Starting phenix.real_space_refine on Sun Aug 24 02:43:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkv_19284/08_2025/8rkv_19284.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 174 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 9765 2.51 5 N 3009 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.95, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 489.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.62 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: 3.65 Time building geometry restraints manager: 1.34 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=" O4' DA 3 60 " pdb=" C1' DA 3 60 " ideal model delta sigma weight residual 1.414 1.376 0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" CB TRP R 202 " pdb=" CG TRP R 202 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.63e+00 bond pdb=" C4' DT 5 18 " pdb=" O4' DT 5 18 " ideal model delta sigma weight residual 1.450 1.412 0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" C1' DC 3 61 " pdb=" N1 DC 3 61 " ideal model delta sigma weight residual 1.490 1.546 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" C3' DA 3 36 " pdb=" O3' DA 3 36 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.49e+00 ... (remaining 17123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 21987 1.68 - 3.35: 1658 3.35 - 5.03: 210 5.03 - 6.71: 45 6.71 - 8.38: 6 Bond angle restraints: 23906 Sorted by residual: angle pdb=" C4' DA 6 57 " pdb=" C3' DA 6 57 " pdb=" O3' DA 6 57 " ideal model delta sigma weight residual 110.00 117.90 -7.90 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C2' DA 6 74 " pdb=" C1' DA 6 74 " pdb=" N9 DA 6 74 " ideal model delta sigma weight residual 113.50 120.55 -7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" C3' DC 3 61 " pdb=" O3' DC 3 61 " pdb=" P DT 3 62 " ideal model delta sigma weight residual 120.20 126.96 -6.76 1.50e+00 4.44e-01 2.03e+01 angle pdb=" O4' DG 6 64 " pdb=" C1' DG 6 64 " pdb=" N9 DG 6 64 " ideal model delta sigma weight residual 108.40 115.03 -6.63 1.50e+00 4.44e-01 1.95e+01 angle pdb=" O3' DG 6 69 " pdb=" C3' DG 6 69 " pdb=" C2' DG 6 69 " ideal model delta sigma weight residual 111.50 117.72 -6.22 1.50e+00 4.44e-01 1.72e+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 - 0.078: 2208 0.078 - 0.156: 372 0.156 - 0.233: 64 0.233 - 0.311: 11 0.311 - 0.389: 5 Chirality restraints: 2660 Sorted by residual: 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 2.42 2.03 0.39 2.00e-01 2.50e+01 3.78e+00 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 -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.10e+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 2.42 2.08 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2657 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 355 " 0.390 9.50e-02 1.11e+02 1.76e-01 2.28e+01 pdb=" NE ARG S 355 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG S 355 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG S 355 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG S 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG 6 69 " 0.051 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" N9 DG 6 69 " -0.071 2.00e-02 2.50e+03 pdb=" C8 DG 6 69 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DG 6 69 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG 6 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG 6 69 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG 6 69 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG 6 69 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG 6 69 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG 6 69 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG 6 69 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG 6 69 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 5 18 " 0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT 5 18 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DT 5 18 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DT 5 18 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT 5 18 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DT 5 18 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DT 5 18 " 0.021 2.00e-02 2.50e+03 pdb=" C5 DT 5 18 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT 5 18 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DT 5 18 " -0.007 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 167 2.59 - 3.17: 14015 3.17 - 3.75: 