Starting phenix.real_space_refine on Mon Aug 25 13:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ooc_17010/08_2025/8ooc_17010.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 17787 2.51 5 N 5035 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28371 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3401 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3414 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 14, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3394 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 283 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3582 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 419} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.69, per 1000 atoms: 0.20 Number of scatterers: 28371 At special positions: 0 Unit cell: (133.164, 161.934, 176.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 15 15.00 Mg 1 11.99 O 5400 8.00 N 5035 7.00 C 17787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 884.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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... Secondary structure from input PDB file: 156 helices and 31 sheets defined 45.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.679A pdb=" N LEU A 264 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.995A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.642A pdb=" N GLN A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.703A pdb=" N CYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 411 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 427 through 438 removed outlier: 3.530A pdb=" N ILE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.527A pdb=" N HIS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 257 through 266 removed outlier: 6.859A pdb=" N GLN B 263 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 264 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.768A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 388 through 402 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.904A pdb=" N LEU B 411 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 427 through 438 removed outlier: 3.863A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'C' and resid 43 through 59 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.817A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 388 through 402 Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.724A pdb=" N LEU C 411 " --> pdb=" O CYS C 407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.528A pdb=" N GLU C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.619A pdb=" N GLY D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.784A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.686A pdb=" N ARG D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 304 through 315 removed outlier: 4.836A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 382 through 396 Processing helix chain 'D' and resid 397 through 415 removed outlier: 3.616A pdb=" N ILE D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 106 through 109 removed outlier: 3.615A pdb=" N PHE E 109 " --> pdb=" O SER E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 208 through 214 removed outlier: 5.013A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.505A pdb=" N ARG E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 Processing helix chain 'E' and resid 304 through 315 removed outlier: 3.936A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 382 through 397 Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.972A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.601A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 Processing helix chain 'F' and resid 209 through 213 removed outlier: 4.178A pdb=" N ARG F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 4.281A pdb=" N ARG F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 256 No H-bonds generated for 'chain 'F' and resid 254 through 256' Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.583A pdb=" N ARG F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 304 through 315 removed outlier: 3.950A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 382 through 397 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.081A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 446 through 449 Processing helix chain 'G' and resid 1223 through 1235 Processing helix chain 'G' and resid 1235 through 1240 removed outlier: 3.780A pdb=" N ILE G1239 " --> pdb=" O ASN G1235 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1270 Processing helix chain 'G' and resid 1270 through 1275 removed outlier: 4.001A pdb=" N PHE G1274 " --> pdb=" O HIS G1270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1316 through 1321 Processing helix chain 'G' and resid 1333 through 1345 removed outlier: 4.525A pdb=" N GLY G1337 " --> pdb=" O ASN G1333 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE G1338 " --> pdb=" O LEU G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1351 through 1357 removed outlier: 3.553A pdb=" N SER G1357 " --> pdb=" O GLU G1353 " (cutoff:3.500A) Processing helix chain 'G' and resid 1365 through 1370 removed outlier: 3.749A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) Processing helix chain 'G' and resid 1374 through 1384 Processing helix chain 'G' and resid 1385 through 1394 Processing helix chain 'G' and resid 1398 through 1407 removed outlier: 3.723A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1417 through 1421 Processing helix chain 'G' and resid 1423 through 1428 Processing helix chain 'G' and resid 1429 through 1435 removed outlier: 4.060A pdb=" N VAL G1433 " --> pdb=" O ASN G1429 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G1435 " --> pdb=" O LYS G1431 " (cutoff:3.500A) Processing helix chain 'G' and resid 1440 through 1446 Processing helix chain 'G' and resid 1447 through 1456 Processing helix chain 'G' and resid 1480 through 1492 removed outlier: 3.668A pdb=" N VAL G1484 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'G' and resid 1493 through 1502 Processing helix chain 'G' and resid 1504 through 1514 Processing helix chain 'G' and resid 1544 through 1551 Processing helix chain 'G' and resid 1552 through 1568 removed outlier: 3.791A pdb=" N GLU G1560 " --> pdb=" O ALA G1556 " (cutoff:3.500A) Processing helix chain 'G' and resid 1579 through 1593 removed outlier: 3.896A pdb=" N ASP G1583 " --> pdb=" O THR G1579 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 475 removed outlier: 4.293A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 