Starting phenix.real_space_refine on Fri Jul 3 21:41:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkv_19284/07_2026/8rkv_19284.map" } resolution = 3.11 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.023 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 174 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 9765 2.51 5 N 3009 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16466 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "3" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 943 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "4" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "5" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "6" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 986 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "7" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "R" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4043 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 19, 'TRANS': 484} Chain breaks: 1 Chain: "S" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4010 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 19, 'TRANS': 480} Chain breaks: 1 Chain: "T" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2393 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 3 Chain: "U" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2419 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 3 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.18 Number of scatterers: 16466 At special positions: 0 Unit cell: (148.512, 98.28, 169.624, 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 44 16.00 P 174 15.00 Mg 2 11.99 O 3472 8.00 N 3009 7.00 C 9765 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: 1.30 Conformation dependent library (CDL) restraints added in 539.6 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 13 sheets defined 45.4% alpha, 16.5% beta 74 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'R' and resid 39 through 53 Processing helix chain 'R' and resid 57 through 73 removed outlier: 3.774A pdb=" N GLY R 62 " --> pdb=" O ARG R 58 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS R 71 " --> pdb=" O GLU R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 90 removed outlier: 3.662A pdb=" N VAL R 79 " --> pdb=" O SER R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 95 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 130 through 146 Processing helix chain 'R' and resid 152 through 170 Proline residue: R 162 - end of helix removed outlier: 3.705A pdb=" N ALA R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 294 through 305 Processing helix chain 'R' and resid 313 through 316 Processing helix chain 'R' and resid 317 through 331 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 332 through 335 Processing helix chain 'R' and resid 349 through 354 Processing helix chain 'R' and resid 357 through 372 removed outlier: 3.590A pdb=" N ARG R 367 " --> pdb=" O GLN R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 376 Processing helix chain 'R' and resid 387 through 392 Processing helix chain 'R' and resid 402 through 411 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.622A pdb=" N CYS R 423 " --> pdb=" O ARG R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 440 removed outlier: 3.540A pdb=" N GLY R 438 " --> pdb=" O TYR R 435 " (cutoff:3.500A) Processing helix chain 'R' and resid 483 through 495 removed outlier: 3.506A pdb=" N SER R 491 " --> pdb=" O ALA R 487 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 495 " --> pdb=" O SER R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 496 through 498 No H-bonds generated for 'chain 'R' and resid 496 through 498' Processing helix chain 'R' and resid 502 through 509 Processing helix chain 'R' and resid 525 through 539 removed outlier: 4.163A pdb=" N ALA R 538 " --> pdb=" O LEU R 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL R 539 " --> pdb=" O ARG R 535 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 54 removed outlier: 3.675A pdb=" N GLU S 54 " --> pdb=" O GLN S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 65 removed outlier: 3.948A pdb=" N GLN S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 73 removed outlier: 3.538A pdb=" N LYS S 71 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 95 removed outlier: 8.747A pdb=" N LEU S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL S 92 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY S 93 " --> pdb=" O ASP S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 123 removed outlier: 4.512A pdb=" N TRP S 111 " --> pdb=" O ILE S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 146 Processing helix chain 'S' and resid 152 through 170 Proline residue: S 162 - end of helix Processing helix chain 'S' and resid 248 through 261 removed outlier: 3.721A pdb=" N LEU S 261 " --> pdb=" O ARG S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 305 Processing helix chain 'S' and resid 313 through 316 Processing helix chain 'S' and resid 317 through 331 Proline residue: S 323 - end of helix Processing helix chain 'S' and resid 332 through 335 Processing helix chain 'S' and resid 342 through 346 Processing helix chain 'S' and resid 349 through 354 Processing helix chain 'S' and resid 357 through 372 removed outlier: 4.080A pdb=" N GLN S 363 " --> pdb=" O ARG S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 392 removed outlier: 3.532A pdb=" N TRP S 390 " --> pdb=" O ARG S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 402 through 407 removed outlier: 3.823A pdb=" N LEU S 406 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 439 Processing helix chain 'S' and resid 461 through 465 Processing helix chain 'S' and resid 483 through 497 removed outlier: 3.699A