27380 3.75 - 4.32: 38765 4.32 - 4.90: 59046 Nonbonded interactions: 139373 Sorted by model distance: nonbonded pdb=" OD1 ASP R 205 " pdb="MG MG R 600 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP S 205 " pdb="MG MG S 600 " model vdw 2.031 2.170 nonbonded pdb=" O3' DT 7 15 " pdb="MG MG S 600 " model vdw 2.062 2.170 nonbonded pdb=" OD2 ASP S 205 " pdb="MG MG S 600 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP R 205 " pdb="MG MG R 600 " model vdw 2.120 2.170 ... (remaining 139368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '4' and (resid 16 through 26 or resid 28 through 33 or resid 35 through 4 \ 0)) selection = (chain '5' and ((resid 16 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or \ name N3 or name C4 or name O4 or name C5 or name C7 or name C6 )) or resid 17 th \ rough 26 or resid 28 through 33 or resid 35 through 40)) } ncs_group { reference = (chain 'R' and (resid 31 through 512 or resid 525 through 600)) selection = chain 'S' } ncs_group { reference = (chain 'T' and (resid 196 through 287 or resid 295 through 339 or resid 354 thro \ ugh 522)) selection = (chain 'U' and (resid 196 through 311 or resid 323 through 522)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.840 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 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 : 0.006 0.075 17128 Z= 0.273 Angle : 0.951 8.384 23906 Z= 0.561 Chirality : 0.063 0.389 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 aren 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 covalent geometry : bond 0.00630 (17128) covalent geometry : angle 0.95061 (23906) hydrogen bonds : bond 0.18944 ( 707) hydrogen bonds : angle 7.72081 ( 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 : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 31 LYS cc_start: 0.6230 (tptt) cc_final: 0.5849 (mmtt) REVERT: R 112 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7752 (mt-10) REVERT: R 124 LYS cc_start: 0.6940 (pptt) cc_final: 0.6331 (pttp) REVERT: R 129 MET cc_start: 0.6915 (ttm) cc_final: 0.6697 (ttm) REVERT: R 165 GLU cc_start: 0.8293 (tp30) cc_final: 0.8049 (tp30) REVERT: R 172 SER cc_start: 0.7118 (t) cc_final: 0.6707 (p) REVERT: R 371 ASP cc_start: 0.8298 (m-30) cc_final: 0.8027 (m-30) REVERT: R 432 ARG cc_start: 0.7444 (ptp90) cc_final: 0.7145 (ptp-110) REVERT: R 451 ARG cc_start: 0.8397 (mtm180) cc_final: 0.8163 (mtm-85) REVERT: R 465 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8153 (mm110) REVERT: S 104 LYS cc_start: 0.6963 (mmtp) cc_final: 0.6532 (mmtt) REVERT: S 143 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7867 (mtt180) REVERT: S 179 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5533 (ppt90) REVERT: S 295 ASN cc_start: 0.8055 (m110) cc_final: 0.7830 (m-40) REVERT: S 349 ASP cc_start: 0.6590 (m-30) cc_final: 0.6366 (t0) REVERT: S 360 GLU cc_start: 0.5932 (mp0) cc_final: 0.5453 (mp0) REVERT: S 375 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7935 (mm-40) REVERT: S 430 MET cc_start: 0.7848 (mtp) cc_final: 0.7610 (mpp) REVERT: S 503 ASN cc_start: 0.7352 (p0) cc_final: 0.7132 (p0) REVERT: T 202 TRP cc_start: 0.5891 (m100) cc_final: 0.5523 (m-10) REVERT: T 327 LEU cc_start: 0.5781 (mm) cc_final: 0.5480 (mm) REVERT: T 363 GLN cc_start: 0.7808 (mt0) cc_final: 0.7607 (mt0) REVERT: T 373 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.4206 (t80) REVERT: T 495 ARG cc_start: 0.6531 (tpt170) cc_final: 0.6283 (ttm110) REVERT: U 233 TYR cc_start: 0.6432 (t80) cc_final: 0.6118 (t80) REVERT: U 245 ASP cc_start: 0.6750 (t0) cc_final: 0.6382 (t0) REVERT: U 285 TYR cc_start: 0.5914 (m-80) cc_final: 0.5703 (m-80) REVERT: U 415 ARG cc_start: 0.5433 (mpp-170) cc_final: 0.5157 (mtm-85) REVERT: U 475 GLN cc_start: 0.5156 (tt0) cc_final: 0.4929 (tt0) REVERT: U 496 THR cc_start: 0.6869 (m) cc_final: 0.6577 (m) outliers start: 27 outliers final: 7 residues processed: 303 average time/residue: 0.1619 time to fit residues: 67.5609 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: R 217 HIS R 427 GLN R 531 GLN S 272 HIS S 295 ASN S 344 GLN S 445 ASN T 206 HIS T 375 GLN T 445 ASN T 481 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174207 restraints weight = 23720.419| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.70 r_work: 0.3950 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17128 Z= 0.175 Angle : 0.703 9.958 23906 Z= 0.388 Chirality : 0.042 0.190 2660 Planarity : 0.005 