082 (p) cc_final: 0.8861 (m) REVERT: F 263 ASP cc_start: 0.7986 (t70) cc_final: 0.7712 (t0) REVERT: F 325 MET cc_start: 0.9042 (ptp) cc_final: 0.8835 (ptp) REVERT: F 364 ASP cc_start: 0.8240 (t0) cc_final: 0.7734 (t70) REVERT: G 1372 ASP cc_start: 0.8366 (t0) cc_final: 0.8137 (t0) REVERT: G 1479 ASP cc_start: 0.7695 (p0) cc_final: 0.7480 (p0) REVERT: G 1554 LYS cc_start: 0.9075 (mttt) cc_final: 0.7637 (tttp) REVERT: G 1557 LYS cc_start: 0.8825 (tptm) cc_final: 0.8496 (mtmt) REVERT: I 204 MET cc_start: 0.8484 (mmm) cc_final: 0.8276 (mmm) REVERT: J 174 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8101 (mt-10) REVERT: J 751 TYR cc_start: 0.8421 (t80) cc_final: 0.8043 (t80) outliers start: 0 outliers final: 1 residues processed: 592 average time/residue: 1.8972 time to fit residues: 1257.7212 Evaluate side-chains 312 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 323 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 248 ASN A 381 GLN A 409 GLN B 19 HIS ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 60 HIS C 86 GLN C 230 HIS C 421 ASN D 24 HIS D 65 GLN E 225 GLN F 357 ASN ** F 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1235 ASN G1287 HIS G1345 HIS I 19 GLN I 23 HIS ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 HIS J 696 GLN J 722 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28847 Z= 0.198 Angle : 0.599 11.000 38993 Z= 0.304 Chirality : 0.044 0.181 4419 Planarity : 0.004 0.057 5049 Dihedral : 8.812 160.840 4060 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.72 % Allowed : 9.47 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.61 (0.13), residues: 3590 helix: 0.50 (0.13), residues: 1521 sheet: 0.58 (0.21), residues: 568 loop : 0.46 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.007 0.001 HIS G1345 PHE 0.017 0.001 PHE G1274 TYR 0.021 0.001 TYR A 193 ARG 0.008 0.001 ARG J 748 *********************** 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 446 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 394 time to evaluate : 3.255 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9036 (tp) cc_final: 0.8749 (tp) REVERT: A 263 GLN cc_start: 0.8268 (mt0) cc_final: 0.8044 (mt0) REVERT: A 286 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: A 419 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7681 (ttm170) REVERT: B 60 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7475 (m90) REVERT: B 114 MET cc_start: 0.8597 (tpt) cc_final: 0.8303 (tpp) REVERT: B 137 THR cc_start: 0.9019 (m) cc_final: 0.8809 (p) REVERT: B 250 ARG cc_start: 0.7694 (ttt90) cc_final: 0.7296 (ttt90) REVERT: C 6 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6937 (mt-10) REVERT: C 8 ARG cc_start: 0.7470 (tpm-80) cc_final: 0.6949 (tpm-80) REVERT: C 433 GLU cc_start: 0.8089 (tp30) cc_final: 0.7828 (tp30) REVERT: D 61 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7979 (mm-30) REVERT: D 65 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: D 137 ILE cc_start: 0.9042 (pt) cc_final: 0.8639 (mp) REVERT: D 200 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8594 (mmtt) REVERT: D 217 MET cc_start: 0.7379 (mtp) cc_final: 0.7038 (mtp) REVERT: D 237 VAL cc_start: 0.9165 (t) cc_final: 0.8913 (p) REVERT: D 304 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7927 (p0) REVERT: E 96 GLN cc_start: 0.7756 (tp40) cc_final: 0.7421 (tm-30) REVERT: F 171 TYR cc_start: 0.9105 (m-80) cc_final: 0.8858 (m-80) REVERT: F 263 ASP cc_start: 0.7794 (t70) cc_final: 0.7397 (OUTLIER) REVERT: F 285 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7978 (mt-10) REVERT: J 174 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8082 (mt-10) outliers start: 52 outliers final: 8 residues processed: 426 average time/residue: 1.7196 time to fit residues: 830.1560 Evaluate side-chains 320 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain J residue 288 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 chunk 269 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 323 optimal weight: 0.5980 chunk 349 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 274 GLN D 343 HIS E 24 HIS E 312 ASN F 301 HIS F 357 ASN I 19 GLN I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 HIS J 722 