pdb=" N ARG S 492 " --> pdb=" O GLU S 488 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 493 " --> pdb=" O ALA S 489 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA S 497 " --> pdb=" O ARG S 493 " (cutoff:3.500A) Processing helix chain 'S' and resid 502 through 512 removed outlier: 3.606A pdb=" N GLN S 508 " --> pdb=" O GLN S 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL S 511 " --> pdb=" O LEU S 507 " (cutoff:3.500A) Processing helix chain 'S' and resid 526 through 535 Processing helix chain 'S' and resid 537 through 541 Processing helix chain 'T' and resid 248 through 261 removed outlier: 3.987A pdb=" N VAL T 252 " --> pdb=" O SER T 248 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG T 257 " --> pdb=" O ALA T 253 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU T 261 " --> pdb=" O ARG T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 Processing helix chain 'T' and resid 295 through 305 removed outlier: 3.924A pdb=" N GLN T 299 " --> pdb=" O ASN T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 330 removed outlier: 3.536A pdb=" N ASN T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 331 through 335 removed outlier: 3.678A pdb=" N LEU T 335 " --> pdb=" O PHE T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 357 through 371 removed outlier: 3.593A pdb=" N VAL T 366 " --> pdb=" O GLU T 362 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG T 367 " --> pdb=" O GLN T 363 " (cutoff:3.500A) Processing helix chain 'T' and resid 385 through 394 Processing helix chain 'T' and resid 403 through 407 removed outlier: 3.788A pdb=" N ASP T 407 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 440 removed outlier: 3.560A pdb=" N ALA T 440 " --> pdb=" O ALA T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 483 through 501 removed outlier: 3.551A pdb=" N THR T 500 " --> pdb=" O THR T 496 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE T 501 " --> pdb=" O ALA T 497 " (cutoff:3.500A) Processing helix chain 'T' and resid 503 through 518 removed outlier: 4.496A pdb=" N VAL T 510 " --> pdb=" O LEU T 506 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL T 511 " --> pdb=" O LEU T 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 261 Processing helix chain 'U' and resid 296 through 305 removed outlier: 3.651A pdb=" N ILE U 300 " --> pdb=" O HIS U 296 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY U 301 " --> pdb=" O LEU U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 323 through 327 Processing helix chain 'U' and resid 331 through 335 Processing helix chain 'U' and resid 359 through 367 removed outlier: 4.467A pdb=" N GLN U 363 " --> pdb=" O ARG U 359 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU U 365 " --> pdb=" O LEU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 372 Processing helix chain 'U' and resid 378 through 382 removed outlier: 3.648A pdb=" N GLY U 382 " --> pdb=" O ALA U 379 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 393 removed outlier: 3.690A pdb=" N TRP U 390 " --> pdb=" O ARG U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 402 through 410 removed outlier: 3.700A pdb=" N LEU U 406 " --> pdb=" O GLU U 403 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP U 407 " --> pdb=" O ARG U 404 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE U 408 " --> pdb=" O ASP U 405 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS U 409 " --> pdb=" O LEU U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 423 Processing helix chain 'U' and resid 435 through 440 removed outlier: 3.509A pdb=" N GLY U 438 " --> pdb=" O TYR U 435 " (cutoff:3.500A) Processing helix chain 'U' and resid 483 through 499 removed outlier: 3.539A pdb=" N LEU U 494 " --> pdb=" O ALA U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 500 through 501 No H-bonds generated for 'chain 'U' and resid 500 through 501' Processing helix chain 'U' and resid 502 through 506 removed outlier: 3.573A pdb=" N SER U 505 " --> pdb=" O SER U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 507 through 520 removed outlier: 3.558A pdb=" N VAL U 511 " --> pdb=" O LEU U 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 33 through 35 removed outlier: 5.782A pdb=" N PHE T 468 " --> pdb=" O ARG T 460 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG T 460 " --> pdb=" O PHE T 468 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN T 461 " --> pdb=" O THR T 443 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N THR T 443 " --> pdb=" O GLN T 461 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU T 446 " --> pdb=" O SER T 414 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER T 414 " --> pdb=" O LEU T 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 33 through 35 removed outlier: 4.693A pdb=" N MET T 430 " --> pdb=" O GLN T 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 184 through 186 Processing sheet with id=AA4, first strand: chain 'R' and resid 237 through 243 removed outlier: 6.003A pdb=" N ILE R 237 " --> pdb=" O ASP R 231 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP R 231 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP R 202 " --> pdb=" O TYR R 285 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 284 " --> pdb=" O HIS R 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 213 through 214 Processing sheet with id=AA6, first strand: chain 'R' and resid 412 through 417 removed outlier: 8.431A pdb=" N THR R 443 " --> pdb=" O GLN R 461 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLN R 461 " --> pdb=" O THR R 443 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP R 449 " --> pdb=" O THR R 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR R 455 " --> pdb=" O ASP R 449 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR R 454 " --> pdb=" O HIS R 473 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS R 473 " --> pdb=" O THR R 454 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE R 456 " --> pdb=" O ARG R 471 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG R 471 " --> pdb=" O ILE R 456 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL R 458 " --> pdb=" O LEU R 469 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU R 429 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 424 " --> pdb=" O TYR R 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 33 through 35 removed outlier: 5.548A pdb=" N PHE U 468 " --> pdb=" O ARG U 460 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG U 460 " --> pdb=" O PHE U 468 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN U 461 " --> pdb=" O THR U 443 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR U 443 " --> pdb=" O GLN U 461 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU U 446 " --> pdb=" O SER U 414 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER U 414 " --> pdb=" O LEU U 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'S' and resid 184 through 186 Processing sheet with id=AB1, first strand: chain 'S' and resid 236 through 243 removed outlier: 6.085A pdb=" N ILE S 237 " --> pdb=" O ASP S 231 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP S 231 " --> pdb=" O ILE S 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY S 239 " --> pdb=" O VAL S 229 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP S 205 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TRP S 202 " --> pdb=" O TYR S 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 411 through 418 removed outlier: 5.661A pdb=" N LYS S 412 " --> pdb=" O PHE S 448 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE S 448 " --> pdb=" O LYS S 412 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER S 414 " --> pdb=" O LEU S 446 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU S 446 " --> pdb=" O SER S 414 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG S 416 " --> pdb=" O VAL S 444 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP S 449 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR S 455 " --> pdb=" O ASP S 449 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR S 454 " --> pdb=" O HIS S 473 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS S 473 " --> pdb=" O THR S 454 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE S 456 " --> pdb=" O ARG S 471 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG S 471 " --> pdb=" O ILE S 456 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL S 458 " --> pdb=" O LEU S 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 237 through 243 removed outlier: 7.023A pdb=" N ILE T 237 " --> pdb=" O ASP T 231 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP T 231 " --> pdb=" O ILE T 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 237 through 243 removed outlier: 6.600A pdb=" N ILE U 237 " --> pdb=" O ASP U 231 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP U 231 " --> pdb=" O ILE U 237 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY U 239 " --> pdb=" O VAL U 229 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TRP U 202 " --> pdb=" O TYR U 285 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 179 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2634 1.32 - 1.44: 5278 1.44 - 1.57: 8810 1.57 - 1.69: 344 1.69 - 1.81: 62 Bond restraints: 17128 Sorted by residual: bond pdb=" C1' DC 3 61 " pdb=" N1 DC 3 61 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" C3' DA 5 19 " pdb=" O3' DA 5 19 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C3' DT 5 18 " pdb=" C2' DT 5 18 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.00e+01 bond pdb=" C3' DA 5 25 " pdb=" C2' DA 5 25 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.96e+01 bond pdb=" C3' DG 4 36 " pdb=" C2' DG 4 36 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.93e+01 ... (remaining 17123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 21769 1.68 - 3.35: 1801 3.35 - 5.03: 266 5.03 - 6.71: 63 6.71 - 8.38: 7 Bond angle restraints: 23906 Sorted by residual: angle pdb=" O4' DG 6 64 " pdb=" C1' DG 6 64 " pdb=" N9 DG 6 64 " ideal model delta sigma weight residual 108.00 115.03 -7.03 7.00e-01 2.04e+00 1.01e+02 angle pdb=" O5' DA 7 10 " pdb=" C5' DA 7 10 " pdb=" C4' DA 7 10 " ideal model delta sigma weight residual 109.40 115.59 -6.19 8.00e-01 1.56e+00 5.99e+01 angle pdb=" O5' DC 5 26 " pdb=" C5' DC 5 26 " pdb=" C4' DC 5 26 " ideal model delta sigma weight residual 109.40 115.31 -5.91 8.00e-01 1.56e+00 5.45e+01 angle pdb=" O4' DT 5 18 " pdb=" C1' DT 5 18 " pdb=" N1 DT 5 18 " ideal model delta sigma weight residual 108.00 102.89 5.11 7.00e-01 2.04e+00 5.33e+01 angle pdb=" O5' DA 6 74 " pdb=" C5' DA 6 74 " pdb=" C4' DA 6 74 " ideal model delta sigma weight residual 109.40 115.13 -5.73 8.00e-01 1.56e+00 5.14e+01 ... (remaining 23901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9128 35.97 - 71.95: 756 71.95 - 107.92: 34 107.92 - 143.89: 2 143.89 - 179.86: 9 Dihedral angle restraints: 9929 sinusoidal: 5295 harmonic: 4634 Sorted by residual: dihedral pdb=" CA ARG R 355 " pdb=" C ARG R 355 " pdb=" N LEU R 356 " pdb=" CA LEU R 356 " ideal model delta harmonic sigma weight residual 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLU S 219 " pdb=" C GLU S 219 " pdb=" N ILE S 220 " pdb=" CA ILE S 220 " ideal model delta harmonic sigma weight residual -180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS R 236 " pdb=" C CYS R 236 " pdb=" N ILE R 237 " pdb=" CA ILE R 237 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 9926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2224 0.084 - 0.169: 360 0.169 - 