203 through 212 removed outlier: 3.962A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 21 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.852A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.873A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 3.934A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 603 through 606 Processing helix chain 'J' and resid 607 through 615 Processing helix chain 'J' and resid 623 through 628 Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.570A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 651 Processing helix chain 'J' and resid 656 through 668 Processing helix chain 'J' and resid 669 through 672 Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 710 removed outlier: 3.636A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 745 Processing helix chain 'J' and resid 748 through 755 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.255A pdb=" N VAL A 67 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER A 332 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 69 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 144 removed outlier: 6.173A pdb=" N GLY A 161 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET A 139 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 159 " --> pdb=" O MET A 139 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A 157 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 143 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 155 " --> pdb=" O GLU A 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 173 current: chain 'A' and resid 201 through 207 removed outlier: 5.975A pdb=" N VAL A 222 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 5.666A pdb=" N LEU A 345 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.325A pdb=" N CYS B 95 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASP B 303 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 97 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY B 66 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 362 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 68 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 141 removed outlier: 6.083A pdb=" N GLY B 161 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET B 139 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 159 " --> pdb=" O MET B 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 173 current: chain 'B' and resid 201 through 207 removed outlier: 6.386A pdb=" N VAL B 222 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 336 through 339 removed outlier: 5.869A pdb=" N LEU B 345 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.223A pdb=" N VAL C 67 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER C 332 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 69 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 66 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 362 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 68 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 364 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 70 " --> pdb=" O THR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 143 removed outlier: 5.700A pdb=" N VAL C 136 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 163 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 138 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 167 " --> pdb=" O SER C 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 201 through 207 removed outlier: 6.491A pdb=" N VAL C 222 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 222 current: chain 'D' and resid 156 through 163 removed outlier: 3.729A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 168 through 173 current: chain 'D' and resid 201 through 206 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 201 through 206 current: chain 'H' and resid 456 through 461 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 339 removed outlier: 6.016A pdb=" N LEU C 345 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 Processing sheet with id=AB6, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.583A pdb=" N THR E 101 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP E 298 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU E 103 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 127 through 147 removed outlier: 6.796A pdb=" N THR E 161 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE E 145 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS E 159 " --> pdb=" O ILE E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 168 through 172 current: chain 'E' and resid 201 through 206 Processing sheet with id=AC1, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AC2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.648A pdb=" N THR F 101 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP F 298 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU F 103 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA F 72 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 356 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 74 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 148 removed outlier: 6.712A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 158 " --> pdb=" O MET F 173 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 173 current: chain 'F' and resid 201 through 207 removed outlier: 6.643A pdb=" N LEU F 224 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG F 206 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 331 through 333 Processing sheet with id=AC6, first strand: chain 'G' and resid 1283 through 1284 removed outlier: 6.081A pdb=" N PHE G1283 " --> pdb=" O SER G1470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 1286 through 1287 Processing sheet with id=AC8, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.073A pdb=" N TYR G1313 " --> pdb=" O VAL G1477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.773A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AD2, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.676A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 97 through 101 Processing sheet with id=AD4, first strand: chain 'J' and resid 203 through 208 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 222 through 223 current: chain 'J' and resid 718 through 720 1165 hydrogen bonds defined for protein. 