0.053 2487 Dihedral : 25.499 177.401 3777 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 12.19 % Favored : 85.52 % 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 aren not related in a simple way. whole: -0.58 (0.21), residues: 1576 helix: -0.50 (0.20), residues: 596 sheet: -0.76 (0.33), residues: 214 loop : 0.04 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 143 TYR 0.024 0.002 TYR T 285 PHE 0.018 0.002 PHE R 284 TRP 0.023 0.002 TRP S 86 HIS 0.007 0.001 HIS T 272 Details of bonding type rmsd covalent geometry : bond 0.00394 (17128) covalent geometry : angle 0.70345 (23906) hydrogen bonds : bond 0.04637 ( 707) hydrogen bonds : angle 5.29777 ( 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 267 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 451 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7962 (mtm-85) REVERT: R 478 GLU cc_start: 0.6662 (pm20) cc_final: 0.5592 (pt0) REVERT: R 480 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: R 491 SER cc_start: 0.8327 (m) cc_final: 0.7826 (t) REVERT: T 232 THR cc_start: 0.4500 (p) cc_final: 0.4296 (p) REVERT: T 261 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7327 (mm) REVERT: T 327 LEU cc_start: 0.5687 (mm) cc_final: 0.5254 (mm) REVERT: T 373 TYR cc_start: 0.5087 (OUTLIER) cc_final: 0.4257 (t80) REVERT: U 223 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6222 (mmm-85) REVERT: U 245 ASP cc_start: 0.6716 (t0) cc_final: 0.6342 (t0) REVERT: U 473 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.5593 (m90) outliers start: 32 outliers final: 16 residues processed: 252 average time/residue: 0.1732 time to fit residues: 60.7263 Evaluate side-chains 206 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 313 ARG Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 299 GLN Chi-restraints excluded: chain S residue 394 LEU Chi-restraints excluded: chain S residue 502 SER Chi-restraints excluded: chain T residue 261 LEU 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 T residue 387 PHE Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 223 ARG Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN R 217 HIS S 272 HIS S 344 GLN S 363 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 = 0.4627 r_free = 0.4627 target = 0.205070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.168218 restraints weight = 23748.184| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.74 r_work: 0.3892 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17128 Z= 0.213 Angle : 0.705 9.214 23906 Z= 0.385 Chirality : 0.043 0.229 2660 Planarity : 0.005 0.057 2487 Dihedral : 25.501 179.429 3763 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.23 % Allowed : 14.41 % Favored : 82.37 % 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 aren not related in a simple way. whole: -0.40 (0.21), residues: 1576 helix: -0.21 (0.21), residues: 594 sheet: -0.76 (0.33), residues: 223 loop : 0.06 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 235 TYR 0.027 0.002 TYR R 233 PHE 0.022 0.002 PHE S 306 TRP 0.021 0.002 TRP S 86 HIS 0.005 0.001 HIS R 283 Details of bonding type rmsd covalent geometry : bond 0.00490 (17128) covalent geometry : angle 0.70471 (23906) hydrogen bonds : bond 0.04702 ( 707) hydrogen bonds : angle 5.13153 ( 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 : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 480 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: R 491 SER cc_start: 0.8353 (m) cc_final: 0.7824 (t) REVERT: S 375 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: S 430 MET cc_start: 0.7748 (mpp) cc_final: 0.7121 (mpp) REVERT: S 471 ARG cc_start: 0.6896 (ppp80) cc_final: 0.6682 (tmm-80) REVERT: T 225 TRP cc_start: 0.7018 (m-90) cc_final: 0.6400 (m-10) REVERT: T 261 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7186 (mm) REVERT: T 327 LEU cc_start: 0.5624 (mm) cc_final: 0.5169 (mm) REVERT: T 373 TYR cc_start: 0.5152 (OUTLIER) cc_final: 0.4490 (t80) REVERT: U 245 ASP cc_start: 0.6713 (t0) cc_final: 0.6219 (t0) REVERT: U 309 HIS cc_start: 0.6072 (m-70) cc_final: 0.5028 (m-70) REVERT: U 372 ARG cc_start: 0.5772 (ttp80) cc_final: 0.5568 (tmm-80) REVERT: U 375 GLN cc_start: 0.6946 (mm110) cc_final: 0.6378 (mm110) REVERT: U 473 HIS cc_start: 0.6292 (OUTLIER) cc_final: 0.5782 (m90) outliers start: 45 outliers final: 28 residues processed: 228 average time/residue: 0.1563 time to fit residues: 49.2930 Evaluate side-chains 