0.253: 58 0.253 - 0.338: 13 0.338 - 0.422: 5 Chirality restraints: 2660 Sorted by residual: chirality pdb=" C3' DA 6 57 " pdb=" C4' DA 6 57 " pdb=" O3' DA 6 57 " pdb=" C2' DA 6 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C1' DG 6 77 " pdb=" O4' DG 6 77 " pdb=" C2' DG 6 77 " pdb=" N9 DG 6 77 " both_signs ideal model delta sigma weight residual False 2.43 2.03 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C1' DG 6 64 " pdb=" O4' DG 6 64 " pdb=" C2' DG 6 64 " pdb=" N9 DG 6 64 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2657 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 355 " 0.390 9.50e-02 1.11e+02 1.76e-01 2.28e+01 pdb=" NE ARG S 355 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG S 355 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG S 355 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG S 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG 6 69 " 0.051 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" N9 DG 6 69 " -0.071 2.00e-02 2.50e+03 pdb=" C8 DG 6 69 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DG 6 69 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG 6 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG 6 69 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG 6 69 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG 6 69 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG 6 69 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG 6 69 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG 6 69 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG 6 69 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 5 18 " 0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT 5 18 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DT 5 18 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DT 5 18 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT 5 18 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DT 5 18 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DT 5 18 " 0.021 2.00e-02 2.50e+03 pdb=" C5 DT 5 18 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT 5 18 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT 5 18 " -0.007 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 167 2.59 - 3.17: 14015 3.17 - 3.75: 27380 3.75 - 4.32: 38765 4.32 - 4.90: 59046 Nonbonded interactions: 139373 Sorted by model distance: nonbonded pdb=" OD1 ASP R 205 " pdb="MG MG R 600 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP S 205 " pdb="MG MG S 600 " model vdw 2.031 2.170 nonbonded pdb=" O3' DT 7 15 " pdb="MG MG S 600 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP S 205 " pdb="MG MG S 600 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP R 205 " pdb="MG MG R 600 " model vdw 2.120 2.170 ... (remaining 139368 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 '4' and (resid 16 through 26 or resid 28 through 33 or resid 35 through 4 \ 0)) selection = (chain '5' and ((resid 16 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or \ name N3 or name C4 or name O4 or name C5 or name C7 or name C6 )) or resid 17 th \ rough 26 or resid 28 through 33 or resid 35 through 40)) } ncs_group { reference = (chain 'R' and (resid 31 through 512 or resid 525 through 600)) selection = chain 'S' } ncs_group { reference = (chain 'T' and (resid 196 through 287 or resid 295 through 339 or resid 354 thro \ ugh 522)) selection = (chain 'U' and (resid 196 through 311 or resid 323 through 522)) } 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: 1.810 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 0.007 0.078 17128 Z= 0.517 Angle : 1.003 8.384 23906 Z= 0.744 Chirality : 0.068 0.422 2660 Planarity : 0.012 0.176 2487 Dihedral : 22.219 179.863 6941 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.94 % Allowed : 8.67 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1576 helix: -2.02 (0.17), residues: 581 sheet: -0.68 (0.33), residues: 208 loop : -0.41 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.004 ARG S 355 TYR 0.030 0.005 TYR R 233 PHE 0.029 0.003 PHE R 284 TRP 0.027 0.003 TRP R 86 HIS 0.011 0.002 HIS S 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.52 (17128) covalent geometry : angle 1.00296 / 0.74 (23906) hydrogen bonds : bond 0.18944 / 21.12 ( 707) hydrogen bonds : angle 7.72081 / 9.54 ( 1811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 31 LYS cc_start: 0.6230 (tptt) cc_final: 0.5849 (mmtt) REVERT: R 112 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7752 (mt-10) REVERT: R 124 LYS cc_start: 0.6940 (pptt) cc_final: 0.6331 (pttp) REVERT: R 129 MET cc_start: 0.6915 (ttm) cc_final: 0.6697 (ttm) REVERT: R 165 GLU cc_start: 0.8293 (tp30) cc_final: 0.8049 (tp30) REVERT: R 172 SER cc_start: 0.7118 (t) cc_final: 0.6707 (p) REVERT: R 371 ASP cc_start: 0.8298 (m-30) cc_final: 0.8027 (m-30) REVERT: R 432 ARG cc_start: 0.7444 (ptp90) cc_final: 0.7145 (ptp-110) REVERT: R 451 ARG cc_start: 0.8397 (mtm180) cc_final: 0.8163 (mtm-85) REVERT: R 465 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8153 (mm110) REVERT: S 104 LYS cc_start: 0.6963 (mmtp) cc_final: 0.6532 (mmtt) REVERT: S 143 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7867 (mtt180) REVERT: S 179 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5533 (ppt90) REVERT: S 295 ASN cc_start: 0.8055 (m110) cc_final: 0.7830 (m-40) REVERT: S 349 ASP cc_start: 0.6590 (m-30) cc_final: 0.6366 (t0) REVERT: S 360 GLU cc_start: 0.5932 (mp0) cc_final: 0.5453 (mp0) REVERT: S 375 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7935 (mm-40) REVERT: S 430 MET cc_start: 0.7848 (mtp) cc_final: 0.7610 (mpp) REVERT: S 503 ASN cc_start: 0.7352 (p0) cc_final: 0.7132 (p0) REVERT: T 202 TRP cc_start: 0.5891 (m100) cc_final: 0.5523 (m-10) REVERT: T 327 LEU cc_start: 0.5781 (mm) cc_final: 0.5480 (mm) REVERT: T 363 GLN cc_start: 0.7808 (mt0) cc_final: 0.7607 (mt0) REVERT: T 373 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.4206 (t80) REVERT: T 495 ARG cc_start: 0.6531 (tpt170) cc_final: 0.6283 (ttm110) REVERT: U 233 TYR cc_start: 0.6432 (t80) cc_final: 0.6118 (t80) REVERT: U 245 ASP cc_start: 0.6750 (t0) cc_final: 0.6382 (t0) REVERT: U 285 TYR cc_start: 0.5914 (m-80) cc_final: 0.5703 (m-80) REVERT: U 415 ARG cc_start: 0.5433 (mpp-170) cc_final: 0.5157 (mtm-85) REVERT: U 475 GLN cc_start: 0.5156 (tt0) cc_final: 0.4929 (tt0) REVERT: U 496 THR cc_start: 0.6869 (m) cc_final: 0.6577 (m) outliers start: 27 outliers final: 7 residues processed: 303 average time/residue: 0.1711 time to fit residues: 71.9083 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 339 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 206 HIS Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 415 ARG Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain U residue 223 ARG Chi-restraints excluded: chain U residue 404 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 427 GLN R 531 GLN S 272 HIS S 295 ASN S 344 GLN S 363 GLN S 445 ASN ** T 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 HIS T 375 GLN ** T 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 481 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.207543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.171902 restraints weight = 23639.492| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.37 r_work: 0.3963 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17128 Z= 0.184 Angle : 0.801 9.349 23906 Z= 0.441 Chirality : 0.053 0.418 2660 Planarity : 0.006 0.058 2487 Dihedral : 25.588 177.436 3777 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.58 % Allowed : 12.04 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1576 helix: -0.82 (0.19), residues: 589 sheet: -0.71 (0.34), residues: 205 loop : 0.00 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 143 TYR 0.026 0.002 TYR T 285 PHE 0.018 0.002 PHE R 284 TRP 0.031 0.002 TRP S 86 HIS 0.008 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (17128) covalent geometry : angle 0.80065 / 0.44 (23906) hydrogen bonds : bond 0.06123 / 6.73 ( 707) hydrogen bonds : angle 5.76427 / 7.08 ( 1811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 371 ASP cc_start: 0.7807 (m-30) cc_final: 0.7443 (m-30) REVERT: R 475 GLN cc_start: 0.6348 (mm-40) cc_final: 0.6075 (mm110) REVERT: R 480 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: R 491 SER cc_start: 0.8187 (m) cc_final: 0.7674 (t) REVERT: S 327 LEU cc_start: 0.6407 (tp) cc_final: 0.6173 (tp) REVERT: S 375 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: T 327 LEU cc_start: 0.5674 (mm) cc_final: 0.5265 (mm) REVERT: T 373 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.4130 (t80) REVERT: T 461 GLN cc_start: 0.7598 (tp40) cc_final: 0.7249 (mm-40) REVERT: U 245 ASP cc_start: 0.6709 (t0) cc_final: 0.6318 (t0) REVERT: U 285 TYR cc_start: 0.5947 (m-80) cc_final: 0.5746 (m-80) REVERT: U 473 HIS cc_start: 0.6060 (OUTLIER) cc_final: 0.5602 (m90) outliers start: 36 outliers final: 17 residues processed: 244 average time/residue: 0.1689 time to fit residues: 58.2054 Evaluate side-chains 205 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 298 SER Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 387 PHE Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 62 optimal weight: 0.0070 chunk 129 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 475 GLN S 272 HIS S 344 GLN T 206 HIS T 272 HIS T 445 ASN U 463 ASN U 475 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.206992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.170842 restraints weight = 23819.722| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.31 r_work: 0.3952 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17128 Z= 0.179 Angle : 0.742 10.185 23906 Z= 0.408 Chirality : 0.050 0.386 2660 Planarity : 0.005 0.067 2487 Dihedral : 25.729 179.314 3754 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.22 % Allowed : 14.62 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1576 helix: -0.44 (0.20), residues: 591 sheet: -0.85 (0.33), residues: 215 loop : 0.02 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 235 TYR 0.022 0.002 TYR R 233 PHE 0.020 0.002 PHE S 306 TRP 0.032 0.002 TRP S 86 HIS 0.008 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (17128) covalent geometry : angle 0.74180 / 0.41 (23906) hydrogen bonds : bond 0.05401 / 5.88 ( 707) hydrogen bonds : angle 5.35189 / 6.57 ( 1811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 480 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6560 (pm20) REVERT: S 430 MET cc_start: 0.7707 (mpp) cc_final: 0.7496 (mpp) REVERT: T 325 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7594 (pmmt) REVERT: T 327 LEU cc_start: 0.5631 (mm) cc_final: 0.5180 (mm) REVERT: T 373 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.4318 (t80) REVERT: T 434 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7101 (mm-30) REVERT: U 245 ASP cc_start: 0.6722 (t0) cc_final: 0.6303 (t0) REVERT: U 436 LEU cc_start: 0.8062 (tp) cc_final: 0.7859 (tp) REVERT: U 473 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5698 (m90) outliers start: 31 outliers final: 21 residues processed: 228 average time/residue: 0.1731 time to fit residues: 54.9573 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 298 SER Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 113 ASN R 217 HIS R 445 ASN S 272 HIS S 344 GLN T 272 HIS T 363 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.203241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166717 restraints weight = 23598.904| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.70 