3333 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: 4.58 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9565 1.34 - 1.46: 3166 1.46 - 1.57: 15863 1.57 - 1.69: 23 1.69 - 1.81: 230 Bond restraints: 28847 Sorted by residual: bond pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CB CYS A 407 " pdb=" SG CYS A 407 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CA PRO G1522 " pdb=" CB PRO G1522 " ideal model delta sigma weight residual 1.533 1.556 -0.023 1.80e-02 3.09e+03 1.59e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CG1 ILE B 102 " pdb=" CD1 ILE B 102 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 28842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38228 2.01 - 4.02: 665 4.02 - 6.03: 84 6.03 - 8.04: 8 8.04 - 10.05: 8 Bond angle restraints: 38993 Sorted by residual: angle pdb=" C1' ADP A 501 " pdb=" C2' ADP A 501 " pdb=" C3' ADP A 501 " ideal model delta sigma weight residual 111.00 100.95 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA PRO G1522 " pdb=" C PRO G1522 " pdb=" N PRO G1523 " ideal model delta sigma weight residual 117.10 126.25 -9.15 2.80e+00 1.28e-01 1.07e+01 angle pdb=" C1' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C3' ADP F 501 " ideal model delta sigma weight residual 111.00 101.27 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C1' ADP D 501 " pdb=" C2' ADP D 501 " pdb=" C3' ADP D 501 " ideal model delta sigma weight residual 111.00 102.27 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " ideal model delta sigma weight residual 111.00 102.41 8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 38988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 17387 35.46 - 70.91: 263 70.91 - 106.36: 28 106.36 - 141.82: 3 141.82 - 177.27: 6 Dihedral angle restraints: 17687 sinusoidal: 7292 harmonic: 10395 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 122.72 177.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 97.98 -157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 148.52 151.49 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 17684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3278 0.048 - 0.096: 879 0.096 - 0.145: 242 0.145 - 0.193: 19 0.193 - 0.241: 1 Chirality restraints: 4419 Sorted by residual: chirality pdb=" CA THR D 81 " pdb=" N THR D 81 " pdb=" C THR D 81 " pdb=" CB THR D 81 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2' ADP D 501 " pdb=" C1' ADP D 501 " pdb=" C3' ADP D 501 " pdb=" O2' ADP D 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 351 " pdb=" N ILE B 351 " pdb=" C ILE B 351 " pdb=" CB ILE B 351 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4416 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 252 " 0.380 9.50e-02 1.11e+02 1.71e-01 2.10e+01 pdb=" NE ARG D 252 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 252 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG D 252 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 252 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 313 " -0.359 9.50e-02 1.11e+02 1.62e-01 2.08e+01 pdb=" NE ARG E 313 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 313 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG E 313 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG E 313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 437 " 0.351 9.50e-02 1.11e+02 1.58e-01 1.86e+01 pdb=" NE ARG F 437 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 437 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG F 437 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG F 437 " 0.002 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 325 2.64 - 3.20: 26583 3.20 - 3.77: 43501 3.77 - 4.33: 65066 4.33 - 4.90: 104124 Nonbonded interactions: 239599 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 801 " model vdw 2.069 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1G ATP J 802 " model vdw 2.096 2.170 nonbonded pdb="MG MG J 801 " pdb=" O1B ATP J 802 " model vdw 2.159 2.170 nonbonded pdb=" ND1 HIS J 197 " pdb=" OD2 ASP J 727 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR E 400 " pdb=" O PHE E 432 " model vdw 2.208 3.040 ... (remaining 239594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 501)) selection = (chain 'F' and resid 20 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.920 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28847 Z= 0.133 Angle : 0.695 10.048 38993 Z= 0.390 Chirality : 0.047 0.241 4419 Planarity : 0.011 0.171 5049 Dihedral : 14.059 177.274 10997 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 3590 helix: -1.47 (0.11), residues: 1523 sheet: 0.59 (0.21), residues: 544 loop : -0.02 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.004 ARG E 313 TYR 0.032 0.005 TYR A 210 PHE 0.020 0.002 PHE G1501 TRP 0.022 0.002 TRP H 450 HIS 0.007 0.001 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00289 (28847) covalent geometry : angle 0.69533 (38993) hydrogen bonds : bond 0.19071 ( 1165) hydrogen bonds : angle 7.48059 ( 3333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7180 Ramachandran restraints generated. 3590 Oldfield, 0 Emsley, 3590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 707 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7672 (ttp80) REVERT: B 181 ILE cc_start: 0.8499 (mm) cc_final: 0.8291 (mt) REVERT: B 265 MET cc_start: 0.8698 (mmt) cc_final: 0.8359 (mmt) REVERT: B 378 ILE cc_start: 0.8669 (mt) cc_final: 0.8307 (mp) REVERT: B 449 THR cc_start: 0.8041 (m) cc_final: 0.7763 (p) REVERT: C 6 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 103 TYR cc_start: 0.8282 (m-80) cc_final: 0.8002 (m-10) REVERT: C 106 GLU cc_start: 0.7902 (tt0) cc_final: 0.7596 (mt-10) REVERT: C 303 ASP cc_start: 0.7487 (t0) cc_final: 0.6616 (t0) REVERT: C 307 MET cc_start: 0.8592 (mmp) cc_final: 0.8201 (mmt) REVERT: C 368 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 134 GLU cc_start: 0.7432 (tt0) cc_final: 0.6774 (tt0) REVERT: D 167 MET cc_start: 0.8664 (mtp) cc_final: 0.8325 (ttm) REVERT: D 184 GLU cc_start: 0.8022 (tp30) cc_final: 0.7576 (tp30) REVERT: D 232 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7666 (mm-40) REVERT: D 441 PHE cc_start: 0.8709 (t80) cc_final: 0.8452 (t80) REVERT: F 167 MET cc_start: 0.7945 (mtp) cc_final: 0.7675 (ttm) REVERT: F 183 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8191 (tptp) REVERT: G 1479 ASP cc_start: 0.7077 (p0) cc_final: 0.6724 (p0) REVERT: G 1538 THR cc_start: 0.8402 (p) cc_final: 0.8188 (t) REVERT: G 1545 MET cc_start: 0.7764 (mmt) cc_final: 0.7407 (mmt) REVERT: I 166 MET cc_start: 0.8411 (ptp) cc_final: 0.8204 (ptp) REVERT: J 142 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mptp) REVERT: J 168 SER cc_start: 0.8875 (m) cc_final: 0.8494 (p) REVERT: J 751 TYR cc_start: 