210 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 436 LEU Chi-restraints excluded: chain R residue 480 GLU Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 277 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 424 LEU Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 261 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 384 GLN Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS R 272 HIS R 295 ASN ** R 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN S 344 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.211912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.177053 restraints weight = 23460.087| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.57 r_work: 0.4002 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17128 Z= 0.139 Angle : 0.616 10.079 23906 Z= 0.337 Chirality : 0.039 0.165 2660 Planarity : 0.005 0.057 2487 Dihedral : 25.392 175.823 3759 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.29 % Allowed : 16.34 % Favored : 81.36 % 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 aren not related in a simple way. whole: 0.06 (0.22), residues: 1576 helix: 0.38 (0.22), residues: 601 sheet: -0.66 (0.34), residues: 213 loop : 0.16 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 389 TYR 0.018 0.001 TYR T 338 PHE 0.014 0.001 PHE S 306 TRP 0.023 0.001 TRP S 86 HIS 0.005 0.001 HIS R 283 Details of bonding type rmsd covalent geometry : bond 0.00306 (17128) covalent geometry : angle 0.61615 (23906) hydrogen bonds : bond 0.03675 ( 707) hydrogen bonds : angle 4.58945 ( 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 241 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: R 445 ASN cc_start: 0.5247 (t0) cc_final: 0.4888 (t0) REVERT: R 478 GLU cc_start: 0.6852 (pm20) cc_final: 0.5662 (pt0) REVERT: R 491 SER cc_start: 0.8305 (m) cc_final: 0.7785 (t) REVERT: S 157 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7695 (mt) REVERT: S 295 ASN cc_start: 0.7888 (m110) cc_final: 0.7537 (m-40) REVERT: S 430 MET cc_start: 0.7765 (mpp) cc_final: 0.7097 (mpp) REVERT: T 225 TRP cc_start: 0.6814 (m-90) cc_final: 0.6273 (m-10) REVERT: T 261 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7018 (mm) REVERT: T 275 TRP cc_start: 0.6047 (OUTLIER) cc_final: 0.5464 (t60) REVERT: T 327 LEU cc_start: 0.5543 (mm) cc_final: 0.5243 (mm) REVERT: T 373 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4816 (t80) REVERT: T 411 MET cc_start: 0.7874 (mmm) cc_final: 0.7637 (mtp) REVERT: U 245 ASP cc_start: 0.6556 (t0) cc_final: 0.6273 (t70) REVERT: U 300 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7987 (mt) REVERT: U 309 HIS cc_start: 0.6122 (m-70) cc_final: 0.5136 (m-70) REVERT: U 375 GLN cc_start: 0.6817 (mm110) cc_final: 0.6300 (mm110) REVERT: U 473 HIS cc_start: 0.6131 (OUTLIER) cc_final: 0.5636 (m90) outliers start: 32 outliers final: 15 residues processed: 232 average time/residue: 0.1445 time to fit residues: 46.8535 Evaluate side-chains 208 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 152 ASN Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP 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 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 101 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 125 optimal weight: 0.0670 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS ** S 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.206101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.168959 restraints weight = 23446.195| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.70 r_work: 0.3908 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17128 Z= 0.202 Angle : 0.682 11.719 23906 Z= 0.366 Chirality : 0.041 0.172 2660 Planarity : 0.005 0.054 2487 Dihedral : 25.394 175.374 3757 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 18.21 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.22), residues: 1576 helix: 0.25 (0.21), residues: 593 sheet: -0.58 (0.35), residues: 209 loop : -0.01 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 188 TYR 0.026 0.002 TYR R 233 PHE 0.022 0.002 PHE S 306 TRP 0.022 0.002 TRP U 225 HIS 0.007 0.001 HIS T 272 Details of bonding type rmsd covalent geometry : bond 0.00466 (17128) covalent geometry : angle 0.68191 (23906) hydrogen bonds : bond 0.04351 ( 707) hydrogen bonds : angle 4.77513 ( 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 237 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: R 137 ARG