r_work: 0.3845 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17128 Z= 0.240 Angle : 0.786 11.988 23906 Z= 0.426 Chirality : 0.051 0.396 2660 Planarity : 0.006 0.066 2487 Dihedral : 25.800 178.726 3751 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.37 % Allowed : 15.91 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1576 helix: -0.50 (0.20), residues: 592 sheet: -0.87 (0.33), residues: 222 loop : -0.20 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 128 TYR 0.033 0.002 TYR R 233 PHE 0.028 0.003 PHE S 306 TRP 0.027 0.003 TRP S 86 HIS 0.015 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (17128) covalent geometry : angle 0.78634 / 0.43 (23906) hydrogen bonds : bond 0.05735 / 6.22 ( 707) hydrogen bonds : angle 5.37187 / 6.59 ( 1811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 480 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: S 375 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8264 (mm-40) REVERT: S 427 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: T 225 TRP cc_start: 0.7130 (m-90) cc_final: 0.6454 (m-10) REVERT: T 325 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7541 (pmmt) REVERT: T 327 LEU cc_start: 0.5653 (mm) cc_final: 0.5192 (mm) REVERT: T 373 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4377 (t80) REVERT: U 245 ASP cc_start: 0.6806 (t0) cc_final: 0.6276 (t0) REVERT: U 404 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.4266 (mmp-170) REVERT: U 473 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5900 (m90) outliers start: 47 outliers final: 25 residues processed: 220 average time/residue: 0.1628 time to fit residues: 50.6142 Evaluate side-chains 200 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 0.0870 chunk 128 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 13 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 HIS T 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.201248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.165157 restraints weight = 23471.214| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.60 r_work: 0.3832 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17128 Z= 0.281 Angle : 0.820 12.483 23906 Z= 0.440 Chirality : 0.053 0.417 2660 Planarity : 0.006 0.059 2487 Dihedral : 25.904 179.110 3751 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.80 % Allowed : 16.49 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1576 helix: -0.66 (0.20), residues: 585 sheet: -0.94 (0.34), residues: 212 loop : -0.48 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 137 TYR 0.037 0.003 TYR R 233 PHE 0.030 0.003 PHE S 306 TRP 0.038 0.003 TRP U 225 HIS 0.016 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.28 (17128) covalent geometry : angle 0.81998 / 0.44 (23906) hydrogen bonds : bond 0.06069 / 6.64 ( 707) hydrogen bonds : angle 5.46695 / 6.72 ( 1811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 171 LYS cc_start: 0.8439 (mptt) cc_final: 0.8196 (mttp) REVERT: R 430 MET cc_start: 0.6201 (ppp) cc_final: 0.5583 (ppp) REVERT: R 431 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: R 480 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6582 (pm20) REVERT: S 375 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8229 (mm-40) REVERT: T 225 TRP cc_start: 0.7230 (m-90) cc_final: 0.6524 (m-10) REVERT: T 325 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7523 (pmmt) REVERT: T 488 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: U 245 ASP cc_start: 0.6815 (t0) cc_final: 0.6435 (t0) REVERT: U 300 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8050 (mt) REVERT: U 404 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.4801 (mmp-170) REVERT: U 415 ARG cc_start: 0.6293 (mpp-170) cc_final: 0.5999 (mtm-85) REVERT: U 473 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5948 (m90) outliers start: 67 outliers final: 40 residues processed: 225 average time/residue: 0.1576 time to fit residues: 50.4616 Evaluate side-chains 211 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 431 TYR Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 234 SER Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 455 THR Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 275 TRP Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 298 SER Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 488 GLU Chi-restraints excluded: chain T residue 507 LEU Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 496 THR Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 475 GLN R 531 GLN S 344 GLN T 363 GLN T 461 GLN U 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.207447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.171409 restraints weight = 23483.291| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.50 r_work: 0.3949 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17128 Z= 0.145 Angle : 0.706 9.981 23906 Z= 0.381 Chirality : 0.047 0.326 2660 Planarity : 0.005 0.056 2487 Dihedral : 25.831 178.658 3751 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.37 % Allowed : 18.