0.8618 (t80) cc_final: 0.8036 (t80) outliers start: 0 outliers final: 0 residues processed: 707 average time/residue: 0.8318 time to fit residues: 657.6004 Evaluate side-chains 361 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 60 HIS B 285 GLN B 421 ASN B 446 ASN C 230 HIS C 237 GLN D 225 GLN D 328 ASN E 312 ASN E 419 GLN F 96 GLN F 394 GLN G1345 HIS G1423 GLN I 199 ASN J 237 HIS J 697 ASN J 722 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.068119 restraints weight = 53423.107| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.90 r_work: 0.2851 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 28847 Z= 0.230 Angle : 0.719 10.867 38993 Z= 0.369 Chirality : 0.048 0.248 4419 Planarity : 0.006 0.074 5049 Dihedral : 9.705 173.920 4058 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.01 % Allowed : 11.13 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.13), residues: 3590 helix: -0.09 (0.12), residues: 1539 sheet: 0.39 (0.21), residues: 548 loop : 0.24 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 21 TYR 0.023 0.002 TYR D 310 PHE 0.024 0.002 PHE E 260 TRP 0.016 0.002 TRP J 129 HIS 0.011 0.002 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00550 (28847) covalent geometry : angle 0.71900 (38993) hydrogen bonds : bond 0.05159 ( 1165) hydrogen bonds : angle 5.26717 ( 3333) *********************** 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 467 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 376 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 157 THR cc_start: 0.8568 (t) cc_final: 0.8298 (m) REVERT: A 373 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7904 (ttp80) REVERT: B 62 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8059 (mpp) REVERT: B 265 MET cc_start: 0.8704 (mmt) cc_final: 0.8419 (mmt) REVERT: B 386 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: B 449 THR cc_start: 0.8026 (m) cc_final: 0.7764 (p) REVERT: C 106 GLU cc_start: 0.8174 (tt0) cc_final: 0.7773 (mt-10) REVERT: C 307 MET cc_start: 0.8685 (mmp) cc_final: 0.8198 (mmt) REVERT: D 232 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7914 (mm110) REVERT: D 441 PHE cc_start: 0.8641 (t80) cc_final: 0.8431 (t80) REVERT: E 159 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8344 (tttm) REVERT: F 183 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8375 (tptp) REVERT: G 1377 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: G 1397 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7511 (mm-40) REVERT: G 1479 ASP cc_start: 0.7202 (p0) cc_final: 0.6982 (p0) REVERT: J 168 SER cc_start: 0.8833 (m) cc_final: 0.8489 (p) REVERT: J 174 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: J 222 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7765 (ttmm) outliers start: 91 outliers final: 35 residues processed: 438 average time/residue: 0.7316 time to fit residues: 363.2230 Evaluate side-chains 351 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 309 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1268 CYS Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 623 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN B 446 ASN D 24 HIS F 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068191 restraints weight = 53317.589| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.94 r_work: 0.2864 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28847 Z= 0.157 Angle : 0.623 10.053 38993 Z= 0.315 Chirality : 0.045 0.374 4419 Planarity : 0.005 0.060 5049 Dihedral : 8.993 178.011 4058 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.72 % Allowed : 12.98 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.14), residues: 3590 helix: 0.45 (0.13), residues: 1533 sheet: 0.34 (0.21), residues: 566 loop : 0.30 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 419 TYR 0.024 0.002 TYR J 751 PHE 0.016 0.002 PHE G1501 TRP 0.012 0.001 TRP J 129 HIS 0.005 0.001 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00368 (28847) covalent geometry : angle 0.62342 (38993) hydrogen bonds : bond 0.04366 ( 1165) hydrogen bonds : angle 4.93197 ( 3333) *********************** 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 428 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 346 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8609 (t) cc_final: 0.8312 (m) REVERT: A 373 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7922 (ttp80) REVERT: B 62 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: B 386 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: B 449 THR cc_start: 0.8073 (m) cc_final: 0.7862 (p) REVERT: C 106 GLU cc_start: 0.8171 (tt0) cc_final: 0.7798 (mt-10) REVERT: C 307 MET cc_start: 0.8693 (mmp) cc_final: 0.8162 (mmt) REVERT: D 220 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: E 159 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8342 (tttm) REVERT: E 263 ASP cc_start: 0.7563 (t0) cc_final: 0.7318 (t70) REVERT: F 183 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8368 (tptp) REVERT: F 333 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: G 1377 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: G 1392 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: G 1397 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7509 (mm-40) REVERT: H 455 MET cc_start: 0.8623 (mmm) cc_final: 0.8152 (mpp) REVERT: I 167 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8040 (mttm) REVERT: J 154 MET cc_start: 0.7795 (tpp) cc_final: 0.6977 (mtt) REVERT: J 168 SER cc_start: 0.8814 (m) cc_final: 0.8487 (p) REVERT: J 174 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: J 222 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7771 (ttmm) REVERT: J 295 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6481 (mtm-85) outliers start: 82 outliers final: 35 residues processed: 404 average time/residue: 0.7640 time to fit residues: 349.7658 Evaluate side-chains 351 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 623 SER Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 313 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 199 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 325 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN D 328 ASN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 GLN F 24 HIS J 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.067733 restraints weight = 53290.906| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.95 r_work: 0.2853 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28847 Z= 0.171 Angle : 0.618 11.017 38993 Z= 0.311 Chirality : 0.045 0.390 