Starting phenix.real_space_refine on Thu Aug 6 17:16:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkv_19284/08_2026/8rkv_19284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkv_19284/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2026/8rkv_19284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2026/8rkv_19284.map" model { file = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2026/8rkv_19284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2026/8rkv_19284.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.86, per 1000 atoms: 0.23 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: 1.39 Conformation dependent library (CDL) restraints added in 613.7 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: 2.22 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: 3.48 Time building geometry restraints manager: 1.87 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: 21744 1.68 - 3.35: 1822 3.35 - 5.03: 266 5.03 - 6.71: 67 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- 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= 0.518 Angle : 1.007 8.384 23906 Z= 0.751 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 1.00715 / 0.75 (23906) hydrogen bonds : bond 0.18944 / 21.21 ( 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 : 0.587 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: 0.8152 (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: 0.7868 (mtt180) REVERT: S 179 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5532 (ppt90) REVERT: S 295 ASN cc_start: 0.8055 (m110) cc_final: 0.7638 (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: 0.7611 (mpp) REVERT: S 503 ASN cc_start: 0.7352 (p0) cc_final: 0.7131 (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: U 233 TYR cc_start: 0.6432 (t80) cc_final: 0.6118 (t80) REVERT: U 245 ASP cc_start: 0.6750 (t0) cc_final: 0.6383 (t0) REVERT: U 285 TYR cc_start: 0.5914 (m-80) cc_final: 0.5702 (m-80) REVERT: U 415 ARG cc_start: 0.5433 (mpp-170) cc_final: 0.4951 (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: 0.1836 time to fit residues: 77.3122 Evaluate side-chains 211 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.207800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.172443 restraints weight = 23658.091| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.43 r_work: 0.3960 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17128 Z= 0.177 Angle : 0.805 9.441 23906 Z= 0.441 Chirality : 0.054 0.424 2660 Planarity : 0.006 0.061 2487 Dihedral : 25.585 175.552 3777 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.65 % Allowed : 12.40 % Favored : 84.95 % 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: -0.81 (0.19), residues: 589 sheet: -0.75 (0.34), residues: 205 loop : 0.01 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 322 TYR 0.026 0.002 TYR T 285 PHE 0.019 0.002 PHE U 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 0.00345 / 0.18 (17128) covalent geometry : angle 0.80525 / 0.44 (23906) hydrogen bonds : bond 0.05887 / 6.49 ( 707) hydrogen bonds : angle 5.72182 / 7.05 ( 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 265 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 371 ASP cc_start: 0.7810 (m-30) cc_final: 0.7440 (m-30) REVERT: R 475 GLN cc_start: 0.6311 (mm-40) cc_final: 0.6089 (mm110) REVERT: R 480 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: R 491 SER cc_start: 0.8187 (m) cc_final: 0.7676 (t) REVERT: S 295 ASN cc_start: 0.8226 (m-40) cc_final: 0.7796 (m-40) REVERT: S 327 LEU cc_start: 0.6384 (tp) cc_final: 0.6145 (tp) REVERT: S 375 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: T 327 LEU cc_start: 0.5670 (mm) cc_final: 0.5275 (mm) REVERT: T 373 TYR cc_start: 0.5007 (OUTLIER) cc_final: 0.4227 (t80) REVERT: T 461 GLN cc_start: 0.7605 (tp40) cc_final: 0.7264 (mm-40) REVERT: U 245 ASP cc_start: 0.6713 (t0) cc_final: 0.6311 (t0) REVERT: U 263 LYS cc_start: 0.8357 (mmpt) cc_final: 0.8126 (mmpt) REVERT: U 285 TYR cc_start: 0.5929 (m-80) cc_final: 0.5727 (m-80) REVERT: U 407 ASP cc_start: 0.4979 (m-30) cc_final: 0.4531 (m-30) REVERT: U 463 ASN cc_start: 0.6538 (m110) cc_final: 0.6331 (m-40) REVERT: U 473 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5595 (m90) outliers start: 37 outliers final: 19 residues processed: 246 average time/residue: 0.1705 time to fit residues: 59.5052 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 193 LEU 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: 9.9990 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 129 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS ** R 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 272 HIS S 344 GLN S 363 GLN T 206 HIS T 272 HIS T 445 ASN U 309 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.201787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.165169 restraints weight = 23918.333| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.89 r_work: 0.3838 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.006 0.078 17128 Z= 0.289 Angle : 0.866 13.760 23906 Z= 0.466 Chirality : 0.056 0.474 2660 Planarity : 0.007 0.082 2487 Dihedral : 25.712 176.871 3754 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.23 % Allowed : 14.77 % Favored : 82.01 % 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: -1.06 (0.20), residues: 1576 helix: -0.93 (0.19), residues: 586 sheet: -1.02 (0.33), residues: 215 loop : -0.23 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 492 TYR 0.036 0.003 TYR R 233 PHE 0.031 0.003 PHE S 306 TRP 0.029 0.003 TRP S 86 HIS 0.006 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (17128) covalent geometry : angle 0.86606 / 0.47 (23906) hydrogen bonds : bond 0.06761 / 7.41 ( 707) hydrogen bonds : angle 5.66980 / 6.98 ( 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 245 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.863 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: R 480 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: S 375 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8248 (mm-40) REVERT: T 325 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7622 (pmmt) REVERT: U 241 ASN cc_start: 0.5917 (OUTLIER) cc_final: 0.5651 (m110) REVERT: U 245 ASP cc_start: 0.6808 (t0) cc_final: 0.6326 (t0) REVERT: U 404 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4867 (mmp-170) REVERT: U 473 HIS cc_start: 0.6452 (OUTLIER) cc_final: 0.5907 (m90) outliers start: 45 outliers final: 31 residues processed: 228 average time/residue: 0.1691 time to fit residues: 55.1012 Evaluate side-chains 213 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 310 LEU 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 33 VAL 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 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 207 THR 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 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 241 ASN 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 453 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 5.9990 chunk 63 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 113 ASN R 217 HIS R 531 GLN S 272 HIS T 272 HIS U 475 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.206828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.170031 restraints weight = 23543.038| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.48 r_work: 0.3930 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17128 Z= 0.153 Angle : 0.719 9.965 23906 Z= 0.392 Chirality : 0.049 0.386 2660 Planarity : 0.005 0.055 2487 Dihedral : 25.733 178.495 3754 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.65 % Allowed : 16.85 % Favored : 80.50 % 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: -0.30 (0.20), residues: 589 sheet: -0.84 (0.34), residues: 217 loop : -0.13 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 223 TYR 0.017 0.002 TYR T 459 PHE 0.016 0.002 PHE T 284 TRP 0.031 0.002 TRP S 86 HIS 0.006 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (17128) covalent geometry : angle 0.71870 / 0.39 (23906) hydrogen bonds : bond 0.04789 / 5.23 ( 707) hydrogen bonds : angle 5.25866 / 6.47 ( 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 237 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 430 MET cc_start: 0.6840 (ppp) cc_final: 0.6545 (ppp) REVERT: R 475 GLN cc_start: 0.6480 (mm-40) cc_final: 0.6245 (mp10) REVERT: T 325 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7586 (pmmt) REVERT: T 373 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.4562 (t80) REVERT: U 245 ASP cc_start: 0.6740 (t0) cc_final: 0.6208 (t0) REVERT: U 375 GLN cc_start: 0.6893 (mm110) cc_final: 0.6375 (mm-40) REVERT: U 436 LEU cc_start: 0.8076 (tp) cc_final: 0.7838 (tp) REVERT: U 473 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5689 (m90) outliers start: 37 outliers final: 17 residues processed: 224 average time/residue: 0.1646 time to fit residues: 52.8033 Evaluate side-chains 206 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 228 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 94 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 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 459 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 0.4980 chunk 128 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 445 ASN S 272 HIS S 344 GLN S 427 GLN T 363 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.201738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164120 restraints weight = 23649.128| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.59 r_work: 0.3839 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17128 Z= 0.271 Angle : 0.813 13.447 23906 Z= 0.435 Chirality : 0.054 0.444 2660 Planarity : 0.006 0.052 2487 Dihedral : 25.815 176.878 3751 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.37 % Allowed : 16.70 % Favored : 78.92 % 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: -0.97 (0.21), residues: 1576 helix: -0.61 (0.20), residues: 588 sheet: -0.89 (0.34), residues: 212 loop : -0.42 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 128 TYR 0.037 0.003 TYR R 233 PHE 0.032 0.003 PHE S 306 TRP 0.029 0.003 TRP U 225 HIS 0.008 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (17128) covalent geometry : angle 0.81305 / 0.43 (23906) hydrogen bonds : bond 0.06076 / 6.67 ( 707) hydrogen bonds : angle 5.43324 / 6.67 ( 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 250 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 475 GLN cc_start: 0.6544 (mm-40) cc_final: 0.6227 (mp10) REVERT: R 480 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: S 375 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8268 (mm-40) REVERT: T 225 TRP cc_start: 0.7180 (m-90) cc_final: 0.6428 (m-10) REVERT: T 325 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7550 (pmmt) REVERT: T 373 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.4587 (t80) REVERT: U 203 GLN cc_start: 0.5390 (tp40) cc_final: 0.5162 (tp-100) REVERT: U 245 ASP cc_start: 0.6791 (t0) cc_final: 0.6147 (t0) REVERT: U 300 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8057 (mt) REVERT: U 375 GLN cc_start: 0.6881 (mm110) cc_final: 0.6383 (mm110) REVERT: U 404 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4317 (mmp-170) REVERT: U 415 ARG cc_start: 0.6238 (mpp-170) cc_final: 0.5763 (mtm-85) REVERT: U 473 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5933 (m90) outliers start: 61 outliers final: 35 residues processed: 232 average time/residue: 0.1660 time to fit residues: 54.8715 Evaluate side-chains 214 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 319 VAL 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 R residue 480 GLU Chi-restraints excluded: chain S residue 33 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 287 ASP 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 415 ARG 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 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 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: 0.8980 chunk 71 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 88 optimal weight: 0.0050 chunk 143 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 445 ASN T 272 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.209789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.173675 restraints weight = 23395.244| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.35 r_work: 0.3977 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17128 Z= 0.139 Angle : 0.704 10.566 23906 Z= 0.379 Chirality : 0.048 0.341 2660 Planarity : 0.005 0.057 2487 Dihedral : 25.747 178.985 3751 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.87 % Allowed : 18.78 % Favored : 78.35 % 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: 0.06 (0.21), residues: 591 sheet: -0.84 (0.34), residues: 211 loop : -0.21 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 143 TYR 0.017 0.001 TYR T 338 PHE 0.014 0.001 PHE S 284 TRP 0.043 0.002 TRP U 225 HIS 0.010 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (17128) covalent geometry : angle 0.70396 / 0.38 (23906) hydrogen bonds : bond 0.04309 / 4.67 ( 707) hydrogen bonds : angle 4.98791 / 6.16 ( 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 231 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.528 Fit side-chains REVERT: R 137 ARG cc_start: 0.6798 (tpp80) cc_final: 0.6544 (tpp80) REVERT: R 480 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: S 157 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7495 (mt) REVERT: S 430 MET cc_start: 0.7662 (mpp) cc_final: 0.6932 (mpp) REVERT: S 471 ARG cc_start: 0.6837 (ppp80) cc_final: 0.6541 (tmm-80) REVERT: T 199 ASN cc_start: 0.4681 (OUTLIER) cc_final: 0.4443 (t0) REVERT: T 325 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7565 (pmmt) REVERT: T 373 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.4929 (t80) REVERT: U 233 TYR cc_start: 0.6297 (t80) cc_final: 0.6041 (t80) REVERT: U 245 ASP cc_start: 0.6736 (t0) cc_final: 0.6104 (t0) REVERT: U 375 GLN cc_start: 0.6897 (mm110) cc_final: 0.6438 (mm110) REVERT: U 407 ASP cc_start: 0.4874 (m-30) cc_final: 0.4016 (m-30) REVERT: U 473 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.5693 (m90) outliers start: 40 outliers final: 17 residues processed: 218 average time/residue: 0.1633 time to fit residues: 51.2242 Evaluate side-chains 206 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 412 LYS Chi-restraints excluded: chain R residue 480 GLU 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 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 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 459 TYR Chi-restraints excluded: chain U residue 248 SER Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 473 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS R 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.204385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.166832 restraints weight = 23527.450| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 2.60 r_work: 0.3882 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17128 Z= 0.209 Angle : 0.751 12.148 23906 Z= 0.401 Chirality : 0.050 0.416 2660 Planarity : 0.006 0.067 2487 Dihedral : 25.795 179.741 3749 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.23 % Allowed : 19.64 % 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: -0.57 (0.21), residues: 1576 helix: -0.07 (0.21), residues: 585 sheet: -0.90 (0.34), residues: 212 loop : -0.32 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 137 TYR 0.032 0.002 TYR R 233 PHE 0.027 0.002 PHE S 306 TRP 0.036 0.003 TRP U 225 HIS 0.019 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (17128) covalent geometry : angle 0.75116 / 0.40 (23906) hydrogen bonds : bond 0.05082 / 5.56 ( 707) hydrogen bonds : angle 5.09856 / 6.29 ( 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 231 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: R 480 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6659 (pm20) REVERT: S 430 MET cc_start: 0.7617 (mpp) cc_final: 0.6886 (mpp) REVERT: S 471 ARG cc_start: 0.6881 (ppp80) cc_final: 0.6559 (tmm-80) REVERT: T 199 ASN cc_start: 0.4821 (OUTLIER) cc_final: 0.4603 (t0) REVERT: T 225 TRP cc_start: 0.6817 (m-90) cc_final: 0.6318 (m-10) REVERT: T 325 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7579 (pmmt) REVERT: T 373 TYR cc_start: 0.5406 (OUTLIER) cc_final: 0.4885 (t80) REVERT: U 245 ASP cc_start: 0.6721 (t0) cc_final: 0.6107 (t0) REVERT: U 300 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8049 (mt) REVERT: U 375 GLN cc_start: 0.6920 (mm110) cc_final: 0.6488 (mm110) REVERT: U 415 ARG cc_start: 0.6177 (mpp-170) cc_final: 0.5758 (mtm-85) REVERT: U 473 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5874 (m90) outliers start: 45 outliers final: 30 residues processed: 213 average time/residue: 0.1669 time to fit residues: 50.9204 Evaluate side-chains 210 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 230 ILE Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR 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 207 THR 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 364 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 227 THR Chi-restraints excluded: chain U residue 300 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS S 272 HIS T 272 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.208026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.171778 restraints weight = 23519.770| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.51 r_work: 0.3946 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3059 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= 0.148 Angle : 0.707 10.755 23906 Z= 0.377 Chirality : 0.048 0.368 2660 Planarity : 0.005 0.088 2487 Dihedral : 25.734 179.267 3749 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.80 % Allowed : 20.50 % Favored : 76.70 % 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: -0.40 (0.22), residues: 1576 helix: 0.12 (0.22), residues: 584 sheet: -0.79 (0.34), residues: 211 loop : -0.26 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 188 TYR 0.016 0.001 TYR T 459 PHE 0.015 0.001 PHE S 306 TRP 0.049 0.002 TRP U 225 HIS 0.006 0.001 HIS R 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (17128) covalent geometry : angle 0.70706 / 0.38 (23906) hydrogen bonds : bond 0.04236 / 4.60 ( 707) hydrogen bonds : angle 4.94432 / 6.09 ( 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 222 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: R 480 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6696 (pm20) REVERT: S 375 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8269 (mm-40) REVERT: S 430 MET cc_start: 0.7608 (mpp) cc_final: 0.6909 (mpp) REVERT: S 471 ARG cc_start: 0.6776 (ppp80) cc_final: 0.6516 (tmm-80) REVERT: T 199 ASN cc_start: 0.4801 (OUTLIER) cc_final: 0.4583 (t0) REVERT: T 225 TRP cc_start: 0.6790 (m-90) cc_final: 0.6311 (m-10) REVERT: T 325 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7547 (pmmt) REVERT: T 373 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4940 (t80) REVERT: U 245 ASP cc_start: 0.6855 (t0) cc_final: 0.6108 (t0) REVERT: U 300 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8045 (mt) REVERT: U 375 GLN cc_start: 0.6935 (mm110) cc_final: 0.6525 (mm110) REVERT: U 415 ARG cc_start: 0.6086 (mpp-170) cc_final: 0.5692 (mtm-85) REVERT: U 473 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5732 (m90) outliers start: 39 outliers final: 27 residues processed: 207 average time/residue: 0.1675 time to fit residues: 49.8710 Evaluate side-chains 211 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 480 GLU 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 166 LYS 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 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 364 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 473 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.207291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.170651 restraints weight = 23611.455| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.49 r_work: 0.3934 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17128 Z= 0.159 Angle : 0.705 10.801 23906 Z= 0.378 Chirality : 0.048 0.383 2660 Planarity : 0.005 0.063 2487 Dihedral : 25.737 179.828 3749 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.58 % Allowed : 20.65 % 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: -0.44 (0.22), residues: 1576 helix: 0.08 (0.21), residues: 592 sheet: -0.69 (0.34), residues: 207 loop : -0.32 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 137 TYR 0.022 0.001 TYR R 233 PHE 0.019 0.002 PHE S 306 TRP 0.059 0.002 TRP U 225 HIS 0.023 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (17128) covalent geometry : angle 0.70539 / 0.38 (23906) hydrogen bonds : bond 0.04351 / 4.74 ( 707) hydrogen bonds : angle 4.92415 / 6.06 ( 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 214 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.522 Fit side-chains REVERT: R 480 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: S 375 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8295 (mm-40) REVERT: S 430 MET cc_start: 0.7628 (mpp) cc_final: 0.6912 (mpp) REVERT: S 471 ARG cc_start: 0.6811 (ppp80) cc_final: 0.6548 (tmm-80) REVERT: T 