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1576 helix: -0.07 (0.21), residues: 590 sheet: -0.85 (0.34), residues: 212 loop : -0.26 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 137 TYR 0.016 0.001 TYR T 459 PHE 0.013 0.001 PHE T 284 TRP 0.033 0.002 TRP U 225 HIS 0.009 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (17128) covalent geometry : angle 0.70600 / 0.38 (23906) hydrogen bonds : bond 0.04384 / 4.73 ( 707) hydrogen bonds : angle 5.05111 / 6.20 ( 1811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.487 Fit side-chains REVERT: S 157 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7501 (mt) REVERT: S 415 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.6091 (ptt90) REVERT: S 430 MET cc_start: 0.7592 (mpp) cc_final: 0.6863 (mpp) REVERT: T 199 ASN cc_start: 0.4746 (OUTLIER) cc_final: 0.4540 (t0) REVERT: T 325 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7558 (pmmt) REVERT: T 373 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.4825 (t80) REVERT: U 245 ASP cc_start: 0.6758 (t0) cc_final: 0.6122 (t0) REVERT: U 375 GLN cc_start: 0.6868 (mm110) cc_final: 0.6621 (mm110) REVERT: U 404 ARG cc_start: 0.5342 (OUTLIER) cc_final: 0.3858 (mmp-170) REVERT: U 473 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5700 (m90) outliers start: 47 outliers final: 23 residues processed: 218 average time/residue: 0.1565 time to fit residues: 48.5431 Evaluate side-chains 201 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 475 GLN Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 415 ARG Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 141 optimal weight: 0.0370 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 445 ASN ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 531 GLN S 272 HIS T 272 HIS U 295 ASN U 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.208510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.172855 restraints weight = 23356.111| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.41 r_work: 0.3960 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17128 Z= 0.138 Angle : 0.682 9.975 23906 Z= 0.369 Chirality : 0.046 0.339 2660 Planarity : 0.005 0.054 2487 Dihedral : 25.797 178.712 3751 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.72 % Allowed : 19.21 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1576 helix: 0.15 (0.22), residues: 591 sheet: -0.69 (0.35), residues: 208 loop : -0.24 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 208 TYR 0.016 0.001 TYR T 459 PHE 0.014 0.001 PHE S 306 TRP 0.023 0.002 TRP U 225 HIS 0.010 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (17128) covalent geometry : angle 0.68172 / 0.37 (23906) hydrogen bonds : bond 0.04247 / 4.58 ( 707) hydrogen bonds : angle 4.94435 / 6.05 ( 1811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.418 Fit side-chains REVERT: R 137 ARG cc_start: 0.6779 (tpp80) cc_final: 0.6529 (tpp80) REVERT: S 375 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: S 415 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.6062 (ptt90) REVERT: S 430 MET cc_start: 0.7598 (mpp) cc_final: 0.6919 (mpp) REVERT: S 471 ARG cc_start: 0.6726 (ppp80) cc_final: 0.6472 (tmm-80) REVERT: T 199 ASN cc_start: 0.4918 (OUTLIER) cc_final: 0.4706 (t0) REVERT: T 225 TRP cc_start: 0.6797 (m-90) cc_final: 0.6428 (m-10) REVERT: T 325 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7582 (pmmt) REVERT: T 373 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4925 (t80) REVERT: U 300 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7956 (mt) REVERT: U 375 GLN cc_start: 0.6776 (mm110) cc_final: 0.6551 (mm110) REVERT: U 404 ARG cc_start: 0.5409 (OUTLIER) cc_final: 0.4042 (mmp-170) REVERT: U 473 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5711 (m90) outliers start: 38 outliers final: 26 residues processed: 207 average time/residue: 0.1577 time to fit residues: 46.1062 Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 531 GLN Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 415 ARG Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.207878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.172237 restraints weight = 23508.675| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.59 r_work: 0.3934 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17128 Z= 0.150 Angle : 0.696 10.325 23906 Z= 0.372 Chirality : 0.046 0.351 2660 Planarity : 0.005 0.050 2487 Dihedral : 25.780 178.877 3749 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.15 % Allowed : 19.71 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1576 helix: 0.10 (0.21), residues: 601 sheet: -0.65 (0.35), residues: 208 loop : -0.32 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 137 TYR 0.019 0.001 TYR R 233 PHE 0.018 0.002 PHE S 306 TRP 0.020 0.002 TRP U 225 HIS 0.014 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (17128) covalent geometry : angle 0.69590 / 0.37 (23906) hydrogen bonds : bond 0.04294 / 4.64 ( 707) hydrogen bonds : angle 4.90020 / 5.98 ( 1811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: S 295 ASN cc_start: 0.8203 (m-40) cc_final: 0.7800 (m-40) REVERT: S 327 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.5378 (mp) REVERT: S 375 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8294 (mm-40) REVERT: S 430 MET cc_start: 0.7628 (mpp) cc_final: 0.6941 (mpp) REVERT: S 471 ARG cc_start: 0.6794 (ppp80) cc_final: 0.6530 (tmm-80) REVERT: T 199 ASN cc_start: 0.4794 (OUTLIER) cc_final: 0.4553 (t0) REVERT: T 225 TRP cc_start: 0.6775 (m-90) cc_final: 0.6290 (m-10) REVERT: T 325 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7594 (pmmt) REVERT: T 338 TYR cc_start: 0.6617 (p90) cc_final: 0.6413 (p90) REVERT: T 373 TYR cc_start: 0.5408 (OUTLIER) cc_final: 0.4969 (t80) REVERT: U 300 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8043 (mt) REVERT: U 375 GLN cc_start: 0.6785 (mm110) cc_final: 0.6563 (mm110) REVERT: U 404 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.4129 (mmp-170) REVERT: U 415 ARG cc_start: 0.6122 (mpp-170) cc_final: 0.5906 (mtm-85) REVERT: U 473 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5761 (m90) outliers start: 44 outliers final: 28 residues processed: 207 average time/residue: 0.1495 time to fit residues: 44.2321 Evaluate side-chains 209 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 29 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.172899 restraints weight = 23647.373| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.53 r_work: 0.3961 