4419 Planarity : 0.005 0.060 5049 Dihedral : 8.717 171.773 4058 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.31 % Allowed : 13.21 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3590 helix: 0.63 (0.13), residues: 1526 sheet: 0.33 (0.21), residues: 556 loop : 0.23 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 126 TYR 0.031 0.002 TYR J 751 PHE 0.017 0.002 PHE G1501 TRP 0.012 0.001 TRP J 129 HIS 0.006 0.001 HIS F 24 Details of bonding type rmsd covalent geometry : bond 0.00402 (28847) covalent geometry : angle 0.61849 (38993) hydrogen bonds : bond 0.04207 ( 1165) hydrogen bonds : angle 4.83688 ( 3333) *********************** 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 434 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 334 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8651 (t) cc_final: 0.8363 (m) REVERT: A 373 ARG cc_start: 0.8385 (ttm110) cc_final: 0.7963 (ttp80) REVERT: B 35 LYS cc_start: 0.7673 (ptmm) cc_final: 0.7433 (tmtt) REVERT: B 62 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: B 421 ASN cc_start: 0.7888 (m-40) cc_final: 0.7650 (m110) REVERT: B 449 THR cc_start: 0.8090 (m) cc_final: 0.7860 (p) REVERT: C 106 GLU cc_start: 0.8171 (tt0) cc_final: 0.7806 (mt-10) REVERT: C 307 MET cc_start: 0.8660 (mmp) cc_final: 0.8091 (mmt) REVERT: D 163 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8746 (ttpp) REVERT: D 220 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: D 234 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7643 (mmm160) REVERT: E 112 GLU cc_start: 0.7609 (tt0) cc_final: 0.7386 (tt0) REVERT: E 159 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8339 (tttm) REVERT: E 263 ASP cc_start: 0.7459 (t0) cc_final: 0.6992 (t0) REVERT: F 222 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (pttm) REVERT: G 1377 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: G 1392 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: G 1397 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: H 455 MET cc_start: 0.8612 (mmm) cc_final: 0.8237 (mpp) REVERT: I 166 MET cc_start: 0.8575 (ptt) cc_final: 0.8360 (ptt) REVERT: I 167 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (mttm) REVERT: J 154 MET cc_start: 0.7726 (tpp) cc_final: 0.6962 (mtt) REVERT: J 168 SER cc_start: 0.8805 (m) cc_final: 0.8481 (p) REVERT: J 174 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: J 222 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7780 (ttmm) REVERT: J 292 ASP cc_start: 0.8527 (m-30) cc_final: 0.8293 (m-30) REVERT: J 295 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6311 (mtm-85) outliers start: 100 outliers final: 44 residues processed: 406 average time/residue: 0.7713 time to fit residues: 354.8976 Evaluate side-chains 356 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 416 ARG Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1397 GLN Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1587 GLU Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 172 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 0.0060 chunk 249 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 341 optimal weight: 3.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068908 restraints weight = 53040.541| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.95 r_work: 0.2878 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28847 Z= 0.128 Angle : 0.580 9.280 38993 Z= 0.291 Chirality : 0.043 0.348 4419 Planarity : 0.004 0.054 5049 Dihedral : 8.314 160.341 4058 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.45 % Allowed : 14.57 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.14), residues: 3590 helix: 0.80 (0.13), residues: 1541 sheet: 0.29 (0.21), residues: 562 loop : 0.28 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 21 TYR 0.032 0.001 TYR J 751 PHE 0.025 0.001 PHE G1274 TRP 0.012 0.001 TRP J 129 HIS 0.005 0.001 HIS E 301 Details of bonding type rmsd covalent geometry : bond 0.00294 (28847) covalent geometry : angle 0.58009 (38993) hydrogen bonds : bond 0.03742 ( 1165) hydrogen bonds : angle 4.68483 ( 3333) *********************** 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 411 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 337 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7602 (mmm-85) REVERT: A 157 THR cc_start: 0.8635 (t) cc_final: 0.8382 (m) REVERT: A 373 ARG cc_start: 0.8398 (ttm110) cc_final: 0.7966 (ttp80) REVERT: B 35 LYS cc_start: 0.7648 (ptmm) cc_final: 0.7436 (tmtt) REVERT: B 62 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8049 (mpp) REVERT: B 421 ASN cc_start: 0.7857 (m-40) cc_final: 0.7616 (m110) REVERT: B 449 THR cc_start: 0.8087 (m) cc_final: 0.7865 (p) REVERT: C 106 GLU cc_start: 0.8130 (tt0) cc_final: 0.7782 (mt-10) REVERT: C 184 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: C 307 MET cc_start: 0.8627 (mmp) cc_final: 0.7988 (mmt) REVERT: D 163 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8762 (ttpp) REVERT: D 234 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7648 (mmm160) REVERT: E 112 GLU cc_start: 0.7567 (tt0) cc_final: 0.7323 (tt0) REVERT: E 159 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8314 (tttm) REVERT: E 263 ASP cc_start: 0.7502 (t0) cc_final: 0.7017 (t0) REVERT: F 162 ILE cc_start: 0.8663 (mt) cc_final: 0.8376 (tp) REVERT: F 222 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (pttm) REVERT: G 1240 MET cc_start: 0.3200 (mmt) cc_final: 0.2986 (pmt) REVERT: G 1265 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7666 (ttm110) REVERT: G 1392 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: H 442 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8004 (ttm-80) REVERT: I 23 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6832 (m170) REVERT: I 166 MET cc_start: 0.8580 (ptt) cc_final: 0.8376 (ptt) REVERT: I 167 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8085 (mttm) REVERT: J 154 MET cc_start: 0.7729 (tpp) cc_final: 0.7071 (mtt) REVERT: J 168 SER cc_start: 0.8804 (m) cc_final: 0.8483 (p) REVERT: J 174 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: J 222 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7752 (ttmm) REVERT: J 292 ASP cc_start: 0.8509 (m-30) cc_final: 0.8274 (m-30) REVERT: J 295 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.6375 (mtm-85) outliers start: 74 outliers final: 33 residues processed: 388 average time/residue: 0.7813 time to fit residues: 343.7226 Evaluate side-chains 354 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1538 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 