cc_start: 0.6946 (tpp80) cc_final: 0.6744 (tpp80) REVERT: R 412 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (ptmt) REVERT: R 480 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: R 491 SER cc_start: 0.8359 (m) cc_final: 0.7841 (t) REVERT: S 295 ASN cc_start: 0.7944 (m110) cc_final: 0.7734 (m-40) REVERT: T 225 TRP cc_start: 0.6983 (m-90) cc_final: 0.6494 (m-10) REVERT: T 261 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7176 (mm) REVERT: T 275 TRP cc_start: 0.6146 (OUTLIER) cc_final: 0.5307 (t60) REVERT: T 327 LEU cc_start: 0.5471 (mm) cc_final: 0.5126 (mm) REVERT: T 373 TYR cc_start: 0.5190 (OUTLIER) cc_final: 0.4739 (t80) REVERT: U 203 GLN cc_start: 0.5514 (tp40) cc_final: 0.5178 (tp-100) REVERT: U 245 ASP cc_start: 0.6680 (t0) cc_final: 0.6339 (t70) REVERT: U 300 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7972 (mt) REVERT: U 309 HIS cc_start: 0.6200 (m-70) cc_final: 0.5126 (m-70) REVERT: U 375 GLN cc_start: 0.7236 (mm110) cc_final: 0.6815 (mm110) REVERT: U 404 ARG cc_start: 0.5512 (OUTLIER) cc_final: 0.4249 (mmp-170) REVERT: U 473 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5800 (m90) outliers start: 43 outliers final: 22 residues processed: 220 average time/residue: 0.1392 time to fit residues: 42.9082 Evaluate side-chains 212 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 480 GLU Chi-restraints excluded: chain R residue 508 GLN Chi-restraints excluded: chain S residue 82 LEU 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 457 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP 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 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS S 272 HIS S 473 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.206865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.170178 restraints weight = 23425.872| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.49 r_work: 0.3930 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17128 Z= 0.182 Angle : 0.660 9.976 23906 Z= 0.356 Chirality : 0.041 0.235 2660 Planarity : 0.005 0.059 2487 Dihedral : 25.390 176.384 3757 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.01 % Allowed : 18.06 % Favored : 77.92 % 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 aren not related in a simple way. whole: -0.13 (0.22), residues: 1576 helix: 0.27 (0.21), residues: 596 sheet: -0.61 (0.34), residues: 214 loop : -0.05 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 471 TYR 0.023 0.002 TYR R 233 PHE 0.020 0.002 PHE S 306 TRP 0.024 0.002 TRP U 225 HIS 0.007 0.001 HIS S 473 Details of bonding type rmsd covalent geometry : bond 0.00415 (17128) covalent geometry : angle 0.66043 (23906) hydrogen bonds : bond 0.04044 ( 707) hydrogen bonds : angle 4.70669 ( 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 249 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 85 ASN cc_start: 0.7972 (m-40) cc_final: 0.7742 (m110) REVERT: R 412 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8127 (ptmt) REVERT: S 375 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8278 (mm-40) REVERT: T 199 ASN cc_start: 0.4743 (OUTLIER) cc_final: 0.4500 (t0) REVERT: T 225 TRP cc_start: 0.7076 (m-90) cc_final: 0.6541 (m-10) REVERT: T 261 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6979 (mm) REVERT: T 275 TRP cc_start: 0.6029 (OUTLIER) cc_final: 0.5213 (t60) REVERT: T 327 LEU cc_start: 0.5409 (mm) cc_final: 0.5056 (mm) REVERT: T 373 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.4830 (t80) REVERT: U 223 ARG cc_start: 0.5557 (mmm-85) cc_final: 0.5200 (mmm-85) REVERT: U 300 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7976 (mt) REVERT: U 309 HIS cc_start: 0.6185 (m-70) cc_final: 0.5176 (m-70) REVERT: U 375 GLN cc_start: 0.7269 (mm110) cc_final: 0.6861 (mm110) REVERT: U 415 ARG cc_start: 0.6114 (mpp-170) cc_final: 0.5795 (mtm-85) REVERT: U 473 HIS cc_start: 0.6289 (OUTLIER) cc_final: 0.5766 (m90) outliers start: 56 outliers final: 28 residues processed: 231 average time/residue: 0.1721 time to fit residues: 55.7936 Evaluate side-chains 218 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 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 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 94 LEU 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 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP 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 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS S 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.206788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.172685 restraints weight = 23329.654| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.59 r_work: 0.3907 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17128 Z= 0.180 Angle : 0.668 11.143 23906 Z= 0.357 Chirality : 0.041 0.236 2660 Planarity : 0.005 0.058 2487 Dihedral : 25.389 176.828 3757 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.37 % Allowed : 19.28 % Favored : 77.35 % 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 aren not related in a simple way. whole: -0.18 (0.22), residues: 1576 helix: 0.24 (0.21), residues: 601 sheet: -0.55 (0.34), residues: 214 loop : -0.13 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 471 TYR 0.021 0.002 TYR R 233 PHE 0.019 0.002 PHE S 306 TRP 0.025 0.002 TRP U 225 HIS 0.010 0.001 HIS S 473 Details of bonding type rmsd covalent geometry : bond 0.00411 (17128) covalent geometry : angle 0.66755 (23906) hydrogen bonds : bond 0.04013 ( 707) hydrogen bonds : angle 4.68877 ( 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 234 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 157 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7701 (mt) REVERT: S 300 ILE cc_start: 0.7090 (mt) cc_final: 0.6813 (tt) REVERT: S 351 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: S 427 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: T 225 TRP cc_start: 0.7114 (m-90) cc_final: 0.6584 (m-10) REVERT: T 261 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7119 (mm) REVERT: T 275 TRP cc_start: 0.6049 (OUTLIER) cc_final: 0.5115 (t60) REVERT: T 327 LEU cc_start: 0.5410 (mm) cc_final: 0.5018 (mm) REVERT: T 373 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4883 (t80) REVERT: U 225 TRP cc_start: 0.5920 (OUTLIER) cc_final: 0.5719 (m-10) REVERT: U 300 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8117 (mp) REVERT: U 309 HIS cc_start: 0.6232 (m-70) cc_final: 0.5183 (m-70) REVERT: U 375 GLN cc_start: 0.7343 (mm110) cc_final: 0.6899 (mm110) REVERT: U 404 ARG cc_start: 0.5512 (OUTLIER) cc_final: 0.4185 (mmp-170) REVERT: U 415 ARG cc_start: 0.6118 (mpp-170) cc_final: 0.5842 (mtm-85) REVERT: U 473 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.5850 (m90) outliers start: 47 outliers final: 27 residues processed: 217 average time/residue: 0.1794 time to fit residues: 54.2697 Evaluate side-chains 210 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 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 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 94 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 291 ASP Chi-restraints excluded: chain S residue 351 GLU Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP 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 T residue 469 LEU Chi-restraints excluded: chain U residue 225 TRP Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 0.0670 chunk 157 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 217 HIS S 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.208583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.173543 restraints weight = 23612.749| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.57 r_work: 0.3961 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17128 Z= 0.157 Angle : 0.651 12.964 23906 Z= 0.348 Chirality : 0.040 0.222 2660 Planarity : 0.005 0.086 2487 Dihedral : 25.314 176.933 3757 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.01 % Allowed : 19.86 % 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 aren not related in a simple way. whole: -0.14 (0.22), residues: 1576 helix: 0.31 (0.22), residues: 609 sheet: -0.35 (0.35), residues: 201 loop : -0.20 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 447 TYR 0.018 0.001 TYR R 233 PHE 0.017 0.002 PHE S 306 TRP 0.017 0.001 TRP S 86 HIS 0.009 0.001 HIS S 473 Details of bonding type rmsd covalent geometry : bond 0.00356 (17128) covalent geometry : angle 0.65111 (23906) hydrogen bonds : bond 0.03692 ( 707) hydrogen bonds : angle 4.57134 ( 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 239 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: R 445 ASN cc_start: 0.5499 (t0) cc_final: 0.5168 (t0) REVERT: S 157 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7695 (mt) REVERT: S 351 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: S 375 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: T 199 ASN cc_start: 0.4880 (OUTLIER) cc_final: 0.4667 (t0) REVERT: T 261 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7034 (mm) REVERT: T 275 TRP cc_start: 0.5985 (OUTLIER) cc_final: 0.5064 (t60) REVERT: T 327 LEU cc_start: 0.5419 (mm) cc_final: 0.5074 (mm) REVERT: T 373 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4955 (t80) REVERT: U 295 ASN cc_start: 0.6652 (p0) cc_final: 0.6424 (p0) REVERT: U 300 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8074 (mp) REVERT: U 309 HIS cc_start: 0.6115 (m-70) cc_final: 0.5092 (m-70) REVERT: U 375 GLN cc_start: 0.7363 (mm110) cc_final: 0.6906 (mm110) REVERT: U 415 ARG cc_start: 0.5997 (mpp-170) cc_final: 0.5764 (mtm-85) REVERT: U 473 HIS cc_start: 0.6354 (OUTLIER) cc_final: 0.5829 (m90) outliers start: 42 outliers final: 29 residues processed: 223 average time/residue: 0.1617 time to fit residues: 51.0243 Evaluate side-chains 222 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 94 LEU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 193 LEU Chi-restraints excluded: chain S residue 351 GLU Chi-restraints excluded: chain S residue 375 GLN Chi-restraints excluded: chain S residue 423 CYS Chi-restraints excluded: chain S residue 457 LEU Chi-restraints excluded: chain T residue 199 ASN Chi-restraints excluded: chain T residue 207 THR Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 275 TRP 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 397 VAL Chi-restraints excluded: chain T residue 459 TYR Chi-restraints excluded: chain T residue 469 LEU Chi-restraints excluded: chain U residue 201 VAL Chi-restraints excluded: chain U residue 300 ILE Chi-restraints excluded: chain U residue 308 CYS Chi-restraints excluded: chain U residue 327 LEU Chi-restraints excluded: chain U residue 404 ARG Chi-restraints excluded: chain U residue 443 THR Chi-restraints excluded: chain U residue 473 HIS Chi-restraints excluded: chain U residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7145 > 50: distance: 138 - 142: 5.432 distance: 142 - 143: 4.924 distance: 142 - 148: 5.506 distance: 143 - 144: 5.109 distance: 143 - 146: 4.863 distance: 144 - 145: 19.431 distance: 144 - 149: 6.722 distance: 146 - 147: 7.619 distance: 147 - 148: 6.585 distance: 149 - 155: 13.804 distance: 150 - 151: 9.113 distance: 150 - 153: 6.919 distance: 151 - 152: 8.415 distance: 151 - 156: 3.599 distance: 153 - 154: 3.536 distance: 154 - 155: 10.029 distance: 156 - 157: 7.037 distance: 157 - 158: 6.337 distance: 157 - 160: 7.061 distance: 158 - 159: 7.978 distance: 158 - 164: 3.756 distance: 159 - 192: 8.605 distance: 160 - 161: 15.898 distance: 161 - 162: 8.411 distance: 161 - 163: 6.315 distance: 164 - 165: 5.225 distance: 165 - 166: 4.537 distance: 165 - 168: 5.081 distance: 166 - 167: 10.753 distance: 166 - 176: 5.040 distance: 167 - 199: 19.619 distance: 168 - 169: 6.649 distance: 169 - 170: 5.055 distance: 169 - 171: 4.381 distance: 170 - 172: 7.332 distance: 171 - 173: 7.352 distance: 172 - 174: 4.130 distance: 173 - 174: 4.678 distance: 174 - 175: 9.085 distance: 177 - 178: 11.112 distance: 177 - 180: 6.600 distance: 178 - 179: 9.536 distance: 178 - 185: 11.380 distance: 179 - 207: 18.064 distance: 180 - 181: 8.750 distance: 181 - 182: 10.410 distance: 182 - 183: 9.147 distance: 183 - 184: 7.815 distance: 185 - 186: 5.147 distance: 186 - 189: 5.365 distance: 187 - 188: 7.730 distance: 187 - 192: 14.994 distance: 188 - 218: 13.101 distance: 189 - 190: 3.434 distance: 189 - 191: 5.908 distance: 192 - 193: 3.260 distance: 193 - 194: 6.649 distance: 193 - 196: 9.073 distance: 194 - 195: 10.246 distance: 194 - 199: 5.730 distance: 195 - 225: 6.508 distance: 196 - 197: 6.439 distance: 196 - 198: 14.257 distance: 199 - 200: 3.593 distance: 200 - 201: 3.512 distance: 200 - 203: 5.010 distance: 201 - 202: 12.582 distance: 202 - 233: 19.457 distance: 203 - 204: 6.585 distance: 204 - 205: 6.453 distance: 204 - 206: 9.549 distance: 207 - 208: 9.605 distance: 208 - 209: 17.789 distance: 208 - 211: 7.629 distance: 209 - 210: 27.374 distance: 209 - 218: 35.922 distance: 211 - 212: 11.824 distance: 212 - 213: 8.516 distance: 213 - 214: 10.764 distance: 214 - 215: 6.743 distance: 215 - 216: 10.207 distance: 215 - 217: 9.707 distance: 218 - 219: 5.893 distance: 219 - 220: 20.025 distance: 219 - 222: 13.840 distance: 220 - 221: 9.555 distance: 220 - 225: 13.947 distance: 222 - 223: 16.860 distance: 222 - 224: 9.502