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17128 Z= 0.139 Angle : 0.685 10.594 23906 Z= 0.366 Chirality : 0.046 0.344 2660 Planarity : 0.005 0.091 2487 Dihedral : 25.741 178.476 3749 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.72 % Allowed : 20.07 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1576 helix: 0.20 (0.22), residues: 598 sheet: -0.63 (0.34), residues: 217 loop : -0.28 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 493 TYR 0.016 0.001 TYR T 459 PHE 0.015 0.001 PHE S 306 TRP 0.018 0.001 TRP U 225 HIS 0.009 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (17128) covalent geometry : angle 0.68537 / 0.37 (23906) hydrogen bonds : bond 0.04094 / 4.42 ( 707) hydrogen bonds : angle 4.81320 / 5.89 ( 1811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: S 327 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5368 (mp) REVERT: S 375 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8281 (mm-40) REVERT: S 430 MET cc_start: 0.7621 (mpp) cc_final: 0.6927 (mpp) REVERT: S 471 ARG cc_start: 0.6759 (ppp80) cc_final: 0.6530 (tmm-80) REVERT: T 199 ASN cc_start: 0.4808 (OUTLIER) cc_final: 0.4600 (t0) REVERT: T 225 TRP cc_start: 0.6758 (m-90) cc_final: 0.6333 (m-10) REVERT: T 325 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7595 (pmmt) REVERT: T 373 TYR cc_start: 0.5368 (OUTLIER) cc_final: 0.4970 (t80) REVERT: U 300 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8024 (mt) REVERT: U 375 GLN cc_start: 0.6791 (mm110) cc_final: 0.6570 (mm110) REVERT: U 404 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.3927 (mmp-170) REVERT: U 415 ARG cc_start: 0.6027 (mpp-170) cc_final: 0.5827 (mtm-85) REVERT: U 473 HIS cc_start: 0.6239 (OUTLIER) cc_final: 0.5736 (m90) outliers start: 38 outliers final: 28 residues processed: 205 average time/residue: 0.1616 time to fit residues: 46.9958 Evaluate side-chains 208 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 327 LEU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 272 HIS Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.207877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.171352 restraints weight = 23503.781| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.47 r_work: 0.3950 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17128 Z= 0.158 Angle : 0.706 13.515 23906 Z= 0.374 Chirality : 0.046 0.357 2660 Planarity : 0.005 0.078 2487 Dihedral : 25.747 179.158 3749 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.72 % Allowed : 20.29 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1576 helix: 0.16 (0.21), residues: 598 sheet: -0.53 (0.35), residues: 207 loop : -0.36 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 137 TYR 0.021 0.001 TYR R 233 PHE 0.019 0.002 PHE S 306 TRP 0.051 0.002 TRP U 225 HIS 0.017 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17128) covalent geometry : angle 0.70561 / 0.37 (23906) hydrogen bonds : bond 0.04273 / 4.63 ( 707) hydrogen bonds : angle 4.83583 / 5.90 ( 1811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 327 LEU cc_start: 0.6486 (tp) cc_final: 0.5382 (mp) REVERT: S 375 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8270 (mm-40) REVERT: S 415 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6118 (ptt90) REVERT: S 430 MET cc_start: 0.7532 (mpp) cc_final: 0.6893 (mpp) REVERT: S 471 ARG cc_start: 0.6695 (ppp80) cc_final: 0.6491 (tmm-80) REVERT: T 199 ASN cc_start: 0.4853 (OUTLIER) cc_final: 0.4647 (t0) REVERT: T 225 TRP cc_start: 0.6757 (m-90) cc_final: 0.6319 (m-10) REVERT: T 325 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7600 (pmmt) REVERT: T 373 TYR cc_start: 0.5328 (OUTLIER) cc_final: 0.4939 (t80) REVERT: U 300 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7976 (mt) REVERT: U 375 GLN cc_start: 0.6785 (mm110) cc_final: 0.6574 (mm110) REVERT: U 404 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.4048 (mmp-170) REVERT: U 415 ARG cc_start: 0.6099 (mpp-170) cc_final: 0.5899 (mtm-85) REVERT: U 473 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5790 (m90) outliers start: 38 outliers final: 27 residues processed: 202 average time/residue: 0.1712 time to fit residues: 48.6372 Evaluate side-chains 211 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 415 ARG Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain S residue 458 VAL Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 278 TYR Chi-restraints excluded: chain T residue 325 LYS Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 397 VAL Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 227 THR Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS T 272 HIS T 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.206902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.171932 restraints weight = 23544.726| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.84 r_work: 0.3903 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17128 Z= 0.167 Angle : 0.715 13.128 23906 Z= 0.379 Chirality : 0.047 0.360 2660 Planarity : 0.005 0.082 2487 Dihedral : 25.763 179.030 3749 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.80 % Allowed : 20.43 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1576 helix: 0.11 (0.21), residues: 598 sheet: -0.51 (0.35), residues: 207 loop : -0.37 (0.24), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 208 TYR 0.023 0.001 TYR R 233 PHE 0.020 0.002 PHE S 306 TRP 0.052 0.002 TRP U 225 HIS 0.009 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (17128) covalent geometry : angle 0.71547 / 0.38 (23906) hydrogen bonds : bond 0.04394 / 4.78 ( 707) hydrogen bonds : angle 4.88092 / 5.94 ( 1811) =============================================================================== Job complete usr+sys time: 4403.94 seconds wall clock time: 76 minutes 6.08 seconds (4566.08 seconds total)