288 THR Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 227 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 168 optimal weight: 0.0370 chunk 243 optimal weight: 0.0980 chunk 330 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN C 19 HIS ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN E 312 ASN J 259 ASN J 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.068133 restraints weight = 53039.353| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.96 r_work: 0.2855 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28847 Z= 0.158 Angle : 0.606 9.717 38993 Z= 0.302 Chirality : 0.044 0.360 4419 Planarity : 0.005 0.056 5049 Dihedral : 8.299 153.417 4058 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.52 % Allowed : 15.33 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.14), residues: 3590 helix: 0.89 (0.13), residues: 1526 sheet: 0.28 (0.21), residues: 562 loop : 0.25 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 21 TYR 0.035 0.002 TYR J 751 PHE 0.030 0.002 PHE J 98 TRP 0.011 0.001 TRP J 129 HIS 0.004 0.001 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00373 (28847) covalent geometry : angle 0.60636 (38993) hydrogen bonds : bond 0.03942 ( 1165) hydrogen bonds : angle 4.69148 ( 3333) *********************** 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 397 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 321 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7590 (mmm-85) REVERT: A 157 THR cc_start: 0.8622 (t) cc_final: 0.8397 (m) REVERT: A 373 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7974 (ttp80) REVERT: B 62 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: B 421 ASN cc_start: 0.7849 (m-40) cc_final: 0.7608 (m110) REVERT: B 449 THR cc_start: 0.8081 (m) cc_final: 0.7853 (p) REVERT: C 106 GLU cc_start: 0.8097 (tt0) cc_final: 0.7796 (mt-10) REVERT: C 184 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 307 MET cc_start: 0.8628 (mmp) cc_final: 0.7972 (mmt) REVERT: D 163 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8778 (ttpp) REVERT: E 112 GLU cc_start: 0.7597 (tt0) cc_final: 0.7341 (tt0) REVERT: E 159 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8340 (tttm) REVERT: E 263 ASP cc_start: 0.7553 (t0) cc_final: 0.7096 (t0) REVERT: F 162 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8346 (mt) REVERT: F 222 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8069 (pttm) REVERT: F 313 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7608 (mmp80) REVERT: G 1392 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: I 23 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6763 (m170) REVERT: I 166 MET cc_start: 0.8594 (ptt) cc_final: 0.8386 (ptt) REVERT: I 167 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8039 (mttm) REVERT: J 154 MET cc_start: 0.7749 (tpp) cc_final: 0.7007 (mtt) REVERT: J 168 SER cc_start: 0.8831 (m) cc_final: 0.8510 (p) REVERT: J 222 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7729 (ttmm) REVERT: J 292 ASP cc_start: 0.8552 (m-30) cc_final: 0.8297 (m-30) REVERT: J 295 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.6402 (mtm-85) outliers start: 76 outliers final: 42 residues processed: 374 average time/residue: 0.7398 time to fit residues: 315.3988 Evaluate side-chains 355 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 86 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 153 optimal weight: 0.0970 chunk 267 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068575 restraints weight = 53053.253| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.97 r_work: 0.2866 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28847 Z= 0.139 Angle : 0.592 10.466 38993 Z= 0.295 Chirality : 0.043 0.333 4419 Planarity : 0.004 0.056 5049 Dihedral : 8.114 146.471 4058 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.42 % Allowed : 16.16 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3590 helix: 0.95 (0.13), residues: 1526 sheet: 0.26 (0.21), residues: 558 loop : 0.24 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 21 TYR 0.029 0.001 TYR J 751 PHE 0.023 0.001 PHE G1274 TRP 0.012 0.001 TRP J 129 HIS 0.004 0.001 HIS J 134 Details of bonding type rmsd covalent geometry : bond 0.00326 (28847) covalent geometry : angle 0.59172 (38993) hydrogen bonds : bond 0.03737 ( 1165) hydrogen bonds : angle 4.64216 ( 3333) *********************** 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 388 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7565 (mmm-85) REVERT: A 157 THR cc_start: 0.8614 (t) cc_final: 0.8384 (m) REVERT: A 261 MET cc_start: 0.8931 (tpp) cc_final: 0.8702 (mpp) REVERT: A 373 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7977 (ttp80) REVERT: B 62 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: B 421 ASN cc_start: 0.7863 (m-40) cc_final: 0.7599 (m110) REVERT: B 449 THR cc_start: 0.8071 (m) cc_final: 0.7844 (p) REVERT: C 106 GLU cc_start: 0.8076 (tt0) cc_final: 0.7793 (mt-10) REVERT: C 184 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: C 307 MET cc_start: 0.8595 (mmp) cc_final: 0.7927 (mmt) REVERT: D 163 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8797 (ttpp) REVERT: D 184 GLU cc_start: 0.8111 (tp30) cc_final: 0.7871 (tm-30) REVERT: E 112 GLU cc_start: 0.7611 (tt0) cc_final: 0.7311 (tt0) REVERT: E 159 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8364 (tttm) REVERT: E 263 ASP cc_start: 0.7583 (t0) cc_final: 0.7219 (t0) REVERT: E 378 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7077 (mp0) REVERT: F 162 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (tp) REVERT: F 222 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8047 (pttm) REVERT: F 313 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7609 (mmp80) REVERT: G 1265 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7594 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: H 442 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: H 463 GLU cc_start: 0.7426 (pm20) cc_final: 0.7134 (pm20) REVERT: H 464 GLU cc_start: 0.8076 (mp0) cc_final: 0.7875 (mp0) REVERT: I 23 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6590 (m170) REVERT: I 167 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8012 (mttm) REVERT: J 154 MET cc_start: 0.7756 (tpp) cc_final: 0.7077 (mtt) REVERT: J 168 SER cc_start: 0.8827 (m) cc_final: 0.8513 (p) REVERT: J 174 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: J 222 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7716 (ttmm) REVERT: J 292 ASP cc_start: 0.8529 (m-30) cc_final: 0.8289 (m-30) REVERT: J 295 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.6491 (mtm-85) REVERT: J 751 TYR cc_start: 0.7672 (t80) cc_final: 0.7178 (t80) outliers start: 73 outliers final: 41 residues processed: 366 average time/residue: 0.7738 time to fit residues: 321.4899 Evaluate side-chains 354 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 222 LYS Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 653 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 148 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN C 28 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.066817 restraints weight = 53243.585| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.94 r_work: 0.2828 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28847 Z= 0.209 Angle : 0.660 11.058 38993 Z= 0.330 Chirality : 0.046 0.321 4419 Planarity : 0.005 0.069 5049 Dihedral : 8.448 147.580 4058 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.75 % Allowed : 16.32 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3590 helix: 0.72 (0.13), residues: 1526 sheet: 0.23 (0.21), residues: 573 loop : 0.13 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 21 TYR 0.025 0.002 TYR J 751 PHE 0.020 0.002 PHE J 612 TRP 0.012 0.002 TRP J 129 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00501 (28847) covalent geometry : angle 0.66044 (38993) hydrogen bonds : bond 0.04350 ( 1165) hydrogen bonds : angle 4.85484 ( 3333) *********************** 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 399 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 316 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7563 (mmm-85) REVERT: A 157 THR cc_start: 0.8692 (t) cc_final: 0.8426 (m) REVERT: A 373 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7957 (ttp80) REVERT: B 62 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8067 (mpp) REVERT: B 421 ASN cc_start: 0.7846 (m-40) cc_final: 0.7598 (m110) REVERT: B 449 THR cc_start: 0.8081 (m) cc_final: 0.7850 (p) REVERT: C 106 GLU cc_start: 0.8091 (tt0) cc_final: 0.7819 (mt-10) REVERT: C 184 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: C 307 MET cc_start: 0.8635 (mmp) cc_final: 0.7970 (mmt) REVERT: D 163 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8791 (ttpp) REVERT: D 184 GLU cc_start: 0.8116 (tp30) cc_final: 0.7823 (tm-30) REVERT: D 234 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7549 (mmm160) REVERT: D 263 ASP cc_start: 0.7717 (m-30) cc_final: 0.7483 (m-30) REVERT: E 112 GLU cc_start: 0.7667 (tt0) cc_final: 0.7380 (tm-30) REVERT: E 159 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8351 (tttm) REVERT: E 430 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8506 (ttpt) REVERT: F 177 MET cc_start: 0.9114 (tpp) cc_final: 0.8686 (tpp) REVERT: F 313 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7613 (mmp80) REVERT: G 1265 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7565 (ptm-80) REVERT: G 1392 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: H 442 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: H 455 MET cc_start: 0.8534 (mmm) cc_final: 0.8236 (mpp) REVERT: I 23 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6635 (m170) REVERT: I 27 LYS cc_start: 0.7107 (mttm) cc_final: 0.6663 (mtpt) REVERT: I 167 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8043 (mttm) REVERT: J 154 MET cc_start: 0.7740 (tpp) cc_final: 0.7162 (mtt) REVERT: J 168 SER cc_start: 0.8830 (m) cc_final: 0.8547 (p) REVERT: J 174 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: J 222 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7782 (ttmm) REVERT: J 292 ASP cc_start: 0.8576 (m-30) cc_final: 0.8321 (m-30) REVERT: J 295 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6583 (mtm-85) REVERT: J 751 TYR cc_start: 0.7780 (t80) cc_final: 0.7284 (t80) outliers start: 83 outliers final: 46 residues processed: 373 average time/residue: 0.7991 time to fit residues: 337.2275 Evaluate side-chains 351 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1377 GLU Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1438 THR Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 MET Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Chi-restraints excluded: chain J residue 653 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 79 optimal weight: 0.8980 chunk 284 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 213 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN E 96 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN J 134 HIS J 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068966 restraints weight = 53029.499| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.99 r_work: 0.2879 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28847 Z= 0.121 Angle : 0.588 11.492 38993 Z= 0.292 Chirality : 0.043 0.329 4419 Planarity : 0.004 0.062 5049 Dihedral : 7.937 138.171 4058 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.99 % Allowed : 17.62 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3590 helix: 0.98 (0.13), residues: 1533 sheet: 0.25 (0.21), residues: 569 loop : 0.19 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 21 TYR 0.023 0.001 TYR J 751 PHE 0.013 0.001 PHE J 612 TRP 0.017 0.001 TRP J 129 HIS 0.004 0.001 HIS J 610 Details of bonding type rmsd covalent geometry : bond 0.00279 (28847) covalent geometry : angle 0.58828 (38993) hydrogen bonds : bond 0.03523 ( 1165) hydrogen bonds : angle 4.63626 ( 3333) *********************** 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 380 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8285 (ttpt) cc_final: 0.8071 (tppp) REVERT: A 126 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7505 (mmm-85) REVERT: A 157 THR cc_start: 0.8626 (t) cc_final: 0.8347 (m) REVERT: A 261 MET cc_start: 0.8896 (tpp) cc_final: 0.8637 (mpp) REVERT: A 373 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7949 (ttp80) REVERT: B 62 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: B 421 ASN cc_start: 0.7905 (m-40) cc_final: 0.7583 (m110) REVERT: B 449 THR cc_start: 0.8063 (m) cc_final: 0.7847 (p) REVERT: C 106 GLU cc_start: 0.8025 (tt0) cc_final: 0.7776 (mt-10) REVERT: C 184 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: C 307 MET cc_start: 0.8568 (mmp) cc_final: 0.7828 (mmt) REVERT: D 163 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8828 (ttpp) REVERT: D 184 GLU cc_start: 0.8109 (tp30) cc_final: 0.7889 (tm-30) REVERT: E 112 GLU cc_start: 0.7555 (tt0) cc_final: 0.7258 (tm-30) REVERT: E 187 MET cc_start: 0.8672 (ttm) cc_final: 0.8330 (ptp) REVERT: E 263 ASP