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28847 Z= 0.316 Angle : 0.639 13.523 38993 Z= 0.318 Chirality : 0.045 0.232 4419 Planarity : 0.005 0.064 5049 Dihedral : 8.429 143.189 4058 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 11.56 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.63 (0.13), residues: 1513 sheet: 0.62 (0.21), residues: 575 loop : 0.32 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 129 HIS 0.008 0.001 HIS B 242 PHE 0.022 0.002 PHE G1274 TYR 0.023 0.002 TYR A 193 ARG 0.006 0.001 ARG J 748 *********************** 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 389 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 315 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (mt0) REVERT: A 159 LEU cc_start: 0.9020 (tp) cc_final: 0.8718 (tp) REVERT: A 286 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: A 419 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7752 (ttm170) REVERT: B 60 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7566 (m90) REVERT: B 250 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7242 (ttt90) REVERT: B 265 MET cc_start: 0.8915 (mmt) cc_final: 0.8573 (mmm) REVERT: C 143 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: C 427 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: D 134 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: D 137 ILE cc_start: 0.8993 (pt) cc_final: 0.8556 (mp) REVERT: D 200 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8601 (mmtt) REVERT: D 217 MET cc_start: 0.7498 (mtp) cc_final: 0.7078 (mtp) REVERT: D 234 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6874 (mtp180) REVERT: D 237 VAL cc_start: 0.9178 (t) cc_final: 0.8881 (p) REVERT: E 96 GLN cc_start: 0.7743 (tp40) cc_final: 0.7460 (tm-30) REVERT: E 112 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: E 135 SER cc_start: 0.8880 (m) cc_final: 0.8501 (p) REVERT: E 418 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8266 (tptt) REVERT: F 171 TYR cc_start: 0.9119 (m-80) cc_final: 0.8852 (m-80) REVERT: F 263 ASP cc_start: 0.7838 (t70) cc_final: 0.7472 (t0) REVERT: F 299 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: G 1240 MET cc_start: 0.6668 (mpm) cc_final: 0.5750 (mtt) REVERT: G 1275 GLU cc_start: 0.7956 (tp30) cc_final: 0.7511 (tp30) REVERT: I 14 GLN cc_start: 0.8848 (mm-40) cc_final: 0.7582 (mm-40) REVERT: J 90 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7653 (tpt90) REVERT: J 174 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8097 (mt-10) REVERT: J 667 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7950 (mt0) outliers start: 74 outliers final: 25 residues processed: 369 average time/residue: 1.7195 time to fit residues: 720.9498 Evaluate side-chains 329 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 207 GLN Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 325 optimal weight: 8.9990 chunk 344 optimal weight: 0.0670 chunk 169 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN D 65 GLN D 232 GLN E 254 GLN F 96 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 645 GLN J 722 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2875 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= 0.218 Angle : 0.576 16.981 38993 Z= 0.282 Chirality : 0.043 0.248 4419 Planarity : 0.004 0.053 5049 Dihedral : 7.881 123.219 4058 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.32 % Allowed : 13.01 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.81 (0.14), residues: 3590 helix: 0.87 (0.13), residues: 1512 sheet: 0.64 (0.21), residues: 588 loop : 0.32 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.006 0.001 HIS I 13 PHE 0.023 0.001 PHE G1274 TYR 0.022 0.001 TYR A 193 ARG 0.007 0.000 ARG J 602 *********************** 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 400 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 330 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: A 159 LEU cc_start: 0.9007 (tp) cc_final: 0.8708 (tp) REVERT: A 263 GLN cc_start: 0.8311 (mt0) cc_final: 0.8079 (mt0) REVERT: A 419 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7776 (ttm170) REVERT: B 60 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7539 (m90) REVERT: B 250 ARG cc_start: 0.7655 (ttt90) cc_final: 0.7257 (ttt90) REVERT: B 265 MET cc_start: 0.8881 (mmt) cc_final: 0.8560 (mmm) REVERT: B 429 GLN cc_start: 0.8595 (mp10) cc_final: 0.8381 (pm20) REVERT: C 427 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: C 433 GLU cc_start: 0.8119 (tp30) cc_final: 0.7815 (tp30) REVERT: D 61 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 65 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: D 137 ILE cc_start: 0.8895 (pt) cc_final: 0.8603 (mp) REVERT: D 200 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8631 (mmtt) REVERT: D 217 MET cc_start: 0.7508 (mtp) cc_final: 0.7116 (mtp) REVERT: D 234 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6856 (mtp180) REVERT: D 237 VAL cc_start: 0.9113 (t) cc_final: 0.8701 (m) REVERT: D 416 ARG cc_start: 0.8479 (mpp80) cc_final: 0.8196 (mpp80) REVERT: E 96 GLN cc_start: 0.7670 (tp40) cc_final: 0.7426 (tm-30) REVERT: E 112 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: E 418 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8228 (tptt) REVERT: F 109 PHE cc_start: 0.8870 (m-80) cc_final: 0.8645 (m-80) REVERT: F 171 TYR cc_start: 0.9099 (m-80) cc_final: 0.8794 (m-80) REVERT: F 263 ASP cc_start: 0.7737 (t70) cc_final: 0.7414 (t0) REVERT: G 1240 MET cc_start: 0.6851 (mpm) cc_final: 0.5920 (mtt) REVERT: J 90 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7526 (tmt170) REVERT: J 174 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8085 (mt-10) REVERT: J 667 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7880 (mt0) outliers start: 70 outliers final: 23 residues processed: 376 average time/residue: 1.7870 time to fit residues: 765.1124 Evaluate side-chains 323 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 207 GLN Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 256 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN E 65 GLN G1376 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2993 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= 0.229 Angle : 0.581 18.263 38993 Z= 0.284 Chirality : 0.043 0.269 4419 Planarity : 0.004 0.053 5049 Dihedral : 7.779 122.299 4058 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.02 % Allowed : 13.97 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.79 (0.14), residues: 3590 helix: 0.90 (0.13), residues: 1520 sheet: 0.67 (0.21), residues: 586 loop : 0.24 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1367 HIS 0.005 0.001 HIS B 242 PHE 0.024 0.001 PHE G1274 TYR 0.023 0.001 TYR A 193 ARG 0.012 0.000 ARG F 234 *********************** 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 371 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 310 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 86 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: A 159 LEU cc_start: 0.9015 (tp) cc_final: 0.8741 (tp) REVERT: A 263 GLN cc_start: 0.8324 (mt0) cc_final: 0.8090 (mt0) REVERT: A 419 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7854 (ttm170) REVERT: B 60 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7644 (m90) REVERT: B 250 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7245 (ttt90) REVERT: B 265 MET cc_start: 0.8913 (mmt) cc_final: 0.8642 (mmm) REVERT: B 429 GLN cc_start: 0.8615 (mp10) cc_final: 0.8390 (pm20) REVERT: C 8 ARG cc_start: 0.7541 (mmm160) cc_final: 0.7267 (mmm160) REVERT: C 143 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: C 427 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: C 433 GLU cc_start: 0.8159 (tp30) cc_final: 0.7873 (tp30) REVERT: D 134 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: D 137 ILE cc_start: 0.8850 (pt) cc_final: 0.8599 (mp) REVERT: D 200 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8615 (mmtt) REVERT: D 217 MET cc_start: 0.7529 (mtp) cc_final: 0.7128 (mtp) REVERT: D 234 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6896 (mtp180) REVERT: D 236 GLU cc_start: 0.7540 (mp0) cc_final: 0.7338 (mp0) REVERT: D 237 VAL cc_start: 0.9132 (t) cc_final: 0.8725 (m) REVERT: D 416 ARG cc_start: 0.8454 (mpp80) cc_final: 0.8183 (mpp80) REVERT: E 96 GLN cc_start: 0.7718 (tp40) cc_final: 0.7472 (tm-30) REVERT: E 418 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8208 (tptt) REVERT: F 28 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7030 (mtt180) REVERT: F 109 PHE cc_start: 0.8804 (m-80) cc_final: 0.8567 (m-80) REVERT: F 171 TYR cc_start: 0.9094 (m-80) cc_final: 0.8842 (m-80) REVERT: F 263 ASP cc_start: 0.7706 (t70) cc_final: 0.7406 (t0) REVERT: G 1240 MET cc_start: 0.6932 (mpm) cc_final: 0.6034 (mtt) REVERT: G 1275 GLU cc_start: 0.7943 (tp30) cc_final: 0.7547 (tp30) REVERT: G 1435 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: I 30 ARG cc_start: 0.8716 (mtp85) cc_final: 0.8490 (mtp85) REVERT: J 94 MET cc_start: 0.7473 (mpm) cc_final: 0.7201 (mpm) REVERT: J 174 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8047 (mt-10) REVERT: J 667 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7817 (mt0) outliers start: 61 outliers final: 27 residues processed: 353 average time/residue: 1.7630 time to fit residues: 708.7060 Evaluate side-chains 328 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 183 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1435 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 207 GLN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Chi-restraints excluded: chain J residue 667 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.0020 chunk 84 optimal weight: 3.9990 chunk 344 optimal weight: 0.0370 chunk 285 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 180 optimal weight: 0.7980 overall best weight: 0.4666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN E 24 HIS E 65 GLN E 359 HIS ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28847 Z= 0.147 Angle : 0.533 17.742 38993 Z= 0.258 Chirality : 0.042 0.264 4419 Planarity : 0.004 0.043 5049 Dihedral : 7.259 123.159 4058 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.75 % Allowed : 14.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 1.07 (0.14), residues: 3590 helix: 1.22 (0.13), residues: 1512 sheet: 0.71 (0.21), residues: 581 loop : 0.35 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G1367 HIS 0.003 0.001 HIS G1345 PHE 0.022 0.001 PHE G1274 TYR 0.021 0.001 TYR A 193 ARG 0.009 0.000 ARG J 602 *********************** 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 403 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 350 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 159 LEU cc_start: 0.8999 (tp) cc_final: 0.8749 (tp) REVERT: A 419 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7633 (ttp80) REVERT: B 60 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7590 (m90) REVERT: B 114 MET cc_start: 0.8623 (tpt) cc_final: 0.8377 (tpp) REVERT: B 250 ARG cc_start: 0.7604 (ttt90) cc_final: 0.7224 (ttt90) REVERT: B 429 GLN cc_start: 0.8583 (mp10) cc_final: 0.8335 (pm20) REVERT: C 8 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7225 (mmm160) REVERT: C 433 GLU cc_start: 0.8153 (tp30) cc_final: 0.7792 (tp30) REVERT: D 137 ILE cc_start: 0.8857 (pt) cc_final: 0.8607 (mp) REVERT: D 217 MET cc_start: 0.7512 (mtp) cc_final: 0.7141 (mtp) REVERT: E 96 GLN cc_start: 0.7607 (tp40) cc_final: 0.7397 (tm-30) REVERT: E 112 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: E 418 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8235 (tptt) REVERT: F 28 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7045 (mtt180) REVERT: F 109 PHE cc_start: 0.8715 (m-80) cc_final: 0.8463 (m-80) REVERT: F 171 TYR cc_start: 0.9017 (m-80) cc_final: 0.8758 (m-80) REVERT: F 263 ASP cc_start: 0.7451 (t70) cc_final: 0.7233 (t0) REVERT: G 1240 MET cc_start: 0.6923 (mpm) cc_final: 0.6079 (mtt) REVERT: G 1275 GLU cc_start: 0.7946 (tp30) cc_final: 0.7523 (tp30) REVERT: G 1562 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8564 (pp) REVERT: G 1585 MET cc_start: 0.8850 (tpp) cc_final: 0.8548 (tpp) REVERT: J 94 MET cc_start: 0.7532 (mpm) cc_final: 0.7293 (mpm) REVERT: J 106 TYR cc_start: 0.7861 (m-80) cc_final: 0.6978 (m-80) REVERT: J 174 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7996 (mt-10) outliers start: 53 outliers final: 18 residues processed: 381 average time/residue: 1.7193 time to fit residues: 753.0734 Evaluate side-chains 328 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 305 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1562 LEU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 HIS D 232 GLN E 65 GLN E 232 GLN F 96 GLN F 452 