199 ASN cc_start: 0.4813 (OUTLIER) cc_final: 0.4586 (t0) REVERT: T 225 TRP cc_start: 0.6806 (m-90) cc_final: 0.6345 (m-10) REVERT: T 325 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7584 (pmmt) REVERT: T 373 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.4997 (t80) REVERT: U 245 ASP cc_start: 0.6786 (t0) cc_final: 0.6353 (t70) REVERT: U 300 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8051 (mt) REVERT: U 375 GLN cc_start: 0.6917 (mm110) cc_final: 0.6554 (mm110) REVERT: U 415 ARG cc_start: 0.6137 (mpp-170) cc_final: 0.5736 (mtm-85) REVERT: U 473 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5751 (m90) outliers start: 36 outliers final: 25 residues processed: 200 average time/residue: 0.1356 time to fit residues: 39.3116 Evaluate side-chains 204 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain R residue 412 LYS Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 291 ASP 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 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 473 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS T 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.205677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.168688 restraints weight = 23479.667| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.50 r_work: 0.3899 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17128 Z= 0.185 Angle : 0.736 11.218 23906 Z= 0.390 Chirality : 0.049 0.401 2660 Planarity : 0.005 0.063 2487 Dihedral : 25.792 179.248 3749 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.51 % Allowed : 21.00 % Favored : 76.49 % 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: -0.54 (0.21), residues: 1576 helix: -0.03 (0.21), residues: 591 sheet: -0.64 (0.34), residues: 207 loop : -0.40 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 137 TYR 0.027 0.002 TYR R 233 PHE 0.023 0.002 PHE S 306 TRP 0.034 0.002 TRP S 86 HIS 0.006 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (17128) covalent geometry : angle 0.73576 / 0.39 (23906) hydrogen bonds : bond 0.04733 / 5.17 ( 707) hydrogen bonds : angle 4.98525 / 6.14 ( 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 220 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 480 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: S 375 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8293 (mm-40) REVERT: S 430 MET cc_start: 0.7542 (mpp) cc_final: 0.6926 (mpp) REVERT: S 471 ARG cc_start: 0.6715 (ppp80) cc_final: 0.6484 (tmm-80) REVERT: T 199 ASN cc_start: 0.4892 (OUTLIER) cc_final: 0.4667 (t0) REVERT: T 325 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7573 (pmmt) REVERT: T 373 TYR cc_start: 0.5436 (OUTLIER) cc_final: 0.4971 (t80) REVERT: U 300 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7997 (mt) REVERT: U 375 GLN cc_start: 0.6959 (mm110) cc_final: 0.6613 (mm110) REVERT: U 415 ARG cc_start: 0.6189 (mpp-170) cc_final: 0.5803 (mtm-85) REVERT: U 473 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5867 (m90) outliers start: 35 outliers final: 28 residues processed: 207 average time/residue: 0.1584 time to fit residues: 46.7240 Evaluate side-chains 210 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 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 207 THR Chi-restraints excluded: chain R residue 228 THR 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 480 GLU 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 166 LYS Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 291 ASP 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 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 443 THR Chi-restraints excluded: chain U residue 473 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 168 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 140 optimal weight: 9.9990 chunk 126 optimal weight: 0.0470 chunk 67 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 151 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 63 optimal weight: 0.0270 chunk 66 optimal weight: 0.0000 overall best weight: 0.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 217 HIS T 272 HIS T 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.212028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.177654 restraints weight = 23662.869| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.45 r_work: 0.4018 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17128 Z= 0.132 Angle : 0.695 11.182 23906 Z= 0.368 Chirality : 0.046 0.350 2660 Planarity : 0.005 0.085 2487 Dihedral : 25.712 177.439 3749 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.22 % Allowed : 21.72 % Favored : 76.06 % 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: -0.20 (0.22), residues: 1576 helix: 0.31 (0.22), residues: 592 sheet: -0.48 (0.35), residues: 196 loop : -0.25 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 137 TYR 0.016 0.001 TYR U 373 PHE 0.011 0.001 PHE S 284 TRP 0.029 0.002 TRP S 86 HIS 0.012 0.001 HIS T 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (17128) covalent geometry : angle 0.69509 / 0.37 (23906) hydrogen bonds : bond 0.03915 / 4.22 ( 707) hydrogen bonds : angle 4.72331 / 5.81 ( 1811) =============================================================================== Job complete usr+sys time: 4460.39 seconds wall clock time: 77 minutes 8.58 seconds (4628.58 seconds total)