cc_start: 0.7605 (t0) cc_final: 0.7281 (t0) REVERT: E 378 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6893 (mm-30) REVERT: F 162 ILE cc_start: 0.8649 (mt) cc_final: 0.8263 (mt) REVERT: F 208 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: F 313 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7617 (mmp80) REVERT: G 1265 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7651 (ptm-80) REVERT: G 1274 PHE cc_start: 0.8650 (t80) cc_final: 0.8374 (t80) REVERT: G 1312 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: G 1392 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: I 23 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6418 (m170) REVERT: I 27 LYS cc_start: 0.7124 (mttm) cc_final: 0.6642 (mtpt) REVERT: J 154 MET cc_start: 0.7838 (tpp) cc_final: 0.7202 (mtt) REVERT: J 168 SER cc_start: 0.8783 (m) cc_final: 0.8536 (p) REVERT: J 174 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: J 292 ASP cc_start: 0.8560 (m-30) cc_final: 0.8293 (m-30) REVERT: J 295 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6439 (mtm-85) REVERT: J 751 TYR cc_start: 0.7665 (t80) cc_final: 0.7318 (t80) outliers start: 60 outliers final: 36 residues processed: 359 average time/residue: 0.7224 time to fit residues: 296.0087 Evaluate side-chains 344 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1448 ILE Chi-restraints excluded: chain G residue 1475 GLU Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 340 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN I 19 GLN I 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.067349 restraints weight = 52839.461| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.96 r_work: 0.2842 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28847 Z= 0.181 Angle : 0.645 11.836 38993 Z= 0.321 Chirality : 0.045 0.375 4419 Planarity : 0.005 0.071 5049 Dihedral : 8.168 136.534 4058 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.95 % Allowed : 17.88 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3590 helix: 0.88 (0.13), residues: 1519 sheet: 0.29 (0.21), residues: 550 loop : 0.09 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 21 TYR 0.023 0.002 TYR J 751 PHE 0.018 0.002 PHE J 612 TRP 0.014 0.002 TRP J 129 HIS 0.005 0.001 HIS G1345 Details of bonding type rmsd covalent geometry : bond 0.00433 (28847) covalent geometry : angle 0.64479 (38993) hydrogen bonds : bond 0.04056 ( 1165) hydrogen bonds : angle 4.75283 ( 3333) ********************** 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 358 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8070 (tppp) REVERT: A 126 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7492 (mmm-85) REVERT: A 157 THR cc_start: 0.8646 (t) cc_final: 0.8387 (m) REVERT: A 373 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7957 (ttp80) REVERT: B 62 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8077 (mpp) REVERT: B 421 ASN cc_start: 0.7931 (m-40) cc_final: 0.7692 (m110) REVERT: B 449 THR cc_start: 0.8053 (m) cc_final: 0.7821 (p) REVERT: C 106 GLU cc_start: 0.8050 (tt0) cc_final: 0.7765 (mt-10) REVERT: C 184 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 307 MET cc_start: 0.8622 (mmp) cc_final: 0.7864 (mmt) REVERT: D 163 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8825 (ttpp) REVERT: D 184 GLU cc_start: 0.8126 (tp30) cc_final: 0.7867 (tm-30) REVERT: D 234 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7439 (ttp80) REVERT: D 263 ASP cc_start: 0.7727 (m-30) cc_final: 0.7493 (m-30) REVERT: E 112 GLU cc_start: 0.7621 (tt0) cc_final: 0.7341 (tt0) REVERT: E 159 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8348 (tttm) REVERT: E 378 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6916 (mm-30) REVERT: F 162 ILE cc_start: 0.8664 (mt) cc_final: 0.8418 (tp) REVERT: F 208 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: F 313 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7623 (mmp80) REVERT: G 1312 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: G 1392 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: H 455 MET cc_start: 0.8420 (mmm) cc_final: 0.8073 (mpp) REVERT: I 23 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6495 (m170) REVERT: I 27 LYS cc_start: 0.7146 (mttm) cc_final: 0.6731 (mtpt) REVERT: J 154 MET cc_start: 0.7905 (tpp) cc_final: 0.7202 (mtt) REVERT: J 168 SER cc_start: 0.8785 (m) cc_final: 0.8559 (p) REVERT: J 174 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: J 292 ASP cc_start: 0.8595 (m-30) cc_final: 0.8322 (m-30) REVERT: J 295 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6493 (mtm-85) REVERT: J 751 TYR cc_start: 0.7824 (t80) cc_final: 0.7519 (t80) outliers start: 59 outliers final: 36 residues processed: 341 average time/residue: 0.7921 time to fit residues: 306.5780 Evaluate side-chains 340 residues out of total 3020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 208 TYR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 394 GLN Chi-restraints excluded: chain G residue 1301 VAL Chi-restraints excluded: chain G residue 1312 GLU Chi-restraints excluded: chain G residue 1341 LYS Chi-restraints excluded: chain G residue 1392 ASP Chi-restraints excluded: chain G residue 1504 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 23 HIS Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain J residue 295 ARG Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 188 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 350 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 446 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066413 restraints weight = 53336.947| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.95 r_work: 0.2824 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28847 Z= 0.221 Angle : 0.682 11.790 38993 Z= 0.341 Chirality : 0.046 0.360 4419 Planarity : 0.005 0.078 5049 Dihedral : 8.450 141.519 4058 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.09 % Allowed : 17.91 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.14), residues: 3590 helix: 0.68 (0.13), residues: 1532 sheet: 0.17 (0.21), residues: 573 loop : 0.01 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 212 TYR 0.024 0.002 TYR J 751 PHE 0.023 0.002 PHE J 35 TRP 0.014 0.002 TRP J 129 HIS 0.006 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00530 (28847) covalent geometry : angle 0.68167 (38993) hydrogen bonds : bond 0.04374 ( 1165) hydrogen bonds : angle 4.89499 ( 3333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10898.15 seconds wall clock time: 185 minutes 39.94 seconds (11139.94 seconds total)