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 GLN J 73 ASN J 237 HIS J 667 GLN ** J 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 28847 Z= 0.409 Angle : 0.676 17.051 38993 Z= 0.333 Chirality : 0.047 0.289 4419 Planarity : 0.005 0.068 5049 Dihedral : 8.047 118.620 4058 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.32 % Allowed : 15.56 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.51 (0.14), residues: 3590 helix: 0.63 (0.13), residues: 1526 sheet: 0.58 (0.21), residues: 591 loop : 0.12 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G1367 HIS 0.007 0.001 HIS B 242 PHE 0.031 0.002 PHE G1274 TYR 0.022 0.002 TYR A 193 ARG 0.010 0.001 ARG F 234 *********************** 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 368 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 298 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (tp) REVERT: A 86 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: A 159 LEU cc_start: 0.8986 (tp) cc_final: 0.8699 (tp) REVERT: A 419 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7608 (ttp80) REVERT: B 60 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7599 (m90) REVERT: B 250 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7294 (ttt90) REVERT: B 394 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8119 (ttt-90) REVERT: B 423 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7341 (mtm180) REVERT: C 304 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8556 (mm-30) REVERT: C 433 GLU cc_start: 0.8248 (tp30) cc_final: 0.7846 (tp30) REVERT: D 137 ILE cc_start: 0.8821 (pt) cc_final: 0.8605 (mp) REVERT: D 200 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8651 (mmtt) REVERT: D 217 MET cc_start: 0.7543 (mtp) cc_final: 0.7124 (mtp) REVERT: D 237 VAL cc_start: 0.9228 (t) cc_final: 0.8863 (p) REVERT: D 416 ARG cc_start: 0.8429 (mpp80) cc_final: 0.8174 (mpp80) REVERT: E 96 GLN cc_start: 0.7712 (tp40) cc_final: 0.7486 (tm-30) REVERT: E 112 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: E 273 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: E 418 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8180 (tptt) REVERT: F 28 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6898 (mtt180) REVERT: F 171 TYR cc_start: 0.9111 (m-80) cc_final: 0.8881 (m-80) REVERT: F 263 ASP cc_start: 0.7675 (t70) cc_final: 0.7444 (t0) REVERT: G 1240 MET cc_start: 0.6948 (mpm) cc_final: 0.6009 (ttt) REVERT: G 1299 THR cc_start: 0.8720 (m) cc_final: 0.8482 (t) REVERT: G 1435 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: G 1578 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: J 106 TYR cc_start: 0.7988 (m-80) cc_final: 0.7117 (m-80) REVERT: J 174 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8110 (mt-10) outliers start: 70 outliers final: 30 residues processed: 353 average time/residue: 1.7077 time to fit residues: 686.4877 Evaluate side-chains 320 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 1256 THR Chi-restraints excluded: chain G residue 1306 SER Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1435 GLU Chi-restraints excluded: chain G residue 1439 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1541 THR Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 218 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28847 Z= 0.207 Angle : 0.580 11.053 38993 Z= 0.284 Chirality : 0.043 0.292 4419 Planarity : 0.004 0.073 5049 Dihedral : 7.605 120.891 4058 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.95 % Allowed : 16.32 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.77 (0.14), residues: 3590 helix: 0.94 (0.13), residues: 1510 sheet: 0.61 (0.21), residues: 589 loop : 0.19 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.005 0.001 HIS G1345 PHE 0.030 0.001 PHE J 98 TYR 0.022 0.001 TYR A 193 ARG 0.017 0.000 ARG F 234 *********************** 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 368 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 309 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8461 (tp) REVERT: A 159 LEU cc_start: 0.8967 (tp) cc_final: 0.8696 (tp) REVERT: A 419 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7576 (ttp80) REVERT: B 250 ARG cc_start: 0.7667 (ttt90) cc_final: 0.7262 (ttt90) REVERT: B 394 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8038 (ttt-90) REVERT: C 427 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 433 GLU cc_start: 0.8207 (tp30) cc_final: 0.7847 (tp30) REVERT: D 65 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: E 96 GLN cc_start: 0.7688 (tp40) cc_final: 0.7469 (tm-30) REVERT: E 112 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: E 273 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: E 418 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8200 (tptt) REVERT: F 28 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6921 (mtt180) REVERT: F 109 PHE cc_start: 0.8705 (m-80) cc_final: 0.8414 (m-80) REVERT: F 171 TYR cc_start: 0.9097 (m-80) cc_final: 0.8844 (m-80) REVERT: F 263 ASP cc_start: 0.7604 (t70) cc_final: 0.7380 (t0) REVERT: F 364 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: G 1240 MET cc_start: 0.6990 (mpm) cc_final: 0.6089 (mtt) REVERT: G 1275 GLU cc_start: 0.8004 (tp30) cc_final: 0.7653 (tp30) REVERT: G 1299 THR cc_start: 0.8713 (m) cc_final: 0.8487 (t) REVERT: G 1435 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: G 1578 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7186 (mtm) REVERT: J 106 TYR cc_start: 0.7946 (m-80) cc_final: 0.7116 (m-80) REVERT: J 174 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8036 (mt-10) outliers start: 59 outliers final: 29 residues processed: 349 average time/residue: 1.7618 time to fit residues: 700.2982 Evaluate side-chains 327 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 288 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain G residue 1256 THR Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1435 GLU Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER 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: 4.9990 chunk 299 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 chunk 318 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 202 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: 0.8546 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28847 Z= 0.181 Angle : 0.576 11.812 38993 Z= 0.281 Chirality : 0.042 0.233 4419 Planarity : 0.004 0.081 5049 Dihedral : 7.365 120.937 4058 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.62 % Allowed : 16.89 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.86 (0.14), residues: 3590 helix: 1.08 (0.13), residues: 1507 sheet: 0.60 (0.21), residues: 587 loop : 0.19 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1367 HIS 0.004 0.001 HIS G1345 PHE 0.027 0.001 PHE G1274 TYR 0.022 0.001 TYR A 193 ARG 0.020 0.000 ARG F 234 *********************** 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 359 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 310 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 159 LEU cc_start: 0.8948 (tp) cc_final: 0.8696 (tp) REVERT: A 419 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7549 (ttp80) REVERT: B 250 ARG cc_start: 0.7626 (ttt90) cc_final: 0.7225 (ttt90) REVERT: B 269 MET cc_start: 0.7805 (mtm) cc_final: 0.6718 (mmt) REVERT: C 424 THR cc_start: 0.9000 (p) cc_final: 0.8768 (t) REVERT: C 433 GLU cc_start: 0.8243 (tp30) cc_final: 0.7936 (tp30) REVERT: D 65 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: D 217 MET cc_start: 0.7509 (mtp) cc_final: 0.7066 (mtp) REVERT: D 234 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7216 (tpt-90) REVERT: E 96 GLN cc_start: 0.7654 (tp40) cc_final: 0.7438 (tm-30) REVERT: E 112 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: E 273 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: E 418 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8195 (tptt) REVERT: F 28 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6951 (mtt180) REVERT: F 109 PHE cc_start: 0.8676 (m-80) cc_final: 0.8407 (m-80) REVERT: F 171 TYR cc_start: 0.9068 (m-80) cc_final: 0.8767 (m-80) REVERT: F 263 ASP cc_start: 0.7514 (t70) cc_final: 0.7308 (t0) REVERT: G 1240 MET cc_start: 0.6980 (mpm) cc_final: 0.6101 (mtt) REVERT: G 1275 GLU cc_start: 0.8009 (tp30) cc_final: 0.7639 (tp30) REVERT: G 1299 THR cc_start: 0.8698 (m) cc_final: 0.8481 (t) REVERT: G 1578 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7155 (mtm) REVERT: J 90 ARG cc_start: 0.7885 (tmt170) cc_final: 0.7591 (tpt170) REVERT: J 93 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8332 (mppt) REVERT: J 106 TYR cc_start: 0.7895 (m-80) cc_final: 0.7078 (m-80) REVERT: J 174 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8016 (mt-10) outliers start: 49 outliers final: 23 residues processed: 349 average time/residue: 1.7485 time to fit residues: 693.0792 Evaluate side-chains 325 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 326 optimal weight: 0.0980 chunk 282 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 GLN F 452 ASN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3434 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= 0.209 Angle : 0.588 11.610 38993 Z= 0.288 Chirality : 0.043 0.295 4419 Planarity : 0.004 0.073 5049 Dihedral : 7.400 118.851 4058 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.19 % Allowed : 17.42 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.83 (0.14), residues: 3590 helix: 1.05 (0.13), residues: 1506 sheet: 0.60 (0.21), residues: 587 loop : 0.18 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G1367 HIS 0.004 0.001 HIS G1345 PHE 0.027 0.001 PHE G1274 TYR 0.023 0.001 TYR A 193 ARG 0.019 0.000 ARG C 8 ********************** 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 338 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 302 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 159 LEU cc_start: 0.8979 (tp) cc_final: 0.8704 (tp) REVERT: A 419 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7577 (ttp80) REVERT: B 250 ARG cc_start: 0.7636 (ttt90) cc_final: 0.7231 (ttt90) REVERT: B 269 MET cc_start: 0.7832 (mtm) cc_final: 0.6745 (mmt) REVERT: C 433 GLU cc_start: 0.8246 (tp30) cc_final: 0.7943 (tp30) REVERT: D 65 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: D 217 MET cc_start: 0.7512 (mtp) cc_final: 0.7106 (mtp) REVERT: E 112 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: E 273 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: E 418 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8230 (tptt) REVERT: F 28 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6926 (mtt180) REVERT: F 109 PHE cc_start: 0.8687 (m-80) cc_final: 0.8413 (m-80) REVERT: F 171 TYR cc_start: 0.9076 (m-80) cc_final: 0.8766 (m-80) REVERT: G 1240 MET cc_start: 0.6974 (mpm) cc_final: 0.6087 (mtt) REVERT: G 1275 GLU cc_start: 0.8018 (tp30) cc_final: 0.7563 (tp30) REVERT: G 1299 THR cc_start: 0.8713 (m) cc_final: 0.8498 (t) REVERT: G 1578 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7151 (mtm) REVERT: H 464 GLU cc_start: 0.8279 (pm20) cc_final: 0.7689 (pm20) REVERT: J 90 ARG cc_start: 0.7842 (tmt170) cc_final: 0.7618 (tpt170) REVERT: J 93 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8298 (mppt) REVERT: J 174 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8006 (mt-10) outliers start: 36 outliers final: 26 residues processed: 325 average time/residue: 1.8469 time to fit residues: 682.5105 Evaluate side-chains 321 residues out of total 3020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 289 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1412 ASP Chi-restraints excluded: chain G residue 1534 LYS Chi-restraints excluded: chain G residue 1578 MET Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 0.0060 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 GLN ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.064075 restraints weight = 54503.523| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.87 r_work: 0.2793 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28847 Z= 0.175 Angle : 0.573 11.739 38993 Z= 0.279 Chirality : 0.042 0.234 4419 Planarity : 0.004 0.068 5049 Dihedral : 7.192 118.697 4058 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.16 % Allowed : 17.72 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: 0.92 (0.14), residues: 3590 helix: 1.13 (0.13), residues: 1512 sheet: 0.61 (0.21), residues: 590 loop : 0.22 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1367 HIS 0.004 0.001 HIS G1345 PHE 0.026 0.001 PHE G1274 TYR 0.022 0.001 TYR A 193 ARG 0.014 0.000 ARG J 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11931.62 seconds wall clock time: 211 minutes 6.12 seconds (12666.12 seconds total)